Actualiser src/global.mk

be consistent across systems (an error would be generated on Ubuntu when
no primers found)

.cproject

@@ -1,151 +1,221 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?fileVersion 4.0.0?>
 
 <cproject>
-<storageModule moduleId="org.eclipse.cdt.core.settings">
+	<storageModule moduleId="org.eclipse.cdt.core.settings">
-<cconfiguration id="cdt.managedbuild.toolchain.gnu.macosx.base.2134184396">
+		<cconfiguration id="cdt.managedbuild.toolchain.gnu.macosx.base.2134184396">
-<storageModule buildSystemId="org.eclipse.cdt.managedbuilder.core.configurationDataProvider" id="cdt.managedbuild.toolchain.gnu.macosx.base.2134184396" moduleId="org.eclipse.cdt.core.settings" name="MacOSX GCC">
+			<storageModule buildSystemId="org.eclipse.cdt.managedbuilder.core.configurationDataProvider" id="cdt.managedbuild.toolchain.gnu.macosx.base.2134184396" moduleId="org.eclipse.cdt.core.settings" name="MacOSX GCC">
-<externalSettings/>
+				<externalSettings/>
-<extensions>
+				<extensions>
-<extension id="org.eclipse.cdt.core.MachO" point="org.eclipse.cdt.core.BinaryParser"/>
+					<extension id="org.eclipse.cdt.core.MachO" point="org.eclipse.cdt.core.BinaryParser"/>
-<extension id="org.eclipse.cdt.core.GASErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
+					<extension id="org.eclipse.cdt.core.GASErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
-<extension id="org.eclipse.cdt.core.GLDErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
+					<extension id="org.eclipse.cdt.core.GLDErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
-<extension id="org.eclipse.cdt.core.GCCErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
+					<extension id="org.eclipse.cdt.core.GCCErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
-<extension id="org.eclipse.cdt.core.MakeErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
+					<extension id="org.eclipse.cdt.core.GmakeErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
-</extensions>
+					<extension id="org.eclipse.cdt.core.CWDLocator" point="org.eclipse.cdt.core.ErrorParser"/>
-</storageModule>
+				</extensions>
-<storageModule moduleId="cdtBuildSystem" version="4.0.0">
+			</storageModule>
-<configuration artifactName="ecoPrimers" buildProperties="" id="cdt.managedbuild.toolchain.gnu.macosx.base.2134184396" name="MacOSX GCC" parent="org.eclipse.cdt.build.core.emptycfg">
+			<storageModule moduleId="cdtBuildSystem" version="4.0.0">
-<folderInfo id="cdt.managedbuild.toolchain.gnu.macosx.base.2134184396.1840911077" name="/" resourcePath="">
+				<configuration artifactName="ecoPrimers" buildProperties="" description="" id="cdt.managedbuild.toolchain.gnu.macosx.base.2134184396" name="MacOSX GCC" parent="org.eclipse.cdt.build.core.emptycfg">
-<toolChain id="cdt.managedbuild.toolchain.gnu.macosx.base.766054112" name="cdt.managedbuild.toolchain.gnu.macosx.base" superClass="cdt.managedbuild.toolchain.gnu.macosx.base">
+					<folderInfo id="cdt.managedbuild.toolchain.gnu.macosx.base.2134184396.1840911077" name="/" resourcePath="">
-<targetPlatform archList="all" binaryParser="org.eclipse.cdt.core.MachO" id="cdt.managedbuild.target.gnu.platform.macosx.base.2057035265" name="Debug Platform" osList="macosx" superClass="cdt.managedbuild.target.gnu.platform.macosx.base"/>
+						<toolChain id="cdt.managedbuild.toolchain.gnu.macosx.base.766054112" name="cdt.managedbuild.toolchain.gnu.macosx.base" superClass="cdt.managedbuild.toolchain.gnu.macosx.base">
-<builder id="cdt.managedbuild.target.gnu.builder.macosx.base.783726363" managedBuildOn="false" name="Gnu Make Builder.MacOSX GCC" superClass="cdt.managedbuild.target.gnu.builder.macosx.base"/>
+							<targetPlatform archList="all" binaryParser="org.eclipse.cdt.core.MachO" id="cdt.managedbuild.target.gnu.platform.macosx.base.2057035265" name="Debug Platform" osList="macosx" superClass="cdt.managedbuild.target.gnu.platform.macosx.base"/>
-<tool id="cdt.managedbuild.tool.macosx.c.linker.macosx.base.914103467" name="MacOS X C Linker" superClass="cdt.managedbuild.tool.macosx.c.linker.macosx.base">
+							<builder id="cdt.managedbuild.target.gnu.builder.macosx.base.783726363" keepEnvironmentInBuildfile="false" managedBuildOn="false" name="Gnu Make Builder" superClass="cdt.managedbuild.target.gnu.builder.macosx.base"/>
-<inputType id="cdt.managedbuild.tool.macosx.c.linker.input.62980206" superClass="cdt.managedbuild.tool.macosx.c.linker.input">
+							<tool id="cdt.managedbuild.tool.macosx.c.linker.macosx.base.914103467" name="MacOS X C Linker" superClass="cdt.managedbuild.tool.macosx.c.linker.macosx.base">
-<additionalInput kind="additionalinputdependency" paths="$(USER_OBJS)"/>
+								<inputType id="cdt.managedbuild.tool.macosx.c.linker.input.62980206" superClass="cdt.managedbuild.tool.macosx.c.linker.input">
-<additionalInput kind="additionalinput" paths="$(LIBS)"/>
+									<additionalInput kind="additionalinputdependency" paths="$(USER_OBJS)"/>
-</inputType>
+									<additionalInput kind="additionalinput" paths="$(LIBS)"/>
-</tool>
+								</inputType>
-<tool id="cdt.managedbuild.tool.macosx.cpp.linker.macosx.base.691108439" name="MacOS X C++ Linker" superClass="cdt.managedbuild.tool.macosx.cpp.linker.macosx.base"/>
+							</tool>
-<tool id="cdt.managedbuild.tool.gnu.assembler.macosx.base.695639877" name="GCC Assembler" superClass="cdt.managedbuild.tool.gnu.assembler.macosx.base">
+							<tool id="cdt.managedbuild.tool.macosx.cpp.linker.macosx.base.691108439" name="MacOS X C++ Linker" superClass="cdt.managedbuild.tool.macosx.cpp.linker.macosx.base"/>
-<inputType id="cdt.managedbuild.tool.gnu.assembler.input.1507665054" superClass="cdt.managedbuild.tool.gnu.assembler.input"/>
+							<tool id="cdt.managedbuild.tool.gnu.assembler.macosx.base.695639877" name="GCC Assembler" superClass="cdt.managedbuild.tool.gnu.assembler.macosx.base">
-</tool>
+								<option id="gnu.both.asm.option.include.paths.1544375094" name="Include paths (-I)" superClass="gnu.both.asm.option.include.paths" valueType="includePath"/>
-<tool id="cdt.managedbuild.tool.gnu.archiver.macosx.base.1786370580" name="GCC Archiver" superClass="cdt.managedbuild.tool.gnu.archiver.macosx.base"/>
+								<inputType id="cdt.managedbuild.tool.gnu.assembler.input.1507665054" superClass="cdt.managedbuild.tool.gnu.assembler.input"/>
-<tool id="cdt.managedbuild.tool.gnu.cpp.compiler.macosx.base.454329831" name="GCC C++ Compiler" superClass="cdt.managedbuild.tool.gnu.cpp.compiler.macosx.base"/>
+							</tool>
-<tool id="cdt.managedbuild.tool.gnu.c.compiler.macosx.base.1928774909" name="GCC C Compiler" superClass="cdt.managedbuild.tool.gnu.c.compiler.macosx.base">
+							<tool id="cdt.managedbuild.tool.gnu.archiver.macosx.base.1786370580" name="GCC Archiver" superClass="cdt.managedbuild.tool.gnu.archiver.macosx.base"/>
-<inputType id="cdt.managedbuild.tool.gnu.c.compiler.input.330854350" superClass="cdt.managedbuild.tool.gnu.c.compiler.input"/>
+							<tool id="cdt.managedbuild.tool.gnu.cpp.compiler.macosx.base.454329831" name="GCC C++ Compiler" superClass="cdt.managedbuild.tool.gnu.cpp.compiler.macosx.base"/>
-</tool>
+							<tool id="cdt.managedbuild.tool.gnu.c.compiler.macosx.base.1928774909" name="GCC C Compiler" superClass="cdt.managedbuild.tool.gnu.c.compiler.macosx.base">
-</toolChain>
+								<option id="gnu.c.compiler.option.include.paths.823251305" superClass="gnu.c.compiler.option.include.paths" valueType="includePath">
-</folderInfo>
+									<listOptionValue builtIn="false" value="/usr/include"/>
-</configuration>
+								</option>
-</storageModule>
+								<inputType id="cdt.managedbuild.tool.gnu.c.compiler.input.330854350" superClass="cdt.managedbuild.tool.gnu.c.compiler.input"/>
-<storageModule moduleId="scannerConfiguration">
+							</tool>
-<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="org.eclipse.cdt.make.core.GCCStandardMakePerProjectProfile"/>
+						</toolChain>
-<profile id="org.eclipse.cdt.make.core.GCCStandardMakePerProjectProfile">
+					</folderInfo>
-<buildOutputProvider>
+				</configuration>
-<openAction enabled="true" filePath=""/>
+			</storageModule>
-<parser enabled="true"/>
+			<storageModule moduleId="org.eclipse.cdt.core.externalSettings"/>
-</buildOutputProvider>
+			<storageModule moduleId="org.eclipse.cdt.core.language.mapping"/>
-<scannerInfoProvider id="specsFile">
+			<storageModule moduleId="scannerConfiguration">
-<runAction arguments="-E -P -v -dD ${plugin_state_location}/${specs_file}" command="gcc" useDefault="true"/>
+				<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="org.eclipse.cdt.make.core.GCCStandardMakePerProjectProfile"/>
-<parser enabled="true"/>
+				<profile id="org.eclipse.cdt.make.core.GCCStandardMakePerProjectProfile">
-</scannerInfoProvider>
+					<buildOutputProvider>
-</profile>
+						<openAction enabled="true" filePath=""/>
-<profile id="org.eclipse.cdt.make.core.GCCStandardMakePerFileProfile">
+						<parser enabled="true"/>
-<buildOutputProvider>
+					</buildOutputProvider>
-<openAction enabled="true" filePath=""/>
+					<scannerInfoProvider id="specsFile">
-<parser enabled="true"/>
+						<runAction arguments="-E -P -v -dD ${plugin_state_location}/${specs_file}" command="gcc" useDefault="true"/>
-</buildOutputProvider>
+						<parser enabled="true"/>
-<scannerInfoProvider id="makefileGenerator">
+					</scannerInfoProvider>
-<runAction arguments="-f ${project_name}_scd.mk" command="make" useDefault="true"/>
+				</profile>
-<parser enabled="true"/>
+				<profile id="org.eclipse.cdt.make.core.GCCStandardMakePerFileProfile">
-</scannerInfoProvider>
+					<buildOutputProvider>
-</profile>
+						<openAction enabled="true" filePath=""/>
-<profile id="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfile">
+						<parser enabled="true"/>
-<buildOutputProvider>
+					</buildOutputProvider>
-<openAction enabled="true" filePath=""/>
+					<scannerInfoProvider id="makefileGenerator">
-<parser enabled="true"/>
+						<runAction arguments="-f ${project_name}_scd.mk" command="make" useDefault="true"/>
-</buildOutputProvider>
+						<parser enabled="true"/>
-<scannerInfoProvider id="specsFile">
+					</scannerInfoProvider>
-<runAction arguments="-E -P -v -dD ${plugin_state_location}/${specs_file}" command="gcc" useDefault="true"/>
+				</profile>
-<parser enabled="true"/>
+				<profile id="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfile">
-</scannerInfoProvider>
+					<buildOutputProvider>
-</profile>
+						<openAction enabled="true" filePath=""/>
-<profile id="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfileCPP">
+						<parser enabled="true"/>
-<buildOutputProvider>
+					</buildOutputProvider>
-<openAction enabled="true" filePath=""/>
+					<scannerInfoProvider id="specsFile">
-<parser enabled="true"/>
+						<runAction arguments="-E -P -v -dD ${plugin_state_location}/${specs_file}" command="gcc" useDefault="true"/>
-</buildOutputProvider>
+						<parser enabled="true"/>
-<scannerInfoProvider id="specsFile">
+					</scannerInfoProvider>
-<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.cpp" command="g++" useDefault="true"/>
+				</profile>
-<parser enabled="true"/>
+				<profile id="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfileCPP">
-</scannerInfoProvider>
+					<buildOutputProvider>
-</profile>
+						<openAction enabled="true" filePath=""/>
-<profile id="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfileC">
+						<parser enabled="true"/>
-<buildOutputProvider>
+					</buildOutputProvider>
-<openAction enabled="true" filePath=""/>
+					<scannerInfoProvider id="specsFile">
-<parser enabled="true"/>
+						<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.cpp" command="g++" useDefault="true"/>
-</buildOutputProvider>
+						<parser enabled="true"/>
-<scannerInfoProvider id="specsFile">
+					</scannerInfoProvider>
-<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.c" command="gcc" useDefault="true"/>
+				</profile>
-<parser enabled="true"/>
+				<profile id="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfileC">
-</scannerInfoProvider>
+					<buildOutputProvider>
-</profile>
+						<openAction enabled="true" filePath=""/>
-<profile id="org.eclipse.cdt.managedbuilder.core.GCCWinManagedMakePerProjectProfile">
+						<parser enabled="true"/>
-<buildOutputProvider>
+					</buildOutputProvider>
-<openAction enabled="true" filePath=""/>
+					<scannerInfoProvider id="specsFile">
-<parser enabled="true"/>
+						<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.c" command="gcc" useDefault="true"/>
-</buildOutputProvider>
+						<parser enabled="true"/>
-<scannerInfoProvider id="specsFile">
+					</scannerInfoProvider>
-<runAction arguments="-E -P -v -dD ${plugin_state_location}/${specs_file}" command="gcc" useDefault="true"/>
+				</profile>
-<parser enabled="true"/>
+				<profile id="org.eclipse.cdt.managedbuilder.core.GCCWinManagedMakePerProjectProfile">
-</scannerInfoProvider>
+					<buildOutputProvider>
-</profile>
+						<openAction enabled="true" filePath=""/>
-<profile id="org.eclipse.cdt.managedbuilder.core.GCCWinManagedMakePerProjectProfileCPP">
+						<parser enabled="true"/>
-<buildOutputProvider>
+					</buildOutputProvider>
-<openAction enabled="true" filePath=""/>
+					<scannerInfoProvider id="specsFile">
-<parser enabled="true"/>
+						<runAction arguments="-E -P -v -dD ${plugin_state_location}/${specs_file}" command="gcc" useDefault="true"/>
-</buildOutputProvider>
+						<parser enabled="true"/>
-<scannerInfoProvider id="specsFile">
+					</scannerInfoProvider>
-<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.cpp" command="g++" useDefault="true"/>
+				</profile>
-<parser enabled="true"/>
+				<profile id="org.eclipse.cdt.managedbuilder.core.GCCWinManagedMakePerProjectProfileCPP">
-</scannerInfoProvider>
+					<buildOutputProvider>
-</profile>
+						<openAction enabled="true" filePath=""/>
-<profile id="org.eclipse.cdt.managedbuilder.core.GCCWinManagedMakePerProjectProfileC">
+						<parser enabled="true"/>
-<buildOutputProvider>
+					</buildOutputProvider>
-<openAction enabled="true" filePath=""/>
+					<scannerInfoProvider id="specsFile">
-<parser enabled="true"/>
+						<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.cpp" command="g++" useDefault="true"/>
-</buildOutputProvider>
+						<parser enabled="true"/>
-<scannerInfoProvider id="specsFile">
+					</scannerInfoProvider>
-<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.c" command="gcc" useDefault="true"/>
+				</profile>
-<parser enabled="true"/>
+				<profile id="org.eclipse.cdt.managedbuilder.core.GCCWinManagedMakePerProjectProfileC">
-</scannerInfoProvider>
+					<buildOutputProvider>
-</profile>
+						<openAction enabled="true" filePath=""/>
-<profile id="org.eclipse.cdt.managedbuilder.xlc.core.XLCManagedMakePerProjectProfile">
+						<parser enabled="true"/>
-<buildOutputProvider>
+					</buildOutputProvider>
-<openAction enabled="false" filePath=""/>
+					<scannerInfoProvider id="specsFile">
-<parser enabled="false"/>
+						<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.c" command="gcc" useDefault="true"/>
-</buildOutputProvider>
+						<parser enabled="true"/>
-<scannerInfoProvider id="specsFile">
+					</scannerInfoProvider>
-<runAction arguments="-E -v ${plugin_state_location}/${specs_file}" command="${XL_compilerRoot}/xlc" useDefault="true"/>
+				</profile>
-<parser enabled="true"/>
+				<scannerConfigBuildInfo instanceId="cdt.managedbuild.toolchain.gnu.macosx.base.2134184396;cdt.managedbuild.toolchain.gnu.macosx.base.2134184396.1840911077;cdt.managedbuild.tool.gnu.c.compiler.macosx.base.1928774909;cdt.managedbuild.tool.gnu.c.compiler.input.330854350">
-</scannerInfoProvider>
+					<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfileC"/>
-</profile>
+					<profile id="org.eclipse.cdt.make.core.GCCStandardMakePerProjectProfile">
-<profile id="org.eclipse.cdt.managedbuilder.xlc.core.XLCManagedMakePerProjectProfileCPP">
+						<buildOutputProvider>
-<buildOutputProvider>
+							<openAction enabled="true" filePath=""/>
-<openAction enabled="false" filePath=""/>
+							<parser enabled="true"/>
-<parser enabled="false"/>
+						</buildOutputProvider>
-</buildOutputProvider>
+						<scannerInfoProvider id="specsFile">
-<scannerInfoProvider id="specsFile">
+							<runAction arguments="-E -P -v -dD ${plugin_state_location}/${specs_file}" command="gcc" useDefault="true"/>
-<runAction arguments="-E -v ${plugin_state_location}/${specs_file}" command="${XL_compilerRoot}/xlC" useDefault="true"/>
+							<parser enabled="true"/>
-<parser enabled="true"/>
+						</scannerInfoProvider>
-</scannerInfoProvider>
+					</profile>
-</profile>
+					<profile id="org.eclipse.cdt.make.core.GCCStandardMakePerFileProfile">
-</storageModule>
+						<buildOutputProvider>
-<storageModule moduleId="org.eclipse.cdt.core.externalSettings"/>
+							<openAction enabled="true" filePath=""/>
-</cconfiguration>
+							<parser enabled="true"/>
-</storageModule>
+						</buildOutputProvider>
-<storageModule moduleId="cdtBuildSystem" version="4.0.0">
+						<scannerInfoProvider id="makefileGenerator">
-<project id="ecoPrimers.null.1292969001" name="ecoPrimers"/>
+							<runAction arguments="-f ${project_name}_scd.mk" command="make" useDefault="true"/>
-</storageModule>
+							<parser enabled="true"/>
+						</scannerInfoProvider>
+					</profile>
+					<profile id="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfile">
+						<buildOutputProvider>
+							<openAction enabled="true" filePath=""/>
+							<parser enabled="true"/>
+						</buildOutputProvider>
+						<scannerInfoProvider id="specsFile">
+							<runAction arguments="-E -P -v -dD ${plugin_state_location}/${specs_file}" command="gcc" useDefault="true"/>
+							<parser enabled="true"/>
+						</scannerInfoProvider>
+					</profile>
+					<profile id="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfileCPP">
+						<buildOutputProvider>
+							<openAction enabled="true" filePath=""/>
+							<parser enabled="true"/>
+						</buildOutputProvider>
+						<scannerInfoProvider id="specsFile">
+							<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.cpp" command="g++" useDefault="true"/>
+							<parser enabled="true"/>
+						</scannerInfoProvider>
+					</profile>
+					<profile id="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfileC">
+						<buildOutputProvider>
+							<openAction enabled="true" filePath=""/>
+							<parser enabled="true"/>
+						</buildOutputProvider>
+						<scannerInfoProvider id="specsFile">
+							<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.c" command="gcc" useDefault="true"/>
+							<parser enabled="true"/>
+						</scannerInfoProvider>
+					</profile>
+					<profile id="org.eclipse.cdt.managedbuilder.core.GCCWinManagedMakePerProjectProfile">
+						<buildOutputProvider>
+							<openAction enabled="true" filePath=""/>
+							<parser enabled="true"/>
+						</buildOutputProvider>
+						<scannerInfoProvider id="specsFile">
+							<runAction arguments="-E -P -v -dD ${plugin_state_location}/${specs_file}" command="gcc" useDefault="true"/>
+							<parser enabled="true"/>
+						</scannerInfoProvider>
+					</profile>
+					<profile id="org.eclipse.cdt.managedbuilder.core.GCCWinManagedMakePerProjectProfileCPP">
+						<buildOutputProvider>
+							<openAction enabled="true" filePath=""/>
+							<parser enabled="true"/>
+						</buildOutputProvider>
+						<scannerInfoProvider id="specsFile">
+							<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.cpp" command="g++" useDefault="true"/>
+							<parser enabled="true"/>
+						</scannerInfoProvider>
+					</profile>
+					<profile id="org.eclipse.cdt.managedbuilder.core.GCCWinManagedMakePerProjectProfileC">
+						<buildOutputProvider>
+							<openAction enabled="true" filePath=""/>
+							<parser enabled="true"/>
+						</buildOutputProvider>
+						<scannerInfoProvider id="specsFile">
+							<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.c" command="gcc" useDefault="true"/>
+							<parser enabled="true"/>
+						</scannerInfoProvider>
+					</profile>
+				</scannerConfigBuildInfo>
+			</storageModule>
+			<storageModule moduleId="org.eclipse.cdt.internal.ui.text.commentOwnerProjectMappings"/>
+		</cconfiguration>
+	</storageModule>
+	<storageModule moduleId="cdtBuildSystem" version="4.0.0">
+		<project id="ecoPrimers.null.1292969001" name="ecoPrimers"/>
+	</storageModule>
 </cproject>

.gitignore

@@ -0,0 +1,15 @@
+*.o
+/src/*.P
+/src/*.a
+/src/ecoPrimer
+/src/libecoPCR/*.P
+/src/libecoPCR/*.a
+/src/libecoPCR/*.o
+/src/libecoprimer/*.P
+/src/libecoprimer/*.a
+/src/libecoprimer/*.o
+/src/libthermo/*.P
+/src/libthermo/*.a
+/src/libthermo/*.o
+phylonorway.*
+src/ecoPrimers

.project

@@ -5,45 +5,26 @@
 	<projects>
 	</projects>
 	<buildSpec>
+		<buildCommand>
+			<name>org.python.pydev.PyDevBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 		<buildCommand>
 			<name>org.eclipse.cdt.managedbuilder.core.genmakebuilder</name>
 			<triggers>clean,full,incremental,</triggers>
 			<arguments>
-				<dictionary>
-					<key>org.eclipse.cdt.make.core.fullBuildTarget</key>
-					<value>all</value>
-				</dictionary>
 				<dictionary>
 					<key>?name?</key>
 					<value></value>
 				</dictionary>
-				<dictionary>
-					<key>org.eclipse.cdt.make.core.enableAutoBuild</key>
-					<value>false</value>
-				</dictionary>
-				<dictionary>
-					<key>org.eclipse.cdt.make.core.enableFullBuild</key>
-					<value>true</value>
-				</dictionary>
-				<dictionary>
-					<key>org.eclipse.cdt.make.core.enableCleanBuild</key>
-					<value>true</value>
-				</dictionary>
-				<dictionary>
-					<key>org.eclipse.cdt.make.core.cleanBuildTarget</key>
-					<value>clean</value>
-				</dictionary>
 				<dictionary>
 					<key>org.eclipse.cdt.make.core.append_environment</key>
 					<value>true</value>
 				</dictionary>
 				<dictionary>
-					<key>org.eclipse.cdt.make.core.contents</key>
+					<key>org.eclipse.cdt.make.core.autoBuildTarget</key>
-					<value>org.eclipse.cdt.make.core.activeConfigSettings</value>
+					<value>all</value>
-				</dictionary>
-				<dictionary>
-					<key>org.eclipse.cdt.make.core.useDefaultBuildCmd</key>
-					<value>true</value>
 				</dictionary>
 				<dictionary>
 					<key>org.eclipse.cdt.make.core.buildArguments</key>
@@ -54,13 +35,37 @@
 					<value>make</value>
 				</dictionary>
 				<dictionary>
-					<key>org.eclipse.cdt.make.core.autoBuildTarget</key>
+					<key>org.eclipse.cdt.make.core.cleanBuildTarget</key>
+					<value>clean</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.contents</key>
+					<value>org.eclipse.cdt.make.core.activeConfigSettings</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.enableAutoBuild</key>
+					<value>false</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.enableCleanBuild</key>
+					<value>true</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.enableFullBuild</key>
+					<value>true</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.fullBuildTarget</key>
 					<value>all</value>
 				</dictionary>
 				<dictionary>
 					<key>org.eclipse.cdt.make.core.stopOnError</key>
 					<value>true</value>
 				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.useDefaultBuildCmd</key>
+					<value>true</value>
+				</dictionary>
 			</arguments>
 		</buildCommand>
 		<buildCommand>
@@ -73,5 +78,6 @@
 		<nature>org.eclipse.cdt.core.cnature</nature>
 		<nature>org.eclipse.cdt.managedbuilder.core.ScannerConfigNature</nature>
 		<nature>org.eclipse.cdt.managedbuilder.core.managedBuildNature</nature>
+		<nature>org.python.pydev.pythonNature</nature>
 	</natures>
 </projectDescription>

.pydevproject

@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<?eclipse-pydev version="1.0"?>
+
+<pydev_project>
+<pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Python 2.6</pydev_property>
+<pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.6</pydev_property>
+</pydev_project>

VERSION

@@ -0,0 +1 @@
+0.5

src/Makefile

@@ -1,4 +1,4 @@
-EXEC=ecoPrimer
+EXEC=ecoPrimers
 
 PRIMER_SRC= ecoprimer.c
 PRIMER_OBJ= $(patsubst %.c,%.o,$(PRIMER_SRC))
@@ -6,10 +6,12 @@ PRIMER_OBJ= $(patsubst %.c,%.o,$(PRIMER_SRC))
 
 SRCS= $(PRIMER_SRC) 
 
-LIB= -lecoPCR -lecoprimer -lz -lm
+LIB= -lecoprimer -lecoPCR -lthermo -lz -lm 
 
 LIBFILE= libecoPCR/libecoPCR.a \
-         libecoprimer/libecoprimer.a
+         libecoprimer/libecoprimer.a \
+         libthermo/libthermo.a \
+	 
 
 
 include global.mk
@@ -25,8 +27,8 @@ all: $(EXEC)
 
 # executable compilation and link
 
-ecoPrimer: $(PRIMER_OBJ) $(LIBFILE) 
+ecoPrimers: $(PRIMER_OBJ) $(LIBFILE) 
-	$(CC) $(LDFLAGS) -O5 -m64 -fast -o $@ $< $(LIBPATH) $(LIB)
+	$(CC) $(LDFLAGS) -O5 -o $@ $< $(LIBPATH) $(LIB)
 	
 
 ########
@@ -41,6 +43,8 @@ libecoPCR/libecoPCR.a:
 libecoprimer/libecoprimer.a:
 	$(MAKE) -C libecoprimer
 	
+libthermo/libthermo.a:
+	$(MAKE) -C libthermo
 	
 ########
 #
@@ -50,9 +54,26 @@ libecoprimer/libecoprimer.a:
 
 clean:
 	rm -f *.o	
+	rm -f *.P
 	rm -f $(EXEC)
 	$(MAKE) -C libecoPCR clean
 	$(MAKE) -C libecoprimer clean
+	$(MAKE) -C libthermo clean
 		
 
-		
+		
+########
+#
+# clean for k2 to remove .o and .P files
+#
+########
+
+k2clean:
+	rm -f *.o	
+	rm -f *.P
+	rm -f libecoPCR/*.o
+	rm -f libecoPCR/*.P
+	rm -f libecoprimer/*.o
+	rm -f libecoprimer/*.P
+	rm -f libthermo/*.o
+	rm -f libthermo/*.P

src/global.mk

@@ -1,9 +1,10 @@
-MACHINE=MAC_OS_X
+MACHINE=LINUX
-LIBPATH= -Llibapat -LlibecoPCR -Llibecoprimer
+LIBPATH= -LlibecoPCR -Llibecoprimer -Llibthermo -L/usr/local/lib
 MAKEDEPEND = gcc -D$(MACHINE) -M $(CPPFLAGS) -o $*.d $<
 
 CC=gcc
-CFLAGS= -W -Wall -O5 -m64 -fast -g
+CFLAGS= -W -Wall -O5
+#CFLAGS= -W -Wall -O5 -m64 -g
 #CFLAGS= -W -Wall -O0 -m64  -g
 #CFLAGS= -W -Wall -O5 -fast -g
 
@@ -17,4 +18,4 @@ default: all
 	@sed 's/\($*\)\.o[ :]*/\1.o $@ : /g' < $*.d > $@; \
 	rm -f $*.d; [ -s $@ ] || rm -f $@
 
-include $(SRCS:.c=.P)
+include $(SRCS:.c=.P)

src/libecoPCR/ecoMalloc.c

@@ -2,7 +2,7 @@
 #include <stdlib.h>
 
 static int eco_log_malloc = 0;
-static size_t eco_amount_malloc=0;
+//static size_t eco_amount_malloc=0;
 static size_t eco_chunk_malloc=0;
 
 void    eco_trace_memory_allocation()
@@ -17,10 +17,10 @@ void    eco_untrace_memory_allocation()
 
 void ecoMallocedMemory()
 {
-	return eco_amount_malloc;
+	//eco_amount_malloc;
 }
 
-void   *eco_malloc(int32_t chunksize,
+void   *eco_malloc(int64_t chunksize,
                    const char *error_message,
                    const char *filename,
                    int32_t    line)
@@ -37,7 +37,7 @@ void   *eco_malloc(int32_t chunksize,
 
 	if (eco_log_malloc)
 		fprintf(stderr,
-			    "Memory segment located at %p of size %d is allocated (file : %s [%d])",
+			    "Memory segment located at %p of size %lld is allocated (file : %s [%d])",
 			    chunk,
 			    chunksize,
 			    filename,
@@ -47,25 +47,33 @@ void   *eco_malloc(int32_t chunksize,
 }
 
 void   *eco_realloc(void *chunk,
-                    int32_t newsize,
+                    int64_t newsize,
                     const char *error_message,
                     const char *filename,
                     int32_t    line)
 {
 	void *newchunk;
 
+	if (newsize == 0)
+	{
+		if (chunk)
+			free(chunk);
+		return NULL;
+	}
+
 	newchunk = realloc(chunk,newsize);
 
-
 	if (!newchunk)
+           {
+        fprintf(stderr,"Requested memory : %lld\n",newsize);
 		ecoError(ECO_MEM_ERROR,error_message,filename,line);
-
+           }
 	if (!chunk)
 		eco_chunk_malloc++;
 
 	if (eco_log_malloc)
 		fprintf(stderr,
-			    "Old memory segment %p is reallocated at %p with a size of %d (file : %s [%d])",
+			    "Old memory segment %p is reallocated at %p with a size of %lld (file : %s [%d])",
 			    chunk,
 			    newchunk,
 			    newsize,

src/libecoPCR/ecoPCR.h

@@ -21,8 +21,8 @@ typedef struct {
 	int32_t  taxid;
 	char     AC[20];
 	int32_t  DE_length;
-	int32_t  SQ_length;
+	uint32_t  SQ_length;
-	int32_t  CSQ_length; /*what is this CSQ_length ? */
+	uint32_t  CSQ_length; /*what is this CSQ_length ? */
 
 	char     data[1];
 
@@ -30,7 +30,7 @@ typedef struct {
 
 typedef struct {
 	int32_t taxid;
-	int32_t SQ_length;
+	uint32_t SQ_length;
 	int32_t isexample;
 	char    *AC;
 	char    *DE;
@@ -130,14 +130,14 @@ typedef struct {
 int32_t is_big_endian();
 int32_t swap_int32_t(int32_t);
 
-void   *eco_malloc(int32_t chunksize,
+void   *eco_malloc(int64_t chunksize,
                    const char *error_message,
                    const char *filename,
                    int32_t    line);
 
 
 void   *eco_realloc(void *chunk,
-                    int32_t chunksize,
+                    int64_t chunksize,
                     const char *error_message,
                     const char *filename,
                     int32_t    line);
@@ -219,7 +219,7 @@ econameidx_t     *read_nameidx(const char *filename,ecotaxonomy_t *taxonomy);
 	 * @return pointer to a taxonomy index structure
 	 */
 
-ecotxidx_t       *read_taxonomyidx(const char *filename);
+ecotxidx_t       *read_taxonomyidx(const char *filename,const char *filename2);
 
 ecotaxonomy_t    *read_taxonomy(const char *prefix,int32_t readAlternativeName);
 

src/libecoPCR/ecofilter.c

@@ -16,4 +16,5 @@ int eco_is_taxid_included(	ecotaxonomy_t *taxonomy,
 			return 1;
 	
 	return 0;
-}
+}
+

src/libecoPCR/ecorank.c

@@ -12,14 +12,14 @@ ecorankidx_t     *read_rankidx(const char *filename)
 	int32_t      i;
 	int32_t      rs;
 	char         *buffer;
-	
+
 	f = open_ecorecorddb(filename,&count,1);
-	
+
 	index = (ecorankidx_t*) ECOMALLOC(sizeof(ecorankidx_t) + sizeof(char*) * (count-1),
 	                                  "Allocate rank index");
-	 
+
-	index->count=count;                                 
+	index->count=count;
-	          
+
 	for (i=0; i < count; i++)
 		{
 			buffer = read_ecorecord(f,&rs);
@@ -27,21 +27,18 @@ ecorankidx_t     *read_rankidx(const char *filename)
 			                                  "Allocate rank label");
 			strncpy(index->label[i],buffer,rs);
 		}
-		
+
 	return index;
 }
 
 int32_t rank_index(const char* label,ecorankidx_t* ranks)
 {
 	char **rep;
-	
+        fprintf(stderr,"Looking for rank -%s-... ",label);
 	rep = bsearch(label,ranks->label,ranks->count,sizeof(char*),compareRankLabel);
-	
+
 	if (rep)
 		return rep-ranks->label;
-	else
-		ECOERROR(ECO_NOTFOUND_ERROR,"Rank label not found");
-		
 	return -1;
 }
 

src/libecoPCR/ecoseq.c

@@ -2,6 +2,7 @@
 #include <stdlib.h>
 #include <string.h>
 #include <zlib.h>
+#include <ctype.h>
 #include <string.h>
 #include <stdio.h>
 
@@ -100,6 +101,8 @@ ecoseq_t *readnext_ecoseq(FILE *f)
 	int32_t  comp_status;
 	unsigned long int seqlength;
 	int32_t  rs;
+	char *c;
+	int32_t i;
 
 	raw = read_ecorecord(f,&rs);
 
@@ -144,6 +147,10 @@ ecoseq_t *readnext_ecoseq(FILE *f)
     if (comp_status != Z_OK)
     	ECOERROR(ECO_IO_ERROR,"I cannot uncompress sequence data");
 
+    for (c=seq->SQ,i=0;i<seqlength;c++,i++)
+    	*c=toupper(*c);
+
+//	fprintf(stderr,"seq name : %30s seq size : %d\n",seq->DE,seq->SQ_length);
 	return seq;
 }
 
@@ -188,7 +195,7 @@ ecoseq_t *ecoseq_iterator(const char *prefix)
 {
 	static FILE    *current_seq_file= NULL;
 	static int32_t current_file_idx = 1;
-	static char    current_prefix[1024];
+	static char    current_prefix[1025];
 	ecoseq_t       *seq;
 
 	if (prefix)

src/libecoPCR/ecotax.c

@@ -10,23 +10,41 @@ static ecotx_t *readnext_ecotaxon(FILE *f,ecotx_t *taxon);
  * @param	pointer to the database (.tdx file)
  * @return	a ecotxidx_t structure
  */
-ecotxidx_t     *read_taxonomyidx(const char *filename)
+ecotxidx_t     *read_taxonomyidx(const char *filename,const char *filename2)
 {
 	int32_t      count;
+	int32_t      count2;
 	FILE         *f;
+	FILE         *f2;
 	ecotxidx_t *index;
 	int32_t      i;
 
-	f = open_ecorecorddb(filename,&count,1);
+	f  = open_ecorecorddb(filename,&count,1);
+	f2 = open_ecorecorddb(filename2,&count2,0);
 
-	index = (ecotxidx_t*) ECOMALLOC(sizeof(ecotxidx_t) + sizeof(ecotx_t) * (count-1),
+
+
+	index = (ecotxidx_t*) ECOMALLOC(sizeof(ecotxidx_t) + sizeof(ecotx_t) * (count+count2-1),
 	                                  "Allocate taxonomy");
 
-	index->count=count;
+	index->count=count+count2;
+
+	fprintf(stderr,"Reading %d taxa...\n",count);
 	for (i=0; i < count; i++){
 		readnext_ecotaxon(f,&(index->taxon[i]));
-		index->taxon[i].parent=index->taxon + (size_t)index->taxon[i].parent;
+		index->taxon[i].parent=index->taxon + (int32_t)index->taxon[i].parent;
 	}
+
+	if (count2>0)
+		fprintf(stderr,"Reading %d local taxa...\n",count2);
+	else
+		fprintf(stderr,"No local taxon\n");
+
+	for (i=0; i < count2; i++){
+		readnext_ecotaxon(f2,&(index->taxon[count+i]));
+		index->taxon[count+i].parent=index->taxon + (int32_t)index->taxon[count+i].parent;
+	}
+
 	return index;
 }
 
@@ -94,7 +112,7 @@ ecotx_t *readnext_ecotaxon(FILE *f,ecotx_t *taxon)
 		raw->taxid      = swap_int32_t(raw->taxid);
 	}
 
-	taxon->parent = (ecotx_t*)(size_t)raw->parent;
+	taxon->parent = (ecotx_t*)raw->parent;
 	taxon->taxid  = raw->taxid;
 	taxon->rank   = raw->rank;
 
@@ -111,6 +129,7 @@ ecotaxonomy_t    *read_taxonomy(const char *prefix,int32_t readAlternativeName)
 {
 	ecotaxonomy_t *tax;
 	char          *filename;
+	char          *filename2;
 	int           buffsize;
 
 	tax = ECOMALLOC(sizeof(ecotaxonomy_t),
@@ -120,14 +139,17 @@ ecotaxonomy_t    *read_taxonomy(const char *prefix,int32_t readAlternativeName)
 
 	filename = ECOMALLOC(buffsize,
 	                     "Allocate filename");
+	filename2= ECOMALLOC(buffsize,
+	                     "Allocate filename");
 
 	snprintf(filename,buffsize,"%s.rdx",prefix);
 
 	tax->ranks = read_rankidx(filename);
 
 	snprintf(filename,buffsize,"%s.tdx",prefix);
+	snprintf(filename2,buffsize,"%s.ldx",prefix);
 
-	tax->taxons = read_taxonomyidx(filename);
+	tax->taxons = read_taxonomyidx(filename,filename2);
 
 	if (readAlternativeName)
 	{
@@ -319,6 +341,9 @@ ecotx_t *eco_getsuperkingdom(ecotx_t *taxon,
 	if (taxonomy && tax!=taxonomy)
 	{
 		rankindex = rank_index("superkingdom",taxonomy->ranks);
+                if (rankindex < 0) {
+		   rankindex = rank_index("domain",taxonomy->ranks);
+                }
 		tax=taxonomy;
 	}
 

src/libecoprimer/Makefile

@@ -10,8 +10,13 @@ SOURCES = goodtaxon.c \
           queue.c \
           libstki.c \
           sortmatch.c \
+          pairtree.c \
           pairs.c \
-          apat_search.c
+          taxstats.c \
+          apat_search.c \
+		  filtering.c \
+		  PrimerSets.c \
+		  ahocorasick.c
 
 SRCS=$(SOURCES)
          

src/libecoprimer/PrimerSets.h

@@ -0,0 +1,58 @@
+#ifndef PRIMERSETS_H_
+#define PRIMERSETS_H_
+
+#include "ecoprimer.h"
+
+#define PRIMERS_IN_SET_COUNT 10
+
+typedef struct {
+	int		*set_wellIdentifiedTaxa;
+	int32_t set_pairs[PRIMERS_IN_SET_COUNT];
+	float set_specificity;
+	float set_coverage;
+	float set_lmean;
+	float set_lcov;
+	float set_score;
+	int32_t set_intaxa;
+	int32_t set_wi_cnt;
+}pairset;
+
+typedef struct{
+	ppair_t* sortedpairs;
+	int32_t sorted_count;
+	pecodnadb_t seqdb;
+	poptions_t options;
+}SetParams;
+
+typedef struct{
+	float t_spc; //specificity contribution
+	float t_cov; //coverage contribution
+	float t_lmd; //link spread difference
+	float len; //length
+	float score; //score
+}primerscore;
+
+void add_pair_in_set (pairset *pair_set, int32_t pset_idx, int32_t prb_idx, SetParams *pparams);
+void get_next_pair_options (int *pair_wi_count_sorted_ids, pairset *pair_set, SetParams *pparams);
+float get_links_distribution (int prb_idx, pairset *prob_set, SetParams *pparams);
+pairset build_primers_set_greedy_spc (SetParams *pparams);
+void get_set_mean_cov_stats (pairset *prob_set, SetParams *pparams);
+void some_other_set_possibilities (pairset *pair_set,
+		ppair_t * sortedpairs, int32_t sorted_count, pecodnadb_t seqdb, poptions_t options);
+void sets_by_SimulatedAnealing (pairset *pair_set,
+		ppair_t * sortedpairs, int32_t sorted_count, pecodnadb_t seqdb, poptions_t options);
+void sets_by_TabuSearch (pairset *pair_set,
+		ppair_t * sortedpairs, int32_t sorted_count, pecodnadb_t seqdb, poptions_t options);
+pairset * sets_by_BruteForce (ppair_t * sortedpairs, 
+		int32_t sorted_count, pecodnadb_t seqdb, poptions_t options);
+pairset * extend_set_randomly (pairset *pair_set, SetParams *params, int extend_to_cnt);
+void build_and_print_sets (ppair_t * sortedpairs, int32_t sorted_count, pecodnadb_t seqdb, poptions_t options);
+int32_t get_next_option_increasing_cov (pairset *pair_set, SetParams *pparams);
+void reset_set_props (pairset *pair_set, SetParams *pparams);
+void primers_graph_graphviz (ppair_t * sortedpairs,
+		int32_t sorted_count, poptions_t options);
+size_t primers_changeSortedArray (ppair_t ** pairs,
+		size_t sorted_count, poptions_t options);
+size_t primers_filterWithGivenLinks (ppair_t ** pairs,
+		size_t sorted_count, poptions_t options);
+#endif 

src/libecoprimer/ahocorasick.c

@@ -0,0 +1,478 @@
+/*
+ * ahocorasick.h
+ *
+ *  Created on: 26 march 2011
+ *      Author: tiayyba
+ */
+#include <inttypes.h>
+#include "hashencoder.h"
+#include "ahocorasick.h"
+
+void ahoc_graphKeywordTree (aho_state *root);
+aho_state *groot = NULL; //just for graph testing
+
+#define BASEATINDEX(w, l, i) (uint8_t)((((w)&(0x3LLU<<(((l)-(i))*2)))>>(((l)-(i))*2)) & 0x3LLU)
+
+void ahoc_addOutputElement (aho_state *node, bool_t isdirect, uint32_t idx)
+{
+	if (!node) return;
+	if (node->output.count == 0)
+		node->output.out_set = ECOMALLOC(sizeof(aho_output),
+                                      "Cannot allocate memory for aho-corasick state output element");
+	else
+		node->output.out_set = ECOREALLOC(node->output.out_set, (node->output.count+1)*sizeof(aho_output),
+                                      "Cannot allocate memory for aho-corasick state output element");
+	node->output.out_set[node->output.count].wordidx = idx;
+	node->output.out_set[node->output.count].isdirect = isdirect;
+	node->output.count++;
+}
+
+//is the passed output element in the set
+bool_t ahoc_isOutputIn (aho_state *node, aho_output ot)
+{
+	uint32_t i;
+
+	for (i=0; i<node->output.count; i++)
+		if (node->output.out_set[i].isdirect == ot.isdirect && node->output.out_set[i].wordidx == ot.wordidx) return TRUE;
+	return FALSE;
+}
+
+//take union of output of the two nodes and put in node1
+void ahoc_unionOutputElements (aho_state *node1, aho_state *node2)
+{
+	uint32_t i;
+
+	for (i=0; i<node2->output.count; i++)
+		if (ahoc_isOutputIn (node1, node2->output.out_set[i]) == FALSE)
+			ahoc_addOutputElement (node1, node2->output.out_set[i].isdirect, node2->output.out_set[i].wordidx);
+}
+
+void ahoc_addKeyword (aho_state *root, word_t w, bool_t isdirect, uint32_t idx, poptions_t options)
+{
+	uint32_t i;
+	aho_state *nextnode = root;
+	uint8_t basecode;
+	static uint32_t state_id = 0;
+	
+	//fprintf (stderr, "%s\n", ecoUnhashWord(w, options->primer_length));
+	for (i=1; i<=options->primer_length; i++)
+	{
+		basecode = BASEATINDEX (w, options->primer_length, i);
+		//fprintf (stderr, "%d", basecode);
+		if (nextnode->next[basecode] == NULL)
+		{
+			//add new state
+			nextnode->next[basecode] =  ECOMALLOC(sizeof(aho_state),
+                                      "Cannot allocate memory for aho-corasick state");
+			nextnode = nextnode->next[basecode];
+			//initialize state
+			nextnode->id = ++state_id;
+			nextnode->next[0]=nextnode->next[1]=nextnode->next[2]=nextnode->next[3]=NULL;
+			nextnode->fail = NULL;
+			nextnode->output.count = 0;
+		}
+		else
+			nextnode = nextnode->next[basecode];
+	}
+	//fprintf (stderr, "\n", basecode);
+	//new pattern addess so add node ouptup element
+	ahoc_addOutputElement (nextnode, isdirect, idx);
+}
+
+void ahoc_buildKeywordTree (aho_state *root, pwordcount_t words, poptions_t options)
+{
+	uint32_t i;
+	if (!root) return;
+
+	//init root
+	root->id = 0;
+	root->next[0]=root->next[1]=root->next[2]=root->next[3]=NULL;
+	root->fail = NULL;
+	root->output.count = 0;
+
+	//now add each word as a pattern in the keyword tree
+	for (i=0; i<words->size; i++)
+	{
+		//add direct word
+		word_t w=WORD(words->words[i]);
+		ahoc_addKeyword (root, w, TRUE, i, options);
+
+		//add reverse word
+		w=ecoComplementWord(w,options->primer_length);
+		ahoc_addKeyword (root, w, FALSE, i, options);
+	}
+
+	//loop on root if some base has no out going edge from roots
+	for (i=0; i<4; i++)
+		if (root->next[i] == NULL)
+			root->next[i] = root;
+}
+
+void ahoc_enqueue (aho_queue *ahoqueue, aho_state *node)
+{
+	queue_node *q;
+	if (node == NULL) return;
+
+	q = ECOMALLOC(sizeof(queue_node),
+            "Cannot allocate memory for aho-corasick queue node");
+	q->state_node = node;
+	q->next = NULL;
+
+	if (ahoqueue->first == NULL)
+	{
+		ahoqueue->first = q;
+		ahoqueue->last = q;
+	}
+	else
+	{
+		ahoqueue->last->next = q;
+		ahoqueue->last = q;
+	}
+}
+
+aho_state *ahoc_dequeue (aho_queue *ahoqueue)
+{
+	aho_state *node = NULL;
+	queue_node *q;
+
+	if (ahoqueue->first == NULL) return node;
+	q = ahoqueue->first;
+	ahoqueue->first = q->next;
+
+	node = q->state_node;
+	ECOFREE (q, "Cannot free memory for aho-corasick queue node");
+	return node;
+}
+
+//set fail links and output sets for the keyword tree
+void ahoc_updateForFailAndOutput (aho_state *root)
+{
+	int32_t i;
+	aho_queue Q;
+	aho_state *node_r;
+	aho_state *node_u;
+	aho_state *node_v;
+
+	//empty queue
+	Q.first = NULL;
+	Q.last = NULL;
+
+	//for us alphabet has 4 elements, A=0, C=1, G=2 and T=3
+	for (i=0; i<4; i++)
+	{
+		if (root->next[i] != root && root->next[i] != NULL)
+		{
+			root->next[i]->fail = root;
+			ahoc_enqueue (&Q, root->next[i]);
+		}
+	}
+
+	//while queue not empty
+	while (Q.first != NULL)
+	{
+		node_r = ahoc_dequeue (&Q);
+		for (i=0; i<4; i++)
+		{
+			if (node_r->next[i] != NULL)
+			{
+				node_u = node_r->next[i];
+				ahoc_enqueue (&Q, node_u);
+				node_v = node_r->fail;
+				while (node_v->next[i] == NULL) 
+					node_v = node_v->fail;
+				node_u->fail = node_v->next[i];
+				ahoc_unionOutputElements (node_u, node_u->fail);
+			}
+		}
+	}
+}
+
+void ahoc_freeKeywordTree (aho_state *node)
+{
+	int i;
+	for (i=0; i<4; i++)
+		if (node->next[i])
+			ahoc_freeKeywordTree (node->next[i]);
+	if (node->output.count > 0)
+		ECOFREE (node->output.out_set, "Free failed for node output");
+	ECOFREE (node, "Free failed for node");
+}
+
+pprimercount_t ahoc_lookforStrictPrimers (pecodnadb_t database, uint32_t seqdbsize,uint32_t exampleCount,
+		                     pwordcount_t words,poptions_t options)
+{
+	aho_state automaton_root;
+	aho_state *curr_state;
+	//uint32_t  inSequenceQuorum;
+	uint32_t  outSequenceQuorum;
+	pprimer_t  data;
+	pprimercount_t primers;
+	uint32_t   i, j, k;
+	int32_t pos;
+	uint32_t lmax;
+	char *base;
+	int8_t code;
+	uint32_t   goodPrimers=0;
+
+
+	//inSequenceQuorum = (uint32_t)floor((float)exampleCount * options->sensitivity_quorum);
+	outSequenceQuorum = (uint32_t)floor((float)(seqdbsize-exampleCount) * options->false_positive_quorum);
+
+	//fprintf(stderr,"  Primers should be at least present in %d/%d example sequences\n",inSequenceQuorum,exampleCount);
+	fprintf(stderr,"  Primers should not be present in more than %d/%d counterexample sequences\n",outSequenceQuorum,(seqdbsize-exampleCount));
+
+	data = ECOMALLOC(words->size * sizeof(primer_t),
+			         "Cannot allocate memory for fuzzy matching results");
+	for (i=0; i < words->size; i++)
+	{
+		data[i].word=WORD(words->words[i]);
+		data[i].inexample = 0;
+		data[i].outexample= 0;
+
+		data[i].directCount=ECOMALLOC(seqdbsize * sizeof(uint32_t),
+		              	"Cannot allocate memory for primer position");
+		data[i].directPos = ECOMALLOC(seqdbsize * sizeof(poslist_t),
+				"Cannot allocate memory for primer position");
+		data[i].reverseCount=ECOMALLOC(seqdbsize * sizeof(uint32_t),
+		 		"Cannot allocate memory for primer position");
+		data[i].reversePos = ECOMALLOC(seqdbsize * sizeof(poslist_t),
+				"Cannot allocate memory for primer position");
+	}
+
+	//build keywords automaton
+	ahoc_buildKeywordTree (&automaton_root, words, options);
+	//set fail links and output sets
+	ahoc_updateForFailAndOutput (&automaton_root);
+
+	//debug; print keywordtree in a gv file
+	//ahoc_graphKeywordTree (&automaton_root);
+
+	//loop on each sequence for its each base and find words
+	for (i=0; i < seqdbsize; i++)
+	{
+		if(database[i]->SQ_length <= options->primer_length) continue;
+
+		lmax = database[i]->SQ_length;
+		if (!options->circular)
+			lmax += options->primer_length-1;
+		curr_state = &automaton_root;
+
+		for (j=0,base=database[i]->SQ; j<lmax; j++,base++)
+		{
+			if (i==(uint32_t)database[i]->SQ_length) base=database[i]->SQ;
+
+			//code = encoder[(*base) - 'A'];
+			code = *base;
+			//if (iii++ < 30)
+			//	fprintf (stderr, "%d:%d,", *base, code);
+			if (code < 0 || code > 3)
+			{
+				//if error char, start from root for next character
+				//+forget any incomplete words
+				curr_state = &automaton_root;
+				continue;
+			}
+			while (curr_state->next[code] == NULL) curr_state = curr_state->fail;
+			curr_state = curr_state->next[code];
+
+			//start position of primer is options->primer_length-1 chars back
+			pos = j-options->primer_length+1;
+			if (pos < 0) pos = database[i]->SQ_length+pos;
+
+			//set output, if there is some output on this state then
+			//+all words in the output set complete here, so increment their
+			//+found properties for current sequence
+			for (k=0; k<curr_state->output.count; k++)
+			{
+				if (curr_state->output.out_set[k].isdirect)
+					data[curr_state->output.out_set[k].wordidx].directCount[i]++;
+				else
+					data[curr_state->output.out_set[k].wordidx].reverseCount[i]++;
+
+				if (options->no_multi_match)
+				{
+					if ((data[curr_state->output.out_set[k].wordidx].directCount[i] + 
+					  data[curr_state->output.out_set[k].wordidx].reverseCount[i]) > 1)
+						//since multimach not allowd, set an indication on 1st seq position that
+						//+ a multimatch was found, so that this word will be filtered out
+						//+ and because of first postion we wont have to search the whole array
+						//+ to find if it voilated nomultimatch constraint for some seq
+						data[curr_state->output.out_set[k].wordidx].directCount[0] = 2;
+					else
+					{
+						if (curr_state->output.out_set[k].isdirect)
+							//direct word found on jth position of ith sequence
+							data[curr_state->output.out_set[k].wordidx].directPos[i].value = (uint32_t)pos;
+						else
+							//reverse word found on jth position of ith sequence
+							data[curr_state->output.out_set[k].wordidx].reversePos[i].value = (uint32_t)pos;
+					}
+				}
+				else
+				{
+					//okay multi match allowed
+					if (curr_state->output.out_set[k].isdirect)
+					{
+						if (data[curr_state->output.out_set[k].wordidx].directCount[i] == 1)
+							data[curr_state->output.out_set[k].wordidx].directPos[i].value = (uint32_t)pos;
+						else
+						{
+							//need to create or extend the positions list
+							if (data[curr_state->output.out_set[k].wordidx].directCount[i] == 2)
+							{
+								//for second element, first was put in .value, so dont forget to copy that in the array too
+								data[curr_state->output.out_set[k].wordidx].directPos[i].pointer = ECOMALLOC(2 * sizeof(uint32_t),
+		                      													"Cannot allocate memory for primer position");
+								data[curr_state->output.out_set[k].wordidx].directPos[i].pointer[0] = data[curr_state->output.out_set[k].wordidx].directPos[i].value;
+								data[curr_state->output.out_set[k].wordidx].directPos[i].pointer[1] = (uint32_t)pos;
+							}
+							else
+							{
+								//for third or greater element
+								data[curr_state->output.out_set[k].wordidx].directPos[i].pointer = ECOREALLOC(data[curr_state->output.out_set[k].wordidx].directPos[i].pointer, 
+																	data[curr_state->output.out_set[k].wordidx].directCount[i] * sizeof(uint32_t),
+		                      													"Cannot allocate memory for primer position");
+								data[curr_state->output.out_set[k].wordidx].directPos[i].pointer[data[curr_state->output.out_set[k].wordidx].directCount[i]-1] = (uint32_t)pos;
+							}
+						}
+					}
+					else
+					{
+						if (data[curr_state->output.out_set[k].wordidx].reverseCount[i] == 1)
+							data[curr_state->output.out_set[k].wordidx].reversePos[i].value = (uint32_t)pos;
+						else
+						{
+							//need to create or extend the positions list
+							if (data[curr_state->output.out_set[k].wordidx].reverseCount[i] == 2)
+							{
+								//for second element, first was put in .value, so dont forget to copy that in the array too
+								data[curr_state->output.out_set[k].wordidx].reversePos[i].pointer = ECOMALLOC(2 * sizeof(uint32_t),
+		                      													"Cannot allocate memory for primer position");
+								data[curr_state->output.out_set[k].wordidx].reversePos[i].pointer[0] = data[curr_state->output.out_set[k].wordidx].reversePos[i].value;
+								data[curr_state->output.out_set[k].wordidx].reversePos[i].pointer[1] = (uint32_t)pos;
+							}
+							else
+							{
+								//for third or greater element
+								data[curr_state->output.out_set[k].wordidx].reversePos[i].pointer = ECOREALLOC(data[curr_state->output.out_set[k].wordidx].reversePos[i].pointer, 
+																	data[curr_state->output.out_set[k].wordidx].reverseCount[i] * sizeof(uint32_t),
+		                      													"Cannot allocate memory for primer position");
+								data[curr_state->output.out_set[k].wordidx].reversePos[i].pointer[data[curr_state->output.out_set[k].wordidx].reverseCount[i]-1] = (uint32_t)pos;
+							}
+						}
+					}
+				}
+				//dont forget to increment inexample or outexample count, but only once for a sequence
+				if ((data[curr_state->output.out_set[k].wordidx].directCount[i] + 
+				  data[curr_state->output.out_set[k].wordidx].reverseCount[i]) == 1)
+				{
+					if (database[i]->isexample)
+						data[curr_state->output.out_set[k].wordidx].inexample++;
+					else
+						data[curr_state->output.out_set[k].wordidx].outexample++;
+				}
+			}
+		}
+	}
+
+	//Only thing that remains is to remove the failed words
+	for (i=0,j=0; i<words->size; i++)
+	{
+		fprintf(stderr,"Primers %5d/%lld analyzed  => sequence : %s in %d example and %d counterexample sequences       \r",
+				i+1,words->size,ecoUnhashWord(data[i].word,options->primer_length),
+				data[i].inexample,data[i].outexample);
+
+		//if (data[i].inexample < inSequenceQuorum || (data[i].directCount[0] == 2 && options->no_multi_match))
+		if (data[i].directCount[0] == 2 && options->no_multi_match)
+		{
+			//bad word, delete from the array
+			for (k=0; k<seqdbsize; k++)
+			{
+				if (data[i].directCount[k] > 1)
+					ECOFREE (data[i].directPos[k].pointer, "Cannot free position pointer.");
+				if (data[i].reverseCount[k] > 1)
+					ECOFREE (data[i].reversePos[k].pointer, "Cannot free position pointer.");
+			}
+			ECOFREE (data[i].directCount, "Cannot free position pointer.");
+			ECOFREE (data[i].directPos, "Cannot free position pointer.");
+			ECOFREE (data[i].reverseCount, "Cannot free position pointer.");
+			ECOFREE (data[i].reversePos, "Cannot free position pointer.");
+		}
+		else
+		{
+			//data[i].good = data[i].inexample >= inSequenceQuorum && data[i].outexample <= outSequenceQuorum;
+			data[i].good = data[i].outexample <= outSequenceQuorum;
+			goodPrimers+=data[i].good? 1:0;
+			if (j < i)
+				data[j] = data[i];
+			j++;
+		}
+	}
+	fprintf(stderr,"\n\nOn %lld analyzed primers %d respect quorum conditions\n",words->size,goodPrimers);
+	fprintf(stderr,"Conserved primers for further analysis : %d/%lld\n",j,words->size);
+
+	primers = ECOMALLOC(sizeof(primercount_t),"Cannot allocate memory for primer table");
+	primers->primers=ECOREALLOC(data,
+			                    j * sizeof(primer_t),
+								"Cannot reallocate memory for fuzzy matching results");
+	primers->size=j;
+
+	//free memory of keyword table
+	for (i=0; i<4; i++)
+		if (automaton_root.next[i] != &automaton_root)
+			ahoc_freeKeywordTree (automaton_root.next[i]);
+
+	return primers;
+}
+
+void ahoc_graphPrintNodesInfo (aho_state *node, FILE* gfile)
+{
+	uint32_t i;
+	fprintf (gfile, "\"%d\"[\n", node->id);
+	fprintf (gfile, "label=\"%d\\n", node->id);
+	for (i=0; i<node->output.count; i++)
+		fprintf (gfile, "%d%c,", node->output.out_set[i].wordidx, node->output.out_set[i].isdirect?'d':'r');
+	fprintf (gfile, "\"\n];\n");
+
+	for (i=0; i<4; i++)
+		if (node->next[i] != NULL && node->next[i] != node)
+			ahoc_graphPrintNodesInfo (node->next[i], gfile);
+}
+
+void ahoc_graphPrintNodesLinks (aho_state *node, FILE* gfile)
+{
+	uint32_t i;
+	static int j=0;
+
+	for (i=0; i<4; i++)
+		if (node->next[i] != NULL && node->next[i] != node)
+		{
+			fprintf (gfile, "\"%d\" -> \"%d\" [\n", node->id, node->next[i]->id);
+			fprintf (gfile, "label=\"%c\"\n];\n", "ACGT"[i]);
+		}
+
+	if (j++ < 40)
+	if (node->fail != NULL && node->fail != groot)
+	{
+		fprintf (gfile, "\"%d\" -> \"%d\" [\n", node->id, node->fail->id);
+		fprintf (gfile, "color= \"red\"\n];\n");
+	}
+
+	for (i=0; i<4; i++)
+		if (node->next[i] != NULL && node->next[i] != node)
+			ahoc_graphPrintNodesLinks (node->next[i], gfile);
+}
+
+void ahoc_graphKeywordTree (aho_state *root)
+{
+	FILE *gfile;
+
+	groot=root;
+	gfile = fopen ("keywordtree.gv", "w");
+	fprintf (gfile, "digraph keywordtree {\n");
+	ahoc_graphPrintNodesInfo (root, gfile);
+	ahoc_graphPrintNodesLinks (root, gfile);
+	fprintf (gfile, "}\n");
+	fclose(gfile);
+}
+

src/libecoprimer/ahocorasick.h

@@ -0,0 +1,43 @@
+/*
+ * ahocorasick.h
+ *
+ *  Created on: 26 march 2011
+ *      Author: tiayyba
+ */
+
+#ifndef H_ahocorasick
+#define H_ahocorasick
+
+#include "ecoprimer.h"
+
+typedef struct aho_output_t{
+	uint32_t wordidx; //index of strict word (dont save the word of 64B)
+	bool_t isdirect; //we need to find both direct and reverse words so we must know which one is it
+}aho_output;
+
+typedef struct aho_output_count_t{
+	uint32_t count;
+	aho_output *out_set;
+}aho_output_count;
+
+typedef struct aho_state_t{
+	int32_t id;
+	struct aho_state_t *next[4]; //for labels A=0,C=1,G=2 and T=3
+	struct aho_state_t *fail;
+	aho_output_count output;
+}aho_state;
+
+typedef struct queue_node_t {
+	aho_state *state_node;
+	struct queue_node_t *next;
+}queue_node;
+
+typedef struct{
+	queue_node *first;
+	queue_node *last;
+}aho_queue;
+
+pprimercount_t ahoc_lookforStrictPrimers (pecodnadb_t database, uint32_t seqdbsize,uint32_t exampleCount,
+		                     pwordcount_t words,poptions_t options);
+#endif /* H_ahocorasick */
+

src/libecoprimer/amplifiatree.c

@@ -0,0 +1,131 @@
+/*
+ * amplifiatree.c
+ *
+ *  Created on: 7 mars 2009
+ *      Author: coissac
+ */
+
+#include  "ecoprimer.h"
+#include <search.h>
+
+static void cleanamplifia(pamplifia_t amplifia);
+static void deleteamplifialist(pamplifialist_t list);
+static int cmpamplifia(const void* p1,const void*p2);
+
+
+static void cleanamplifiatlist(pamplifiacount_t list)
+{
+	if (list->amplifias)
+		ECOFREE(list->amplifias,
+				"Free amplifia list");
+}
+
+static void cleanamplifia(pamplifia_t amplifia)
+{
+   cleanamplifiatlist(&(amplifia->pcr));
+}
+
+static pamplifialist_t newamplifialist(pamplifialist_t parent, size_t size)
+{
+	pamplifialist_t tmp;
+
+	tmp=ECOMALLOC(sizeof(amplifialist_t)+sizeof(amplifia_t)*(size-1),
+			      "Cannot allocate new amplifia list");
+
+	tmp->amplifiaslots=size;
+	tmp->amplifiacount=0;
+	tmp->next=NULL;
+
+	if (parent)
+		parent->next=(void*)tmp;
+
+	return tmp;
+}
+
+static void deleteamplifialist(pamplifialist_t list)
+{
+	size_t i;
+
+	if (list)
+	{
+		if (list->next)
+		{
+			deleteamplifialist(list->next);
+			list->next=NULL;
+		}
+		for (i=0; i < list->amplifiacount; i++)
+			cleanamplifia((list->amplifias)+i);
+
+		ECOFREE(list,"Delete amplifia list");
+	}
+
+}
+
+static int cmpamplifia(const void* p1,const void*p2)
+{
+	pamplifia_t pr1,pr2;
+
+	pr1=(pamplifia_t)p1;
+	pr2=(pamplifia_t)p2;
+
+	if (pr1->p1 < pr2->p1) return -1;
+	if (pr1->p1 > pr2->p1) return  1;
+
+	if (pr1->asdirect1 < pr2->asdirect1) return -1;
+	if (pr1->asdirect1 > pr2->asdirect1) return  1;
+
+	if (pr1->p2 < pr2->p2) return -1;
+	if (pr1->p2 > pr2->p2) return  1;
+
+	if (pr1->asdirect2 < pr2->asdirect2) return -1;
+	if (pr1->asdirect2 > pr2->asdirect2) return  1;
+
+	return 0;
+}
+
+pamplifia_t amplifiaintree (amplifia_t key,
+		            pamplifiatree_t amplifialist)
+{
+	if (!amplifialist->tree)
+		return NULL;
+
+	return *((pamplifia_t*)tsearch((const void *)(&key),
+								&(amplifialist->tree),
+						        cmpamplifia
+							  ));
+}
+
+pamplifia_t insertamplifia(amplifia_t key,
+		           pamplifiatree_t list)
+{
+	pamplifia_t current;
+	pamplifia_t found;
+
+	if (list->last->amplifiacount==list->last->amplifiaslots)
+	{
+		list->last->next=newamplifialist(list,100);
+		list->last=list->last->next;
+	}
+
+	current = list->last->amplifias + list->last->amplifiacount;
+	*current=key;
+
+	found = *((pamplifia_t*)tsearch((const void *)current,
+			                    &(list->tree),
+			                    cmpamplifia));
+	if (found==current)
+		list->last->amplifiacount++;
+
+	return found;
+}
+
+pamplifiatree_t initamplifiatree(pamplifiatree_t tree)
+{
+	if (!tree)
+		tree = ECOMALLOC(sizeof(amplifiatree_t),"Cannot allocate amplifia tree");
+
+	tree->first=newamplifialist(NULL,500);
+	tree->last=tree->first;
+
+	tree->tree=NULL;
+}

src/libecoprimer/apat_search.c

@@ -36,10 +36,10 @@ int32_t ManberNoErr(pecoseq_t pseq,ppattern_t pat,
         ppatternParam_t param,
         StackiPtr stkpos)
 {
-        int32_t     pos;
+        uint32_t     pos;
         uint32_t    smask, r;
         uint8_t     *data;
-        int32_t    end;
+        uint32_t    end;
 
         end = (size_t)(pseq->SQ_length);
 
@@ -84,11 +84,11 @@ int32_t ManberSub(pecoseq_t pseq,ppattern_t pat,
         StackiPtr stkpos)
 {
         int       e, found;
-        int32_t     pos;
+        uint32_t     pos;
         uint32_t    smask, cmask, sindx;
         uint32_t    *pr, r[2 * MAX_PAT_ERR + 2];
         uint8_t     *data;
-        int32_t    end;
+        uint32_t    end;
 
         end = (size_t)(pseq->SQ_length);
 
@@ -103,8 +103,7 @@ int32_t ManberSub(pecoseq_t pseq,ppattern_t pat,
         for (e = 0, pr = r + 3 ; e <= param->maxerr ; e++, pr += 2)
                 *pr = cmask;
 
-        cmask = ~ param->omask;  // A VOIR !!!!! omask (new) doit <20>tre compos<6F> de + et - ... Ancien omask : bits
+        cmask = ~ param->omask;
-
                                         /* init. scan           */
         data   = (uint8_t*)(pseq->SQ);
 

src/libecoprimer/aproxpattern.c

@@ -39,8 +39,8 @@ ppattern_t buildPatternFromWord(word_t word, uint32_t patlen)
 }
 
 
-#ifdef IS_UPPER(c)
+#ifdef IS_UPPER
-#undef IS_UPPER(c)
+#undef IS_UPPER
 #endif
 
 /* -------------------------------------------- */
@@ -59,9 +59,9 @@ void encodeSequence(ecoseq_t *seq)
      data = (uint8_t*)(seq->SQ);
      cseq = seq->SQ;
 
-     for (i=0;i<seq->SQ_length;i++,data++,cseq++)
+     for (i=0;i<(int)(seq->SQ_length);i++,data++,cseq++)
      {
-         *data = encoder[(IS_UPPER(*cseq) ? *cseq - 'A' : 'Z')];
+         *data = encoder[(IS_UPPER(*cseq) ? *cseq : 'Z') - 'A'];
      }
 }
 
@@ -82,7 +82,7 @@ pprimercount_t lookforAproxPrimer(pecodnadb_t database, uint32_t seqdbsize,uint3
 	uint32_t  inSequenceQuorum;
 	uint32_t  outSequenceQuorum;
 	bool_t    conserved = TRUE;
-	
+
 	//poslist_t ttt;
 
 
@@ -97,7 +97,8 @@ pprimercount_t lookforAproxPrimer(pecodnadb_t database, uint32_t seqdbsize,uint3
 
 	params.circular = options->circular;
 	params.maxerr   = options->error_max;
-	params.omask    = (1 << options->strict_three_prime) -1;
+//	params.omask    = (1 << options->strict_three_prime) -1;
+	params.omask    = 0;
 	params.patlen   = options->primer_length;
 
 	positions.val=NULL;
@@ -200,7 +201,7 @@ pprimercount_t lookforAproxPrimer(pecodnadb_t database, uint32_t seqdbsize,uint3
 		data[w].good = data[w].inexample >= inSequenceQuorum && data[w].outexample <= outSequenceQuorum;
 		goodPrimers+=data[w].good? 1:0;
 
-		fprintf(stderr,"Primers %5d/%d analyzed  => sequence : %s in %d example and %d counterexample sequences       \r",
+		fprintf(stderr,"Primers %5d/%lld analyzed  => sequence : %s in %d example and %d counterexample sequences       \r",
 				i+1,words->size,ecoUnhashWord(data[w].word,options->primer_length),
 				data[w].inexample,data[w].outexample);
 
@@ -223,8 +224,8 @@ pprimercount_t lookforAproxPrimer(pecodnadb_t database, uint32_t seqdbsize,uint3
 		ECOFREE(data[w].reversePos,"Free direct count table");
 	}
 
-	fprintf(stderr,"\n\nOn %d analyzed primers %d respect quorum conditions\n",words->size,goodPrimers);
+	fprintf(stderr,"\n\nOn %lld analyzed primers %d respect quorum conditions\n",words->size,goodPrimers);
-	fprintf(stderr,"Conserved primers for further analysis : %d/%d\n",w,words->size);
+	fprintf(stderr,"Conserved primers for further analysis : %d/%lld\n",w,words->size);
 
 	primers = ECOMALLOC(sizeof(primercount_t),"Cannot allocate memory for primer table");
 	primers->primers=ECOREALLOC(data,

src/libecoprimer/ecoprimer.h

@@ -13,6 +13,7 @@
 #include <stdio.h>
 #include "ecotype.h"
 #include "../libecoPCR/ecoPCR.h"
+#include "../libthermo/nnparams.h"
 #include "apat.h"
 
 #define DEBUG
@@ -47,6 +48,7 @@ typedef uint64_t word_t, *pword_t;
 #define WORDMASK(s)       ((1LLU << ((s) * 2)) -1)
 #define LSHIFTWORD(x,s)    (((x) << 2) & WORDMASK(s))
 #define RSHIFTWORD(x,s)    (((x) & WORDMASK(s))>> 2)
+#define ERRORMASK(s)       ((int32_t)((1LLU << (s)) -1))
 
 #define RAPPENDBASE(x,s,c) (LSHIFTWORD((x),(s)) | (word_t)(c))
 #define LAPPENDBASE(x,s,c) (RSHIFTWORD((x),(s)) | ((word_t)((~(c)) & 3) << (((s)-1) *2)))
@@ -65,42 +67,61 @@ typedef uint64_t word_t, *pword_t;
 #define MINI(x,y) (((x) < (y)) ? (x):(y))
 #define MAXI(x,y) (((x) < (y)) ? (y):(x))
 
+#define FWORDSIZE (13)
+#define FWORDMASK WORDMASK(FWORDSIZE)
+#define FILTERWORD(x) ((uint32_t)((x) & FWORDMASK))
+#define CFILTERWORD(x,s) ((uint32_t)(((x) >> (((s)-FWORDSIZE)*2)) & FWORDMASK))
+
+
+
 typedef struct {
 	pword_t    words;
 	uint32_t    *strictcount;
 	uint32_t     inseqcount;
 	uint32_t     outseqcount;
-	uint32_t     size;
+	uint64_t     size;
 } wordcount_t, *pwordcount_t;
 
 
 typedef union {
 	uint32_t *pointer;
 	uint32_t value;
-} poslist_t, *ppostlist_t;
+} poslist_t, *pposlist_t;
+
+
+/**
+ * primer_t structure store fuzzy match positions for a primer
+ * on all sequences
+ */
 
 typedef struct {
-    word_t     word;
+    word_t     word;              //< code for the primer
-	uint32_t   *directCount;
+	uint32_t   *directCount;      //< Occurrence count on direct strand
-	ppostlist_t directPos;
+	pposlist_t directPos;        //< list of position list on direct strand
 
-	uint32_t   *reverseCount;
+	uint32_t   *reverseCount;     //< Occurrence count on reverse strand
-	ppostlist_t reversePos;
+	pposlist_t reversePos;       //< list of position list on reverse strand
-	bool_t     good;
+
-	uint32_t   inexample;
+	bool_t     good;              //< primer match more than quorum example and no
-	uint32_t   outexample;
+	                              //  more counterexample quorum.
+
+	uint32_t   inexample;         //< count of example sequences matching primer
+	uint32_t   outexample;        //< count of counterexample sequences matching primer
 } primer_t, *pprimer_t;
 
+/**
+ * primercount_t structure store fuzzy match positions for all primers
+ * on all sequences as a list of primer_t
+ */
 typedef struct {
 	pprimer_t   primers;
 	uint32_t    size;
 } primercount_t, *pprimercount_t;
 
 typedef struct {
-	word_t      word;
+	pprimer_t   primer;
 	uint32_t    position;
 	bool_t      strand;
-	bool_t     	good; /*TR: Added*/
 } primermatch_t, *pprimermatch_t;
 
 /*TR: Added*/
@@ -109,6 +130,21 @@ typedef struct {
 	uint32_t	matchcount;
 } primermatchcount_t, *pprimermatchcount_t;
 
+typedef struct {
+	pecoseq_t  sequence;
+	bool_t     strand;
+	const char *amplifia;
+	int32_t	   length;
+	uint32_t   begin;
+	uint32_t   end;
+} amplifia_t, *pamplifia_t;
+
+typedef struct {
+	pamplifia_t amplifias;
+	uint32_t    ampcount;
+	uint32_t	ampslot;
+} amplifiacount_t, *pamplifiacount_t;
+
 typedef struct {
 	char *amplifia;
 	int32_t *taxonids;
@@ -124,30 +160,64 @@ typedef struct {
 } taxampset_t, *ptaxampset_t;
 
 typedef struct {
-	word_t 			w1;
+	pprimer_t 		p1;
-	word_t 			w2;
+	bool_t			asdirect1;
-	uint32_t   		inexample; /*inexample count*/
+	pprimer_t 		p2;
-	uint32_t   		outexample; /*outexample count*/
+	bool_t			asdirect2;
-	
+
-	uint32_t 		mind;
+	amplifiacount_t pcr;
-	uint32_t		maxd;
+
-	
+	uint32_t   		inexample;         //< example sequence count
-	uint32_t		ampsetcount;
+	uint32_t   		outexample;        //< counterexample sequence count
-	uint32_t		ampsetindex;
+	uint32_t   		intaxa;            //< example taxa count
-	pampseqset_t	ampset;
+	uint32_t   		outtaxa;            //< counterexample taxa count
-	
+	uint32_t		notwellidentifiedtaxa;
-	uint32_t		taxsetcount;
+
-	uint32_t		taxsetindex;
+	int				*wellIdentifiedSeqs; //< an array having elements equla to total seqs
-	ptaxampset_t	taxset;
+									 // values are either 0 or 1, if seq is well identified
-	
+									 // its 1 else 0
-	uint32_t		oktaxoncount;
+	int				*coveredSeqs; //< an array having elements equal to total seqs, 1 if seq is covered else 0
-} pairs_t, *ppairs_t;
+
+					// these statistics are relative to inexample sequences
+
+	uint32_t 		mind;				//< minimum distance between primers
+	uint32_t		maxd;				//< maximum distance between primers
+	uint32_t        sumd;				//< distance sum
+	uint32_t        amplifiacount;
+	float			yule;
+	float			quorumin;
+	float           quorumout;
+	float           bs;
+	float           bc;
+	int32_t        refsequence;
+//
+//	uint32_t		taxsetcount;
+//	uint32_t		taxsetindex;
+//	ptaxampset_t	taxset;
+//
+//	uint32_t		oktaxoncount;
+	uint32_t		curseqid;
+	float			p1temp;			//strict primer1 melting temperature
+	float			p1mintemp;		//approx primer1 minimum melting temperature
+	float			p2temp;			//strict primer2 melting temperature
+	float			p2mintemp;		//approx primer2 minimum melting temperature
+} pair_t, *ppair_t;
 
 /*TR: Added*/
+
 typedef struct {
-	ppairs_t 	pairs;
+	size_t  	paircount;
-	uint32_t	paircount;
+	size_t      pairslots;
-}pairscount_t, *ppairscount_t;
+    void*       next;
+	pair_t 	    pairs[1];
+} pairlist_t, *ppairlist_t;
+
+typedef struct {
+	ppairlist_t first;
+	ppairlist_t last;
+	void       *tree;
+	int32_t     count;
+} pairtree_t, *ppairtree_t;
 
 typedef struct {
 	pword_t     words;
@@ -168,15 +238,34 @@ typedef struct {
 	uint32_t    size;
 } merge_t, *pmerge_t;
 
+typedef struct {
+	const char 		*amplifia;
+	bool_t     	strand;
+	int32_t	   	length;
+	int32_t		taxoncount;
+	void		*taxontree;
+}amptotaxon_t, *pamptotaxon_t;
 
 typedef struct {
+	int32_t 	taxid;
+	void		*amptree;
+}taxontoamp_t, *ptaxontoamp_t;
+
+typedef struct {
+	bool_t         printAC;
+	bool_t         statistics;
+	bool_t         filtering;
 	uint32_t        lmin;                   //**< Amplifia minimal length
 	uint32_t        lmax;                   //**< Amplifia maximal length
 	uint32_t        error_max;              //**< maximum error count in fuzzy search
 	uint32_t        primer_length;          //**< minimal length of the primers
 	int32_t		  *restricted_taxid;      //**< limit amplification below these taxid
 	int32_t       *ignored_taxid;         //**< no amplification below these taxid
+	int32_t		  *exception_taxid;
 	char          *prefix;
+	char          *reference;
+	pecoseq_t      refseq;
+	uint32_t       refseqid;
 	uint32_t		  circular;
 	uint32_t        doublestrand;
 	float         strict_quorum;
@@ -186,9 +275,26 @@ typedef struct {
 	uint32_t      strict_three_prime;
 	int32_t		  r;                      //**< count of restrited taxa (restricted_taxid array size)
 	int32_t		  g;                      //**< count of ignored taxa (ignored_taxid array size)
+	int32_t		  e;                      //**< count of ignored taxa (ignored_taxid array size)
 	bool_t        no_multi_match;
 	char		  taxonrank[20];  //TR to count ranks against a pair
 	int32_t		  taxonrankidx;   //TR to count ranks against a pair
+
+	// Some statistics useful for options filters
+
+	int32_t       dbsize;
+	int32_t		  insamples;
+	int32_t		  outsamples;
+	int32_t       intaxa;
+	int32_t       outtaxa;
+	int			  saltmethod;
+	float		  salt;
+	PNNParams	  pnparm;
+	bool_t		  print_sets_of_primers;
+	float		  specificity_threshold;
+	int			  links_cnt;
+	float		  max_links_percent;
+	bool_t		  filter_on_links;
 } options_t, *poptions_t;
 
 typedef ecoseq_t  **pecodnadb_t;
@@ -196,12 +302,15 @@ typedef ecoseq_t  **pecodnadb_t;
 void sortword(pword_t table,uint32_t N);
 
 
-pecodnadb_t readdnadb(const char *name, uint32_t *size);
+pecodnadb_t readdnadb(const char *name, ecotaxonomy_t *taxonomy, uint32_t *size,poptions_t options);
 
 int isGoodTaxon(ecotaxonomy_t *taxonomy,int32_t taxon,poptions_t options);
+int isExampleTaxon(ecotaxonomy_t *taxonomy,int32_t taxon,poptions_t options);
+int isCounterExampleTaxon(ecotaxonomy_t *taxonomy,int32_t taxon,poptions_t options);
 
 uint32_t ecoWordCount(uint32_t wordsize, uint32_t circular, ecoseq_t *seq);
-pword_t ecoHashSequence(pword_t dest, uint32_t wordsize, uint32_t circular, uint32_t doublestrand, ecoseq_t *seq,uint32_t *size);
+pword_t ecoHashSequence(pword_t dest, uint32_t wordsize, uint32_t circular, uint32_t doublestrand, ecoseq_t *seq,uint32_t *size,int32_t *neededWords,uint32_t neededWordCount,
+	    int32_t quorum);
 uint32_t ecoCompactHashSequence(pword_t dest,uint32_t size);
 const char* ecoUnhashWord(word_t word,uint32_t size);
 word_t ecoComplementWord(word_t word,uint32_t size);
@@ -209,8 +318,8 @@ uint32_t ecoFindWord(pwordcount_t table,word_t word);
 
 
 void ecomerge(pwordcount_t data,uint32_t s1,uint32_t s2,uint32_t remainingSeq,uint32_t seqQuorum);
-pwordcount_t initCountTable(pwordcount_t table, uint32_t wordsize, uint32_t circular, uint32_t doublestrand,ecoseq_t *seq);
+pwordcount_t initCountTable(pwordcount_t table, uint32_t wordsize, uint32_t circular, uint32_t doublestrand,uint32_t seqQuorum,ecoseq_t *seq,int32_t *neededWords,uint32_t neededWordCount);
-void addSeqToWordCountTable(pwordcount_t table, uint32_t wordsize, uint32_t circular, uint32_t doublestrand,uint32_t exampleCount,uint32_t seqQuorum,ecoseq_t *seq);
+void addSeqToWordCountTable(pwordcount_t table, uint32_t wordsize, uint32_t circular, uint32_t doublestrand,uint32_t exampleCount,uint32_t seqQuorum,ecoseq_t *seq,int32_t *neededWords,uint32_t neededWordCount);
 
 pqueue_t newQueue(pqueue_t queue, uint32_t size);
 pqueue_t resizeQueue(pqueue_t queue, uint32_t size);
@@ -232,7 +341,26 @@ pprimercount_t lookforAproxPrimer(pecodnadb_t database, uint32_t seqdbsize,uint3
 
 void sortmatch(pprimermatch_t table,uint32_t N);
 
+ppairtree_t initpairtree(ppairtree_t tree);
+ppair_t pairintree (pair_t key,ppairtree_t pairlist);
+ppair_t insertpair(pair_t key,ppairtree_t list);
+
+
 /*TR: Added*/
-pairscount_t buildPrimerPairs(pecodnadb_t seqdb,uint32_t seqdbsize,pprimercount_t primers,poptions_t options);
+ppairtree_t buildPrimerPairs(pecodnadb_t seqdb,uint32_t seqdbsize,pprimercount_t primers,poptions_t options);
+
+int32_t counttaxon(int32_t taxid);
+int32_t getrankdbstats(pecodnadb_t seqdb,
+					   uint32_t seqdbsize,
+					   ecotaxonomy_t *taxonomy,
+					   poptions_t options);
+float taxonomycoverage(ppair_t pair, poptions_t options, pecodnadb_t seqdb,uint32_t seqdbsize);
+char ecoComplementChar(char base);
+void taxonomyspecificity (ppair_t pair, pecodnadb_t seqdb,uint32_t seqdbsize);
+
+int32_t *filteringSeq(pecodnadb_t database, uint32_t seqdbsize,
+					 uint32_t exampleCount,poptions_t options,uint32_t *size,int32_t  sequenceQuorum);
+
+void printSeqTest(pecodnadb_t seqdb,uint32_t seqdbsize);
 
 #endif /* EPSORT_H_ */

src/libecoprimer/filtering.c

@@ -0,0 +1,222 @@
+/*
+ * filtering.c
+ *
+ *  Created on: 12 mai 2009
+ *      Author: coissac
+ */
+
+#include "ecoprimer.h"
+#include <string.h>
+#include <math.h>
+
+#include "hashencoder.h"
+
+static int32_t *ecoFilteringHashSequence(int32_t *dest,
+										 uint32_t circular,
+										 uint32_t doublestrand,
+										 ecoseq_t *seq,
+										 uint32_t *size);
+
+
+
+
+
+static	int32_t *ecoFilteringHashSequence(int32_t *dest,
+										  uint32_t circular,
+										  uint32_t doublestrand,
+										  ecoseq_t *seq,
+										  uint32_t *size)
+{
+
+	/*
+	 * This function aims at building a vector of count for every possible hash codes
+	 *
+	 * The function must be applied once on each sequence
+	 *
+	 * The function allocates memory on the first call for the dest table
+	 * The function also allocates memory for the static temporary table in_last_seq and
+	 * the function must be called with *dest == -1 in order to free this temporary table
+	 *
+	 */
+	static char    *in_last_seq=NULL;
+	uint32_t i=0;
+	uint32_t j;
+	char *base;
+	int8_t code;
+	int32_t error=0;
+	word_t word=0;
+	word_t antiword=0;
+	uint32_t goodword;
+	uint32_t lmax=0;
+
+	// run on the first call;
+
+	if (dest==(void*)-1)
+	{
+		if (in_last_seq) ECOFREE(in_last_seq,"Free in last seq table");
+		return NULL;
+	}
+
+
+	/* FWORDSIZE = 13 => *size =    67 108 864
+	 * FWORDSIZE = 14 => *size =   268 435 456
+	 * FWORDSIZE = 15 => *size = 1 073 741 824
+	 */
+
+	*size = pow(4,FWORDSIZE);
+
+	/*
+	 * in_last_seq is a vector of char as it is just to avoid counting twice (or more) a hash code (a DNA word)
+	 * it is set to zero (with memset) and then filled with ones for each word belonging to the sequence
+	 */
+
+	if (!in_last_seq)
+		in_last_seq = ECOMALLOC(*size*sizeof(char),
+								"Cannot allocate filtering hash table");
+
+	memset(in_last_seq,0,*size*sizeof(char));
+
+	/*
+	 * Allocate (on first call) the memory for the table of counts
+	 */
+
+	if (!dest)
+	{
+		dest = ECOMALLOC(*size*sizeof(int32_t),
+				               "Cannot allocate filtering hash table");
+		memset(dest,0,*size*sizeof(int32_t));
+	}
+
+	lmax = seq->SQ_length;
+	if (!circular)
+       lmax-= FWORDSIZE-1;
+
+
+
+//	DEBUG_LOG("Sequence %s @ %d : %18.18s",seq->AC,i,(seq->SQ+i));
+
+	/*
+	 * Compute first word of seq
+	 */
+
+	for (i=0, base = seq->SQ; i < FWORDSIZE && i < lmax; i++,base++)
+	{
+		error<<= 1;
+		error&=ERRORMASK(FWORDSIZE);
+
+		code = encoder[(*base) - 'A'];
+		if (code <0)
+		{
+			code = 0;
+			error|= 1;
+		}
+
+
+		word=RAPPENDBASE(word,FWORDSIZE,code);
+		if (doublestrand)
+			antiword=LAPPENDBASE(antiword,FWORDSIZE,code);
+	}
+
+	if (!error && i==FWORDSIZE)
+	{
+
+		goodword=(uint32_t)((doublestrand) ? MINI(word,antiword):word);
+
+		/*
+		 * FB: I don't think the test is necessary as the table has just been initialized
+		 */
+		if (!in_last_seq[goodword])
+		{
+			in_last_seq[goodword]=1;
+			dest[goodword]++;
+		}
+	}
+
+	/*
+	 * compute and store counts (avoid counting twice a word) for the other words of the seq
+	 */
+
+	for (j=1; j < lmax; j++,i++,base++)
+	{
+
+//		DEBUG_LOG("Sequence %s @ %d : %18.18s",seq->AC,j,(seq->SQ+j));
+
+							/* roll over the sequence for circular ones */
+		if (i==(uint32_t)seq->SQ_length) base=seq->SQ;
+
+		error<<= 1;
+		error&=ERRORMASK(FWORDSIZE);
+
+		//code = -1;
+		//if((*base) >= 'A' && (*base) <= 'Z')
+		code = encoder[(*base) - 'A'];
+		if (code <0)
+		{
+			code = 0;
+			error|= 1;
+		}
+
+		word=RAPPENDBASE(word,FWORDSIZE,code);
+		if (doublestrand)
+			antiword=LAPPENDBASE(antiword,FWORDSIZE,code);
+
+		if (!error)
+		{
+			if (doublestrand)
+				goodword=(uint32_t)MINI(word,antiword);
+			else
+				goodword=word;
+			if (!in_last_seq[goodword])
+			{
+				in_last_seq[goodword]=1;
+				dest[goodword]++;
+			}
+		}
+
+	}
+
+
+	return dest;
+
+}
+
+
+int32_t *filteringSeq(pecodnadb_t database, uint32_t seqdbsize,
+					 uint32_t exampleCount,poptions_t options,uint32_t *size,int32_t  sequenceQuorum)
+{
+	int32_t *wordscount=NULL;
+	int32_t keep=0;
+	uint32_t i,j=0;
+
+	for (i=0;i<seqdbsize;i++)
+    {
+    	if (database[i]->isexample && database[i]->SQ_length > options->primer_length)
+    	{
+    		j++;
+    		wordscount=ecoFilteringHashSequence(wordscount,
+									 options->circular,
+                                     options->doublestrand,
+                                     database[i],
+                                     size);
+    	}
+    	fprintf(stderr,"  Filtered sequences %5u/%5u          \r",j,exampleCount);
+
+    }
+
+	fprintf(stderr,"\n");
+
+	for (i=0;i<*size;i++)
+		if (wordscount[i] >= sequenceQuorum)
+			keep++;
+
+
+	(void)ecoFilteringHashSequence((int32_t*)-1,
+									options->circular,
+	                                options->doublestrand,
+	                                NULL,
+	                                NULL);
+
+	fprintf(stderr,"ok\n Considered word of size %d for filtering : %d\n",FWORDSIZE,keep);
+	return wordscount;
+
+}

src/libecoprimer/goodtaxon.c

@@ -12,16 +12,53 @@ int isGoodTaxon(ecotaxonomy_t *taxonomy,int32_t taxon,poptions_t options)
 {
 	int result;
 
-	result=( (options->r == 0) || (eco_is_taxid_included(taxonomy,
+	result=((options->r == 0) || (eco_is_taxid_included(taxonomy,
 			                            options->restricted_taxid,
 			                            options->r,
 			                            taxonomy->taxons->taxon[taxon].taxid)
 		   )) &&
-		   ((options->g == 0) || !(eco_is_taxid_included(taxonomy,
+		   ((options->e == 0) || !(eco_is_taxid_included(taxonomy,
-				                        options->ignored_taxid,
+				                        options->exception_taxid,
-		   		                        options->g,
+		   		                        options->e,
 		   		                        taxonomy->taxons->taxon[taxon].taxid)
 		   ));
 
 	return result;
 }
+
+int isExampleTaxon(ecotaxonomy_t *taxonomy,int32_t taxon,poptions_t options)
+{
+	int result;
+
+	result=( (options->r == 0) || (eco_is_taxid_included(taxonomy,
+			                            options->restricted_taxid,
+			                            options->r,
+			                            taxonomy->taxons->taxon[taxon].taxid)
+		   )) &&
+		   ((options->e == 0) || !(eco_is_taxid_included(taxonomy,
+				                        options->exception_taxid,
+		   		                        options->e,
+		   		                        taxonomy->taxons->taxon[taxon].taxid)
+		   ));
+
+	return result;
+}
+
+
+int isCounterExampleTaxon(ecotaxonomy_t *taxonomy,int32_t taxon,poptions_t options)
+{
+	int result;
+
+	result=((options->g != 0) && (eco_is_taxid_included(taxonomy,
+								   options->ignored_taxid,
+								   options->g,
+								   taxonomy->taxons->taxon[taxon].taxid))
+           ) || ((options->e != 0) && (eco_is_taxid_included(taxonomy,
+				                        options->exception_taxid,
+		   		                        options->e,
+		   		                        taxonomy->taxons->taxon[taxon].taxid))
+           );
+
+
+	return result;
+}

src/libecoprimer/hashencoder.h

@@ -0,0 +1,13 @@
+/*
+ * hashencoder.h
+ *
+ *  Created on: 12 mai 2009
+ *      Author: coissac
+ */
+
+#ifndef HASHENCODER_H_
+#define HASHENCODER_H_
+
+extern int8_t encoder[];
+
+#endif /* HASHENCODER_H_ */

src/libecoprimer/hashsequence.c

@@ -10,7 +10,9 @@
 
 static int cmpword(const void *x,const void *y);
 
-static int8_t encoder[] = {0,                                            // A
+#include "hashencoder.h"
+
+int8_t encoder[] = {0,                                            // A
 		                   -1,                                           // b
 		                   1,                                            // C
 	       	               -1,-1,-1,                                     // d, e, f
@@ -31,8 +33,29 @@ uint32_t ecoWordCount(uint32_t wordsize, uint32_t circular, ecoseq_t *seq)
 	return wordcount;
 }
 
-pword_t ecoHashSequence(pword_t dest, uint32_t wordsize, uint32_t circular, uint32_t doublestrand, ecoseq_t *seq,uint32_t *size)
+pword_t ecoHashSequence(pword_t dest,
+					    uint32_t wordsize,
+					    uint32_t circular,
+					    uint32_t doublestrand,
+					    ecoseq_t *seq,
+					    uint32_t *size,
+					    int32_t  *neededWords,
+					    uint32_t neededWordCount,
+					    int32_t quorum)
 {
+
+	/*
+	 * dest            / out    : words of the hashed sequence position per position
+	 * wordsize        / in     : size of the word to be hashed (record error for that size) BUT not equal to FWORDSIZE ...
+	 *                            ... the size of the word REALLY returned as a result
+	 * circular        / in     : is the sequence circular
+	 * doublestrand    / in     : if we have to hash on both strands of the sequence
+	 * seq             / in     : the sequence in ecoseq format
+	 * size            / out    : number of hashed words (size of the dest vector)
+	 * neededWordCount / in     : table hash codes of word counts in the full DB (used to filter words)
+	 * quorum          / in     : minimum quorum used to filter words based on the neededWordCount table
+	 */
+
 	uint32_t i=0;
 	uint32_t j;
 	char *base;
@@ -40,6 +63,7 @@ pword_t ecoHashSequence(pword_t dest, uint32_t wordsize, uint32_t circular, uint
 	int32_t error=0;
 	word_t word=0;
 	word_t antiword=0;
+	word_t goodword;
 	uint32_t lmax=0;
 
 	(*size)=0;
@@ -53,11 +77,13 @@ pword_t ecoHashSequence(pword_t dest, uint32_t wordsize, uint32_t circular, uint
 				         "I cannot allocate memory for sequence hashing"
 				        );
 
-//	DEBUG_LOG("Sequence %s @ %d : %18.18s",seq->AC,i,(seq->SQ+i));
+	//DEBUG_LOG("Sequence %s @ %d : %18.18s",seq->AC,i,(seq->SQ+i));
 
 	for (i=0, base = seq->SQ; i < wordsize && i < lmax; i++,base++)
 	{
+
 		error<<= 1;
+		error&=ERRORMASK(wordsize);
 
 		code = encoder[(*base) - 'A'];
 		if (code <0)
@@ -68,10 +94,22 @@ pword_t ecoHashSequence(pword_t dest, uint32_t wordsize, uint32_t circular, uint
 
 
 		word=RAPPENDBASE(word,wordsize,code);
+
 		if (doublestrand)
 			antiword=LAPPENDBASE(antiword,wordsize,code);
+
+		if (neededWordCount && i>=(FWORDSIZE-1))
+		{
+
+			goodword = (doublestrand) ? MINI(FILTERWORD(word),CFILTERWORD(antiword,wordsize)):FILTERWORD(word);
+			if (neededWords[(uint32_t)goodword]<quorum)
+				error|= (1 << (FWORDSIZE-1));
+
+		}
+
 	}
 
+
 	if (!error && i==wordsize)
 	{
 		dest[*size]=(doublestrand) ? MINI(word,antiword):word;
@@ -82,12 +120,14 @@ pword_t ecoHashSequence(pword_t dest, uint32_t wordsize, uint32_t circular, uint
 	for (j=1; j < lmax; j++,i++,base++)
 	{
 
-//		DEBUG_LOG("Sequence %s @ %d : %18.18s",seq->AC,j,(seq->SQ+j));
+		//DEBUG_LOG("Sequence %s @ %d : %18.18s",seq->AC,j,(seq->SQ+j));
 
 							/* roll over the sequence for circular ones */
+
 		if (i==(uint32_t)seq->SQ_length) base=seq->SQ;
 
 		error<<= 1;
+		error&=ERRORMASK(wordsize);
 
 		code = encoder[(*base) - 'A'];
 		if (code <0)
@@ -100,6 +140,17 @@ pword_t ecoHashSequence(pword_t dest, uint32_t wordsize, uint32_t circular, uint
 		if (doublestrand)
 			antiword=LAPPENDBASE(antiword,wordsize,code);
 
+		if (neededWordCount)
+		{
+			goodword = (doublestrand) ? MINI(FILTERWORD(word),CFILTERWORD(antiword,wordsize)):FILTERWORD(word);
+			if (neededWords[(uint32_t)goodword]<quorum)
+				error|= (1 << (FWORDSIZE-1));
+//			else
+//				DEBUG_LOG("%s goodword = %p %d/%d (pos:%d error:%d)",seq->AC,goodword,neededWords[(uint32_t)goodword],quorum,i,error);
+
+		}
+
+
 		if (!error)
 		{
 			dest[*size]=(doublestrand) ? MINI(word,antiword):word;
@@ -107,24 +158,34 @@ pword_t ecoHashSequence(pword_t dest, uint32_t wordsize, uint32_t circular, uint
 		}
 
 	}
-
+	//DEBUG_LOG("%s goodword = %d",seq->AC,*size);
 	return dest;
 
 }
 
 uint32_t ecoCompactHashSequence(pword_t table,uint32_t size)
 {
+	/*
+	 *
+	 * MULTIWORD is a word occurring more than once in a sequence
+	 *
+	 */
+
 	uint32_t i,j;
 	word_t  current;
+//	bool_t here=FALSE;
 
 	sortword(table,size);
 
 	current = 0;
 	current=SETMULTIWORD(current);   /* build impossible word for the first loop cycle */
 
+//	if (strcmp(ecoUnhashWord(table[size-1],18),"GTTTGTTCAACGATTAAA")==0)
+//		here=TRUE;
+
 	for (i=0,j=0; j < size;j++)
 	{
-		if (table[j]!=current)
+		if (WORD(table[j])!=current)
 		{
 			current =table[j];
 			table[i]=current;
@@ -134,6 +195,9 @@ uint32_t ecoCompactHashSequence(pword_t table,uint32_t size)
 			table[i]=SETMULTIWORD(table[i]);
 	}
 
+//		if (strcmp(ecoUnhashWord(WORD(table[i-1]),18),"TACGACCTCGATGTTGGA")==0)
+//			DEBUG_LOG("winner %d",i)
+
 	return i;
 }
 
@@ -201,3 +265,8 @@ uint32_t ecoFindWord(pwordcount_t table,word_t word)
 		return ~0;
 }
 
+char ecoComplementChar(char base)
+{
+	return (base < 4)? ~base & 3: 4;
+}
+

src/libecoprimer/libstki.c

@@ -250,8 +250,7 @@ void CursiToTop(StackiPtr stki)
 
 } /* end of CursiToTop */
 
-void CursiToBottom(stki)
+void CursiToBottom(StackiPtr stki)
-        StackiPtr stki;
 {
         stki->cursor = 0;
 

src/libecoprimer/libstki.h

@@ -16,6 +16,7 @@
 
 
 #include "ecotype.h"
+#include <stdint.h>
 
 /* ==================================================== */
 /* Constantes de dimensionnement                        */
@@ -85,5 +86,6 @@ bool_t            SearchDownStacki   (StackiPtr  stki  , int32_t sval       );
 bool_t            BinSearchStacki    (StackiPtr  stki  , int32_t sval       );
 bool_t            SameStacki         (StackiPtr  stki1 , StackiPtr stki2  );
 bool_t            ReverseStacki      (StackiPtr  stki                     );
+void              CursiToBottom      (StackiPtr stki  );
 
 #endif /* _H_libstki */

src/libecoprimer/merge.c

@@ -10,7 +10,7 @@
 static pmerge_t mergeInit(pmerge_t merge,pwordcount_t data,uint32_t s1,uint32_t s2);
 
 
-static pmerge_t mergeInit(pmerge_t merge, pwordcount_t data,uint32_t s1,uint32_t s2)
+static pmerge_t mergeInit(pmerge_t merge, pwordcount_t data, uint32_t s1, uint32_t s2)
 {
 	merge->words = data->words;
 	merge->count = data->strictcount;
@@ -26,23 +26,52 @@ typedef enum {S1=1,S2=2,STACK=3} source_t;
 
 void ecomerge(pwordcount_t data,uint32_t s1,uint32_t s2,uint32_t remainingSeq,uint32_t seqQuorum)
 {
+
+	/*
+	 * data          / in out : the table that contains the two parts to be merged
+	 * s1            / in     : end of the first part of the table
+	 * s2            / in     : end of the second part of the table
+	 * remainingSeq  / in     : the number of remaining seqs to be added to the table
+	 * seqQuorum     / in     : the minimum number of sequences in which a pattern must appear
+	 */
+
 	merge_t   merged;
 	source_t  source;
 	word_t    currentword,tmpword;
 	uint32_t  currentcount,tmpcount;
 	int       same;
 	queue_t   queue;
-	int       nsame=0;
+	// int       nsame=0;
 	uint32_t  maxcount=0;
 	bool_t    writed=TRUE;
 
 //	DEBUG_LOG("Coucou %p  s1= %d s2= %d",data,s1,s2)
 
+	/*
+	 * init the merged structure (used only for coding convenience, never returned, allocated on the C-stack)
+	 * note that :
+	 *     merged.words : hashcodes           (initialized to data->words)
+	 *     merged.count : counts of each word (initialized to data->strictcount)
+	 *     merged.read1 : index of the first word of the first subtable   (initialized to 0)
+	 *     merged.read1 : index of the first word of the first subtable   (initialized to 0)
+	 *     merged.read2 : index of the first word of the second subtable  (initialized to s1)
+	 *     merged.size  : total size of the table (initialized to s1+s2)
+	 *
+	 * allocate a new stack of size min(s1, s2)
+	 */
+
 	(void)mergeInit(&merged,data,s1,s2);
 	(void)newQueue(&queue,MINI(s1,s2));
 
-	while (merged.read1 < s1 && merged.read2 < merged.size)
+
+	/* true until
+	 * merged.read1 == s1 AND merged.read2 == merged.size, i.e. ALL words have been processed
+	 */
+	while (merged.read1 < s1 || merged.read2 < merged.size)
 	{
+		/*
+		 * initialize current{word,count} from either STACK (if not empty) or first table (S1)
+		 */
 		if (! queue.empty)
 		{
 			currentword  = queue.words[queue.pop];
@@ -56,18 +85,34 @@ void ecomerge(pwordcount_t data,uint32_t s1,uint32_t s2,uint32_t remainingSeq,ui
 			source=S1;
 		}
 
-		if (WORD(currentword) > WORD(merged.words[merged.read2]))
+		/*
+		 * IF there are some words in the second subtable remaining to be processed AND
+		 *    its first word is lower than current word
+		 * THEN initialize current{word,count} from the second table (S2)
+		 *
+		 */
+		if (merged.read2 < merged.size &&
+				WORD(currentword) > WORD(merged.words[merged.read2]))
 		{
 			currentword  = merged.words[merged.read2];
 			currentcount = merged.count[merged.read2];
 			source  = S2;
 		}
 
+		/*
+		 * record if the two words in the both subtable are the same
+		 */
 		same = (source != S2) && (WORD(currentword) == WORD(merged.words[merged.read2]));
-		nsame+=same;
+		// nsame+=same;
 
 //		DEBUG_LOG("Merging : r1 = %d s1 = %d r2 = %d size = %d word = %s source=%u same=%u",merged.read1,s1,merged.read2-s1,merged.size,ecoUnhashWord(currentword,18),source,same)
 
+
+		/*
+		 * merge step (AND apply the quorum property)
+		 * update merged.read1 AND/OR merged.read2
+		 * record the word and its count in the table
+		 */
 		tmpword = merged.words[merged.write];
 		tmpcount= merged.count[merged.write];
 
@@ -113,7 +158,15 @@ void ecomerge(pwordcount_t data,uint32_t s1,uint32_t s2,uint32_t remainingSeq,ui
 //	DEBUG_LOG("r1 : %d r2 : %d qsize : %d nsame : %d tot : %d write : %s count : %d source : %d size : %d pop : %d push : %d  empty : %d",merged.read1,merged.read2-s1,qsize,nsame,qsize+nsame,ecoUnhashWord(currentword,18),currentcount,source,queue.size,queue.pop,queue.push,queue.empty)
 
 
+	/*
+	 * finish the merging with words not processed (AND apply the quorum property)
+	 * they are stored in the second subtable (IF)
+	 *              OR in the queue           (ELSE)
+	 */
+
 	if (merged.read2 < merged.size)
+		{
+			//DEBUG_LOG("end1 %d %d/%d  %d/%d",merged.write,merged.read1,s1,merged.read2,merged.size);
 		for (;merged.read2 < merged.size;merged.read2++)
 		{
 			merged.words[merged.write]=merged.words[merged.read2];
@@ -122,7 +175,10 @@ void ecomerge(pwordcount_t data,uint32_t s1,uint32_t s2,uint32_t remainingSeq,ui
 	        	merged.write++;
 
 		}
-	else while (! queue.empty)
+		}
+	else {
+		//DEBUG_LOG("end2 %d %d/%d  %d/%d",merged.write,merged.read1,s1,merged.read2,merged.size);
+		while (! queue.empty)
 		{
 //			DEBUG_LOG("write : %s count : %d write : %d size : %d pop : %d push : %d  empty : %d",ecoUnhashWord(queue.words[queue.pop],18),queue.count[queue.pop],merged.write,queue.size,queue.pop,queue.push,queue.empty)
 			merged.words[merged.write]=queue.words[queue.pop];
@@ -131,6 +187,7 @@ void ecomerge(pwordcount_t data,uint32_t s1,uint32_t s2,uint32_t remainingSeq,ui
 	        if (remainingSeq + merged.count[merged.write] >= seqQuorum)
 	        	merged.write++;
 		}
+		}
 
 	data->size = merged.write;
 

src/libecoprimer/pairs.c

@@ -7,34 +7,41 @@
 
 #include  "ecoprimer.h"
 #include  <string.h>
+#include  <stdlib.h>
+#include "../libthermo/thermostats.h"
 
-primermatchcount_t buildPrimerPairsForOneSeq(uint32_t seqid,pprimercount_t primers,poptions_t options);
+static void buildPrimerPairsForOneSeq(uint32_t seqid,
+									  pecodnadb_t seqdb,
+		 							  pprimercount_t primers,
+								 	  ppairtree_t pairs,
+									  poptions_t options);
 
-int32_t pairinlist (ppairs_t pairlist, word_t w1, word_t w2, uint32_t size)
-{
-	uint32_t i;
-	
-	for (i = 0; i < size; i++)
-	{
-		if (w1 == pairlist[i].w1 && w2 == pairlist[i].w2) return i;
-		if (w1 == pairlist[i].w2 && w2 == pairlist[i].w1) return i;
-	}
-	return -1;
-}
 
-char *addamplifiasetelem (ppairs_t pair, char* amplifia, int32_t taxid)
+
+
+
+
+/*************************************
+ *
+ *       pair collection management
+ *
+ *************************************/
+
+#ifdef MASKEDCODE
+
+char *addamplifiasetelem (ppair_t pair, char* amplifia, int32_t taxid)
 {
 	uint32_t i;
 	uint32_t j;
 	char *ampused = NULL;
-	
+
 	if(pair->ampsetcount == 0)
 	{
 		pair->ampsetcount = 500;
 		pair->ampsetindex = 0;
 		pair->ampset = ECOMALLOC(pair->ampsetcount * sizeof(ampseqset_t),"Cannot allocate amplifia set");
 	}
-	
+
 	for (i = 0; i < pair->ampsetindex; i++)
 	{
 		if (strcmp (pair->ampset[i].amplifia, amplifia) == 0)
@@ -43,43 +50,43 @@ char *addamplifiasetelem (ppairs_t pair, char* amplifia, int32_t taxid)
 			break;
 		}
 	}
-	
+
 	if (i == 0)
 	{
 		pair->ampset[i].seqidcount = 100;
 		pair->ampset[i].seqidindex = 0;
 		pair->ampset[i].taxonids = ECOMALLOC(pair->ampset[i].seqidcount * sizeof(uint32_t),"Cannot allocate amplifia sequence table");
 	}
-	
+
 	if (pair->ampsetindex == pair->ampsetcount)
 	{
 		pair->ampsetcount += 500;
 		pair->ampset = ECOREALLOC(pair->ampset, pair->ampsetcount * sizeof(ampseqset_t), "Cannot allocate amplifia set");
 	}
-	
+
 	if (pair->ampset[i].seqidindex == pair->ampset[i].seqidcount)
 	{
 		pair->ampset[i].seqidcount += 100;
 		pair->ampset[i].taxonids = ECOREALLOC(pair->ampset[i].taxonids, pair->ampset[i].seqidcount * sizeof(int32_t), "Cannot allocate amplifia sequence table");
 	}
-	
+
 	if (pair->ampset[i].amplifia == NULL)
 	{
 		pair->ampset[i].amplifia = amplifia;
 		pair->ampsetindex++;
 	}
-	
+
 	for (j = 0; j < pair->ampset[i].seqidindex; j++)
 	{
 		if (pair->ampset[i].taxonids[j] == taxid) break;
 	}
-	
+
 	if (j == pair->ampset[i].seqidindex)
 		pair->ampset[i].taxonids[pair->ampset[i].seqidindex++] = taxid;
 	return ampused;
 }
 
-void addtaxampsetelem (ppairs_t pair, int32_t taxid, char *amplifia)
+void addtaxampsetelem (ppair_t pair, int32_t taxid, char *amplifia)
 {
 	uint32_t i;
 	uint32_t j;
@@ -90,42 +97,42 @@ void addtaxampsetelem (ppairs_t pair, int32_t taxid, char *amplifia)
 		pair->taxsetindex = 0;
 		pair->taxset = ECOMALLOC(pair->taxsetcount * sizeof(taxampset_t),"Cannot allocate taxon set");
 	}
-	
+
 	for (i = 0; i < pair->taxsetindex; i++)
 	{
 		if (pair->taxset[i].taxonid == taxid) break;
 	}
-	
+
 	if (i == 0)
 	{
 		pair->taxset[i].amplifiacount = 100;
 		pair->taxset[i].amplifiaindex = 0;
 		pair->taxset[i].amplifia = ECOMALLOC(pair->taxset[i].amplifiacount * sizeof(char *),"Cannot allocate amplifia table");
 	}
-	
+
 	if (pair->taxsetindex == pair->taxsetcount)
 	{
 		pair->taxsetcount += 500;
 		pair->taxset = ECOREALLOC(pair->taxset, pair->taxsetcount * sizeof(taxampset_t), "Cannot allocate taxon set");
 	}
-	
+
 	if (pair->taxset[i].amplifiaindex == pair->taxset[i].amplifiacount)
 	{
 		pair->taxset[i].amplifiacount += 100;
 		pair->taxset[i].amplifia = ECOREALLOC(pair->taxset[i].amplifia, pair->taxset[i].amplifiacount * sizeof(char *), "Cannot allocate amplifia table");
 	}
-	
+
 	if (pair->taxset[i].taxonid == 0)
 	{
 		pair->taxset[i].taxonid = taxid;
 		pair->taxsetindex++;
 	}
-	
+
 	for (j = 0; j < pair->taxset[i].amplifiaindex; j++)
 	{
 		if (strcmp(pair->taxset[i].amplifia[j], amplifia) == 0) break;
 	}
-	
+
 	if (j == pair->taxset[i].amplifiaindex)
 	{
 		pair->taxset[i].amplifia[j] = amplifia;
@@ -135,140 +142,67 @@ void addtaxampsetelem (ppairs_t pair, int32_t taxid, char *amplifia)
 
 char *getamplifia (pecoseq_t seq, uint32_t start, uint32_t len)
 {
+	fprintf(stderr,"start : %d length : %d\n",start,len);
 	char *amplifia = ECOMALLOC((len + 1) * sizeof(char),"Cannot allocate amplifia");
 	char *seqc = &seq->SQ[start];
-	
+
 	strncpy(amplifia, seqc, len);
 	return amplifia;
 }
 
+#endif
 
 /*TR: Added*/
-pairscount_t buildPrimerPairs(pecodnadb_t seqdb,uint32_t seqdbsize,pprimercount_t primers,poptions_t options)
+ppairtree_t buildPrimerPairs(pecodnadb_t seqdb,uint32_t seqdbsize,pprimercount_t primers,poptions_t options)
 {
 	uint32_t i;
-	uint32_t j;
+	ppairtree_t primerpairs;
-	uint32_t k;
-	uint32_t d;
-	uint32_t strt;
-	uint32_t end;
-	uint32_t paircount = 0;
-	uint32_t pairslots = 500;
-	int32_t foundindex;
-	ppairs_t pairs;
-	pairscount_t primerpairs;
-	primermatchcount_t seqmatchcount;
-	word_t w1;
-	word_t w2;
-	char *amplifia;
-	char *oldamp;
 	
-
+	primerpairs = initpairtree(NULL);
-	pairs = ECOMALLOC(pairslots * sizeof(pairs_t),"Cannot allocate pairs table");
 
 	for (i=0; i < seqdbsize; i++)
 	{
-		seqmatchcount = buildPrimerPairsForOneSeq(i, primers, options);
+		buildPrimerPairsForOneSeq(i, seqdb, primers, primerpairs, options);
-		if (seqmatchcount.matchcount == 0) continue;
-		
-		for (j=0; j < seqmatchcount.matchcount; j++)
-		{		
-			strt = 0;
-			w1 = seqmatchcount.matches[j].word;
-			/*first word should b on direct strand*/
-			if (!seqmatchcount.matches[j].strand)
-				w1 = ecoComplementWord(w1, options->primer_length);
-			else
-				strt = options->primer_length;
-			
-			for (k=j+1; k < seqmatchcount.matchcount; k++)
-			{
-				end = 0;
-				w2 = seqmatchcount.matches[k].word;
-				/*second word should be on reverse strand*/
-				if (seqmatchcount.matches[k].strand)
-					w2 = ecoComplementWord(w2, options->primer_length);
-				else
-					end = options->primer_length;
-
-				if (!(seqmatchcount.matches[j].good || seqmatchcount.matches[k].good)) continue;
-				if (w1 == w2) continue;
-				
-				d = seqmatchcount.matches[k].position - seqmatchcount.matches[j].position;
-				if (d >= options->lmin && d <= options->lmax)
-				{
-					/*get amplified string*/
-					amplifia = getamplifia (seqdb[i], seqmatchcount.matches[j].position + strt, d - strt - end);
-
-					foundindex = pairinlist(pairs, w1, w2, paircount);
-					if (foundindex != -1) /*pair is found*/
-					{
-						if (seqdb[i]->isexample)
-							pairs[foundindex].inexample++;
-						else
-							pairs[foundindex].outexample++;
-								
-						if (pairs[foundindex].mind > d) pairs[foundindex].mind = d;
-						else if (pairs[foundindex].maxd < d) pairs[foundindex].maxd = d;
-						
-						oldamp = addamplifiasetelem (&pairs[foundindex], amplifia, seqdb[i]->ranktaxonid);
-						/*if exact same string is already in amplifia set then use that for taxon set, it will help for
-						 * calculating the fully identified taxons i.e specificity, we will compare pointrs instead of strings
-						 * because same string means same pointer*/
-						if (oldamp)
-						{
-							ECOFREE (amplifia, "free amplifia");
-							amplifia = oldamp;
-						}
-						addtaxampsetelem (&pairs[foundindex], seqdb[i]->ranktaxonid, amplifia);
-
-						continue;
-					}
-
-					if (paircount == pairslots)
-					{
-						pairslots += 500;
-						pairs = ECOREALLOC(pairs, pairslots * sizeof(pairs_t), "Cannot allocate pairs table");
-					}
-					pairs[paircount].w1 = w1;
-					pairs[paircount].w2 = w2;
-					if (seqdb[i]->isexample) pairs[paircount].inexample = 1;
-					else pairs[paircount].outexample = 1;
-					pairs[paircount].mind = d;
-					pairs[paircount].maxd = d;
-					oldamp = addamplifiasetelem (&pairs[paircount], amplifia, seqdb[i]->ranktaxonid);
-					addtaxampsetelem (&pairs[paircount], seqdb[i]->ranktaxonid, amplifia);
-
-					paircount++;
-				}
-				else if (d > options->lmax)
-					break; /*once if the distance is greater than lmax then it will keep on increasing*/
-			}
-		}
-		ECOFREE(seqmatchcount.matches, "Cannot free matches table");
 	}
-	primerpairs.pairs = ECOREALLOC(pairs, paircount * sizeof(pairs_t), "Cannot allocate pairs table");
-	primerpairs.paircount = paircount;
 	return primerpairs;
 }
 
-primermatchcount_t buildPrimerPairsForOneSeq(uint32_t seqid,pprimercount_t primers,poptions_t options)
+#define DMAX (2000000000)
-{
-	uint32_t i,j,k;
-	uint32_t matchcount=0;
-	pprimermatch_t matches = NULL;
-	primermatchcount_t seqmatchcount;
 
-	seqmatchcount.matchcount = 0;
+static void buildPrimerPairsForOneSeq(uint32_t seqid,
-	seqmatchcount.matches = NULL;
+									  pecodnadb_t seqdb,
+		 							  pprimercount_t primers,
+								 	  ppairtree_t pairs,
+									  poptions_t options)
+{
+	static uint32_t    paircount=0;
+	uint32_t           i,j,k;
+	uint32_t           matchcount=0;
+	pprimermatch_t     matches = NULL;
+	//primermatchcount_t seqmatchcount;
+	ppair_t            pcurrent;
+	pair_t			   current;
+	pprimer_t		   wswp;
+	bool_t			   bswp;
+	size_t			   distance;
+	bool_t             strand;
+	//char 			   prmr[50];
+	//float			   mtemp;
+	word_t 			   w1, w1a, omask = (0x1L << (options->strict_three_prime*2)) -1;
+	word_t 			   w2, w2a;//, wtmp;
+	uint32_t   		   bp1,bp2;
+		
+	//prmr[options->primer_length] = '\0';
 	
 	for (i=0;i < primers->size; i++)
 	{
 		matchcount+=primers->primers[i].directCount[seqid];
 		matchcount+=primers->primers[i].reverseCount[seqid];
 	}
-	
+
-	if (matchcount <= 0) return seqmatchcount;
+	if (matchcount <= 0)
+		return;
+
 	matches = ECOMALLOC(matchcount * sizeof(primermatch_t),"Cannot allocate primers match table");
 
 	for (i=0,j=0;i < primers->size; i++)
@@ -277,17 +211,15 @@ primermatchcount_t buildPrimerPairsForOneSeq(uint32_t seqid,pprimercount_t prime
 		{
 			if (primers->primers[i].directCount[seqid]==1)
 			{
-				matches[j].word = primers->primers[i].word;
+			matches[j].primer = primers->primers+i;
-				matches[j].strand=TRUE;
+			matches[j].strand=TRUE;
-				matches[j].good=primers->primers[i].good;/*TR: Added*/
 				matches[j].position=primers->primers[i].directPos[seqid].value;
 				j++;
 			}
 			else for (k=0; k < primers->primers[i].directCount[seqid]; k++,j++)
 			{
-				matches[j].word = primers->primers[i].word;
+				matches[j].primer = primers->primers+i;
 				matches[j].strand=TRUE;
-				matches[j].good=primers->primers[i].good;/*TR: Added*/
 				matches[j].position=primers->primers[i].directPos[seqid].pointer[k];
 			}
 		}
@@ -296,26 +228,233 @@ primermatchcount_t buildPrimerPairsForOneSeq(uint32_t seqid,pprimercount_t prime
 		{
 			if (primers->primers[i].reverseCount[seqid]==1)
 			{
-				matches[j].word = primers->primers[i].word;
+			matches[j].primer = primers->primers+i;
-				matches[j].strand=FALSE;
+			matches[j].strand=FALSE;
-				matches[j].good=primers->primers[i].good;/*TR: Added*/
 				matches[j].position=primers->primers[i].reversePos[seqid].value;
 				j++;
 			}
 			else for (k=0; k < primers->primers[i].reverseCount[seqid]; k++,j++)
 			{
-				matches[j].word = primers->primers[i].word;
+				matches[j].primer = primers->primers+i;
 				matches[j].strand=FALSE;
-				matches[j].good=primers->primers[i].good;/*TR: Added*/
 				matches[j].position=primers->primers[i].reversePos[seqid].pointer[k];
 			}
 		}
 	}
 
-	sortmatch(matches,matchcount); // sort in asscending order by position
+	if (matchcount>1)
-	
+	{
-	/*TR: Added*/
+//		fprintf(stderr,"\n====================================\n");
-	seqmatchcount.matches = matches;
+
-	seqmatchcount.matchcount = matchcount;
+		sortmatch(matches,matchcount); // sort in ascending order by position
-	return seqmatchcount;
+
+		for (i=0; i < matchcount;i++)
+		{
+			// For all primers matching the sequence
+
+			/*for(j=i+1;
+			       (j<matchcount)
+			    && ((distance=matches[j].position - matches[i].position - options->primer_length) < options->lmax);
+			   j++
+			   )//*/
+			for (j=i+1; j<matchcount; j++)
+			{
+				if (matches[j].position - matches[i].position <= options->primer_length) continue;
+				distance = matches[j].position - matches[i].position - options->primer_length;
+				if (distance >= options->lmax) break;
+				
+
+			   // For all not too far primers
+
+		       if ( (matches[i].primer->good || matches[j].primer->good)
+		    		&& (distance > options->lmin)
+		    		)
+		       {
+		    	   // If possible primer pair
+		    	   current.p1 = matches[i].primer;
+		    	   current.asdirect1=matches[i].strand;
+		    	   current.p2 = matches[j].primer;
+		    	   current.asdirect2= !matches[j].strand;
+		    	   current.maxd=DMAX;
+		    	   current.mind=DMAX;
+		    	   current.sumd=0;
+		    	   current.amplifiacount=0;
+	    		   current.inexample=0;
+	    		   current.outexample=0;
+				   current.curseqid = 0;
+				   current.refsequence=-1;
+				   //current.p1temp = 100;
+				   //current.p1mintemp = 100;
+				   //current.p2temp = 100;
+				   //current.p2mintemp = 100;
+
+		    	   // Standardize the pair
+	    		   strand = current.p2->word > current.p1->word;
+		    	   if (!strand)
+		    	   {
+		    		   wswp = current.p1;
+		    		   current.p1=current.p2;
+		    		   current.p2=wswp;
+
+		    		   bswp = current.asdirect1;
+		    		   current.asdirect1=current.asdirect2;
+		    		   current.asdirect2=bswp;
+		    	   }
+
+		    	   
+		    	   //Code to make sure that if -3 option is given then
+		    	   //3' end must match upto given number of base pairs
+		    	   if (options->strict_three_prime > 0)
+		    	   {
+		    		   w1 = current.p1->word;
+		    		   w2 = current.p2->word;
+		    		   if (!current.asdirect1) //make sure that word is from 5' to 3'
+		    			   w1=ecoComplementWord(w1,options->primer_length);
+
+		    		   if (!current.asdirect2) //make sure that word is from 5' to 3'
+		    			   w2=ecoComplementWord(w2,options->primer_length);
+		    		   //now both w1 and w2 are from 5' to 3' end
+		    		   bp1 = matches[i].position;
+		    		   bp2 = matches[j].position;
+		    		   if (!strand)
+		    		   {
+			    		   bp1 = matches[j].position;
+			    		   bp2 = matches[i].position;
+		    		   }
+		    		   //get word of first approximate repeat
+		    		   w1a = extractSite(seqdb[seqid]->SQ,bp1,options->primer_length,strand);
+		    		   //get word of second approximate repeat
+		    		   w2a = extractSite(seqdb[seqid]->SQ,bp2,options->primer_length,!strand);
+		    		   		    		  		    		   
+		    		   w1 = w1 & omask;   //keep only strict_three_prime bases on the right (3') end
+		    		   w2 = w2 & omask;   //keep only strict_three_prime bases on the right (3') end
+		    		   w1a = w1a & omask; //keep only strict_three_prime bases on the right (3') end
+		    		   w2a = w2a & omask; //keep only strict_three_prime bases on the right (3') end
+		    		
+		    		   //now check that both words and primers of amplifia have same bases on 3' end
+		    		   if ((w1 ^ w1a) != 0) continue; 
+		    		   if ((w2 ^ w2a) != 0) continue;
+		    	   }
+		    	   
+		    	   
+
+		    	   // Look for the new pair in already seen pairs
+
+		    	   pcurrent = insertpair(current,pairs);
+
+
+		    	   if (seqdb[seqid]->isexample)
+
+				   {
+		    		   //pcurrent->inexample++;
+		    		   pcurrent->sumd+=distance;
+		    		   pcurrent->amplifiacount++;
+
+		    		   if ((pcurrent->maxd==DMAX) || (distance > pcurrent->maxd))
+			    		   pcurrent->maxd = distance;
+
+			    	   if (distance < pcurrent->mind)
+			    		   pcurrent->mind = distance;
+		    	   }
+		    	   //else
+		    		 //  pcurrent->outexample++;
+
+		    	   //for each pair we save current sequence id in the pair
+		    	   //when we see this pair for the first time in currnet sequence
+		    	   //because we want to increment inexample & outexample count
+		    	   //only once for one sequence
+				  if (pcurrent->curseqid != (seqid+1))
+				   {
+						if (seqdb[seqid]->isexample)
+							pcurrent->inexample++;
+		    	        else
+		    		        pcurrent->outexample++;
+
+						if (pcurrent->curseqid != 0)
+							pcurrent->curseqid = seqid+1;
+					}
+
+					/*if ((pcurrent->outexample+pcurrent->inexample)==0)
+					{
+						fprintf(stderr,"pcurrent->outexample+pcurrent->inexample=0!\n");
+						exit(0);
+					}*/
+
+		    	   if (pcurrent->curseqid == 0)//((pcurrent->outexample+pcurrent->inexample)==1)
+		    	   {
+					   pcurrent->curseqid = seqid+1;
+					   paircount++;
+					   pcurrent->pcr.ampslot=200;
+					   pcurrent->pcr.ampcount=0;
+					   pcurrent->pcr.amplifias = ECOMALLOC(sizeof(amplifia_t)*pcurrent->pcr.ampslot,
+							                               "Cannot allocate amplifia table");
+		    	   }
+		    	   else
+		    	   {
+		    		   if (pcurrent->pcr.ampslot==pcurrent->pcr.ampcount)
+		    		   {
+		    			   pcurrent->pcr.ampslot+=200;
+		    			   pcurrent->pcr.amplifias = ECOREALLOC(pcurrent->pcr.amplifias,
+															    sizeof(amplifia_t)*pcurrent->pcr.ampslot,
+		    			   							            "Cannot allocate amplifia table");
+		    		   }
+		    	   }
+
+		    	   if (seqid==options->refseqid)
+		    		   pcurrent->refsequence=seqid;
+		    	   pcurrent->pcr.amplifias[pcurrent->pcr.ampcount].length=distance;
+		    	   pcurrent->pcr.amplifias[pcurrent->pcr.ampcount].sequence=seqdb[seqid];
+		    	   pcurrent->pcr.amplifias[pcurrent->pcr.ampcount].strand=strand;
+		    	   pcurrent->pcr.amplifias[pcurrent->pcr.ampcount].begin=matches[i].position + options->primer_length;
+		    	   pcurrent->pcr.amplifias[pcurrent->pcr.ampcount].end=  matches[j].position - 1;
+
+		    	   if (strand)
+		    	   	   pcurrent->pcr.amplifias[pcurrent->pcr.ampcount].amplifia=  seqdb[seqid]->SQ + matches[i].position + options->primer_length;
+		    	   else
+		    	   	   pcurrent->pcr.amplifias[pcurrent->pcr.ampcount].amplifia=  seqdb[seqid]->SQ + matches[j].position - 1 ;
+
+		    	   
+		    	   /*strncpy (prmr, seqdb[seqid]->SQ + matches[i].position, options->primer_length);
+		    	   mtemp = nparam_CalcSelfTM (options->pnparm, prmr, options->primer_length) - 273.0;
+		    	   if (mtemp < pcurrent->p1mintemp)
+		    		   pcurrent->p1mintemp = mtemp;
+		    	   //fprintf (stderr, "prmr1: %s\n", seqdb[seqid]->SQ);
+		    	   strncpy (prmr, seqdb[seqid]->SQ + matches[j].position, options->primer_length);
+		    	   mtemp = nparam_CalcSelfTM (options->pnparm, prmr, options->primer_length) - 273.0;
+		    	   if (mtemp < pcurrent->p2mintemp)
+		    		   pcurrent->p2mintemp = mtemp;
+		    	   //fprintf (stderr, "prmr2: %s\n", prmr);
+
+		    	   if (pcurrent->p1temp == 100)
+		    		   pcurrent->p1temp = nparam_CalcSelfTM (options->pnparm, ecoUnhashWord(pcurrent->p1->word, options->primer_length), 0) - 273.0;
+		    	   if (pcurrent->p2temp == 100)
+		    		   pcurrent->p2temp = nparam_CalcSelfTM (options->pnparm, ecoUnhashWord(pcurrent->p2->word, options->primer_length), 0) - 273.0;
+		    	   */
+		    	   pcurrent->pcr.ampcount++;
+//		    	   fprintf(stderr,"%c%c W1 : %s   direct : %c",
+//		    			   "bG"[(int)pcurrent->p1->good],
+//		    			   "bG"[(int)pcurrent->p2->good],
+//		    			   ecoUnhashWord(pcurrent->p1->word, options->primer_length),
+//		    			   "><"[(int)pcurrent->asdirect1]
+//		    			   );
+//
+//		    	   fprintf(stderr,"   W2 : %s   direct : %c distance : %d (min/max/avg : %d/%d/%f) in/out: %d/%d %c (%d pairs)\n",
+//		    			   ecoUnhashWord(pcurrent->p2->word, options->primer_length),
+//		    			   "><"[(int)pcurrent->asdirect2],
+//		    			   distance,
+//		    			   pcurrent->mind,pcurrent->maxd,
+//		    			   (pcurrent->inexample) ? (float)pcurrent->sumd/pcurrent->inexample:0.0,
+//		    			   pcurrent->inexample,pcurrent->outexample,
+//		    			   " N"[(pcurrent->outexample+pcurrent->inexample)==1],
+//		    			   paircount
+//
+//		    			   );
+//
+
+		       }
+		}
+		 }
+	}
+   pairs->count=paircount;
+
 }

src/libecoprimer/pairtree.c

@@ -0,0 +1,136 @@
+/*
+ * pairtree.c
+ *
+ *  Created on: 7 mars 2009
+ *      Author: coissac
+ */
+
+#include  "ecoprimer.h"
+#include <search.h>
+
+static void cleanpair(ppair_t pair);
+static void deletepairlist(ppairlist_t list);
+static int cmppair(const void* p1,const void*p2);
+
+
+static void cleanamplifiatlist(pamplifiacount_t list)
+{
+	if (list->amplifias)
+		ECOFREE(list->amplifias,
+				"Free amplifia list");
+}
+
+static void cleanpair(ppair_t pair)
+{
+   cleanamplifiatlist(&(pair->pcr));
+}
+
+static ppairlist_t newpairlist(ppairlist_t parent, size_t size)
+{
+	ppairlist_t tmp;
+
+	tmp=ECOMALLOC(sizeof(pairlist_t)+sizeof(pair_t)*(size-1),
+			      "Cannot allocate new pair list");
+
+	tmp->pairslots=size;
+	tmp->paircount=0;
+	tmp->next=NULL;
+
+	if (parent)
+		parent->next=(void*)tmp;
+
+
+	return tmp;
+}
+
+static void deletepairlist(ppairlist_t list)
+{
+	size_t i;
+
+	if (list)
+	{
+		if (list->next)
+		{
+			deletepairlist(list->next);
+			list->next=NULL;
+		}
+		for (i=0; i < list->paircount; i++)
+			cleanpair((list->pairs)+i);
+
+		ECOFREE(list,"Delete pair list");
+	}
+
+}
+
+static int cmppair(const void* p1,const void*p2)
+{
+	ppair_t pr1,pr2;
+
+	pr1=(ppair_t)p1;
+	pr2=(ppair_t)p2;
+
+	if (pr1->p1 < pr2->p1) return -1;
+	if (pr1->p1 > pr2->p1) return  1;
+
+	if (pr1->asdirect1 < pr2->asdirect1) return -1;
+	if (pr1->asdirect1 > pr2->asdirect1) return  1;
+
+	if (pr1->p2 < pr2->p2) return -1;
+	if (pr1->p2 > pr2->p2) return  1;
+
+	if (pr1->asdirect2 < pr2->asdirect2) return -1;
+	if (pr1->asdirect2 > pr2->asdirect2) return  1;
+
+	return 0;
+}
+
+ppair_t pairintree (pair_t key,
+		            ppairtree_t pairlist)
+{
+	if (!pairlist->tree)
+		return NULL;
+
+	return *((ppair_t*)tsearch((const void *)(&key),
+								&(pairlist->tree),
+						        cmppair
+							  ));
+}
+
+ppair_t insertpair(pair_t key,
+		           ppairtree_t list)
+{
+	ppair_t current;
+	ppair_t found;
+
+	if (list->last->paircount==list->last->pairslots)
+	{
+		list->last->next=newpairlist(list->last,100);
+		list->last=list->last->next;
+	}
+
+	current = list->last->pairs + list->last->paircount;
+	*current=key;
+
+	found = *((ppair_t*)tsearch((const void *)current,
+			                    &(list->tree),
+			                    cmppair));
+	if (found==current)
+		list->last->paircount++;
+
+	return found;
+}
+
+ppairtree_t initpairtree(ppairtree_t tree)
+{
+
+	if (!tree)
+		tree = ECOMALLOC(sizeof(pairtree_t),"Cannot allocate pair tree");
+
+	tree->first=newpairlist(NULL,300);
+	tree->last=tree->first;
+
+	tree->tree=NULL;
+	tree->count=0;
+
+	return tree;
+}

src/libecoprimer/readdnadb.c

@@ -7,7 +7,7 @@
 
 #include "ecoprimer.h"
 
-pecodnadb_t readdnadb(const char *name, uint32_t *size)
+pecodnadb_t readdnadb(const char *name, ecotaxonomy_t *taxonomy, uint32_t *size,poptions_t options)
 {
 	ecoseq_t      *seq;
 	uint32_t       buffsize=100;
@@ -18,18 +18,42 @@ pecodnadb_t readdnadb(const char *name, uint32_t *size)
 
 	for(seq=ecoseq_iterator(name), *size=0;
 	    seq;
-	    seq=ecoseq_iterator(NULL), (*size)++
+	    seq=ecoseq_iterator(NULL)
 	   )
 	{
-		if (*size==buffsize)
+	  if (isExampleTaxon(taxonomy,seq->taxid,options) ||
-		{
+		  isCounterExampleTaxon(taxonomy,seq->taxid,options))
-			buffsize*=2;
+	  {
-			db = ECOREALLOC(db,buffsize*sizeof(ecoseq_t*),"I cannot allocate db memory");
+			if (*size==buffsize)
-		}
+			{
-		db[*size]=seq;
+				buffsize*=2;
+				db = ECOREALLOC(db,buffsize*sizeof(ecoseq_t*),"I cannot allocate db memory");
+			}
+			db[*size]=seq;
+			(*size)++;
+	  }
+	  else
+	  {
+		  delete_ecoseq(seq);
+	  }
 	};
 
 	db = ECOREALLOC(db,(*size)*sizeof(ecoseq_t*),"I cannot allocate db memory");
 
 	return db;
 }
+
+
+void printSeqTest(pecodnadb_t seqdb,uint32_t seqdbsize)
+{
+	uint32_t i;
+	char ch[11];
+	ch [10] = '\0';
+	
+	for (i=0; i < seqdbsize; i++)
+	{
+		strncpy (ch, seqdb[i]->SQ, 10);
+		fprintf (stderr, "seq %d = %s\n", i, ch);
+	}
+	exit (0);
+}

src/libecoprimer/smothsort.c

@@ -35,6 +35,7 @@
  * @author Pekka Pessi <Pekka.Pessi@nokia.com>
  */
 
+#include <stdlib.h> /* FB for NULL */
 
 #include <assert.h>
 #include <stdio.h>

src/libecoprimer/strictprimers.c

@@ -5,16 +5,55 @@
  *      Author: coissac
  */
 
+#define _GNU_SOURCE
 #include "ecoprimer.h"
 #include <string.h>
 #include <math.h>
+#include <sys/resource.h>
+#include <unistd.h>
+#include <stdio.h>
 
-pwordcount_t initCountTable(pwordcount_t table, uint32_t wordsize, uint32_t circular, uint32_t doublestrand,ecoseq_t *seq)
+#ifndef RUSAGE_SELF
+#define   RUSAGE_SELF     0
+#define   RUSAGE_CHILDREN     -1
+#endif
+
+static double timeval_subtract (struct timeval *x, struct timeval *y);
+
+
+ /* Subtract the `struct timeval' values X and Y,
+	Return elapsed secondes as a double.  */
+
+double timeval_subtract (struct timeval *x, struct timeval *y)
+{
+   struct timeval result;
+
+   /* Perform the carry for the later subtraction by updating y. */
+   if (x->tv_usec < y->tv_usec) {
+	 int nsec = (y->tv_usec - x->tv_usec) / 1000000 + 1;
+	 y->tv_usec -= 1000000 * nsec;
+	 y->tv_sec += nsec;
+   }
+   if (x->tv_usec - y->tv_usec > 1000000) {
+	 int nsec = (x->tv_usec - y->tv_usec) / 1000000;
+	 y->tv_usec += 1000000 * nsec;
+	 y->tv_sec -= nsec;
+   }
+
+   /* Compute the time remaining to wait.
+	  tv_usec is certainly positive. */
+   result.tv_sec = x->tv_sec - y->tv_sec;
+   result.tv_usec = x->tv_usec - y->tv_usec;
+
+   return (double)result.tv_sec + (double)result.tv_usec/1e6;
+ }
+
+pwordcount_t initCountTable(pwordcount_t table, uint32_t wordsize, uint32_t circular, uint32_t doublestrand,uint32_t seqQuorum,ecoseq_t *seq,int32_t *neededWords,uint32_t neededWordCount)
 {
 	uint32_t i;
 	uint32_t buffsize;
 	//wordcount_t t;
-	
+
 	if (!table)
 		table = ECOMALLOC(sizeof(wordcount_t),"Cannot allocate memory for word count structure");
 
@@ -26,7 +65,7 @@ pwordcount_t initCountTable(pwordcount_t table, uint32_t wordsize, uint32_t circ
 
 	if (seq)
 	{
-		table->words = ecoHashSequence(NULL,wordsize,circular,doublestrand,seq,&buffsize);
+		table->words = ecoHashSequence(NULL,wordsize,circular,doublestrand,seq,&buffsize,neededWords,neededWordCount,seqQuorum);
 		table->size  = ecoCompactHashSequence(table->words,buffsize);
 
 		table->inseqcount=1;
@@ -40,7 +79,7 @@ pwordcount_t initCountTable(pwordcount_t table, uint32_t wordsize, uint32_t circ
 	return table;
 }
 
-void addSeqToWordCountTable(pwordcount_t table, uint32_t wordsize, uint32_t circular, uint32_t doublestrand,uint32_t exampleCount,uint32_t seqQuorum,ecoseq_t *seq)
+void addSeqToWordCountTable(pwordcount_t table, uint32_t wordsize, uint32_t circular, uint32_t doublestrand,uint32_t exampleCount,uint32_t seqQuorum,ecoseq_t *seq,int32_t *neededWords,uint32_t neededWordCount)
 {
 	uint32_t buffersize;
 	pword_t newtable;
@@ -50,33 +89,52 @@ void addSeqToWordCountTable(pwordcount_t table, uint32_t wordsize, uint32_t circ
 	buffersize = table->size + ecoWordCount(wordsize,circular,seq);
 
 	table->words = ECOREALLOC(table->words,buffersize*sizeof(word_t),
-							  "Cannot allocate memory to extend word table");
+							  "\n\nCannot allocate memory to extend word table" );
-
 
+	/*
+	 * newtable is a pointer on the memory planed to be used for the new sequence (ecoWordCount new hash codes max)
+	 */
 	newtable = table->words + table->size;
 
 //	DEBUG_LOG("Words = %x (%u) new = %x", table->words,table->size,newtable);
 
-	(void)ecoHashSequence(newtable,wordsize,circular,doublestrand,seq,&newsize);
+	(void)ecoHashSequence(newtable,wordsize,circular,doublestrand,seq,&newsize,neededWords,neededWordCount,seqQuorum);
 //	DEBUG_LOG("new seq wordCount : %d",newsize);
 
+	/*
+	 * at this stage, new hash codes have been added in the table but the table is not sorted
+	 */
+
 	newsize = ecoCompactHashSequence(newtable,newsize);
 
+	/*
+	 * new hash codes have now been sorted BUT the whole table is not.
+	 * MULTIWORDS have been tagged (and compacted)
+	 */
+
 //	DEBUG_LOG("compacted wordCount : %d",newsize);
 	buffersize = table->size + newsize;
 
+	/*
+	 * buffersize is now set to the REAL size used by the table (but the memory chunck may be larger)
+	 */
+
 	// resize the count buffer
 
 	table->inseqcount++;
 
-
+	//fprintf (stderr, "\nOldAddress: %x", table->strictcount);
-	table->strictcount = ECOREALLOC(table->strictcount,buffersize*sizeof(uint32_t),
+	table->strictcount = ECOREALLOC(table->strictcount,(buffersize+5000)*sizeof(uint32_t),
 								"Cannot allocate memory to extend example word count table");
+	//fprintf (stderr, " NewAddress: %x\n", table->strictcount);
+	
 
 	for (i=table->size; i < buffersize; i++)
 		table->strictcount[i]=1;
 
-
+	/*
+	 * new words in the table are set to a count of ONE
+	 */
 
 	// Now we have to merge in situ the two tables
 
@@ -88,45 +146,96 @@ void addSeqToWordCountTable(pwordcount_t table, uint32_t wordsize, uint32_t circ
 pwordcount_t lookforStrictPrimer(pecodnadb_t database, uint32_t seqdbsize,
 								 uint32_t exampleCount,poptions_t options)
 {
-	uint32_t i;
+	struct rusage start;
+	struct rusage usage;
+	double seconde;
+	char   *logfilename;
+	FILE   *logfile;
+	uint32_t i, j;
+	bool_t first=TRUE;
 	pwordcount_t strictprimers=NULL;
+	uint64_t totallength=0;
 	uint32_t  sequenceQuorum = (uint32_t)floor((float)exampleCount * options->strict_quorum);
+	int32_t *neededWords;
+	uint32_t neededWordCount;
+
+	fprintf(stderr,"Filtering... ");
+
+	if (options->filtering)
+		neededWords = filteringSeq(database,seqdbsize,exampleCount,options,&neededWordCount,(int32_t)sequenceQuorum);
+	else
+	{
+		neededWordCount=0;
+		neededWords=NULL;
+	}
+
+	if (options->statistics)
+	{
+		asprintf(&logfilename,"ecoprimer_%d.log",getpid());
+		logfile = fopen(logfilename,"w");
+		fprintf(logfile,"# seq\tlength\tsize\ttime\tspeed\n");
+		fclose(logfile);
+	}
+
 
 	fprintf(stderr,"  Primers should be at least present in %d/%d example sequences\n",sequenceQuorum,exampleCount);
 
 	strictprimers = initCountTable(NULL,options->primer_length,
                                                  options->circular,
                                                  options->doublestrand,
-                                   NULL);
+                                                 0,
+                                   NULL,NULL,0);
 
 
+	getrusage(RUSAGE_SELF,&start);
+
     for (i=0;i<seqdbsize;i++)
     {
-    	if (database[i]->isexample)
+    	if (database[i]->isexample && database[i]->SQ_length > options->primer_length)
     	{
-    		if (strictprimers->size)
+
+    		if (first)
     		{
-    			uint32_t s;
+    			strictprimers = initCountTable(strictprimers,options->primer_length,
-    			s = strictprimers->size;
+                                                             options->circular,
+                                                             options->doublestrand,
+                                                             sequenceQuorum,
+                                               database[i],neededWords,neededWordCount);
+    			first=FALSE;
+    		}
+    		else
+    		{
+//  			uint32_t s;
+//    			s = strictprimers->size;
 //    			DEBUG_LOG("stack size : %u",s);
     			addSeqToWordCountTable(strictprimers,options->primer_length,
     					                             options->circular,
     					                             options->doublestrand,
     					                             exampleCount,
     					                             sequenceQuorum,
-    					               database[i]);
+    					               database[i],neededWords,neededWordCount);
+    		};
+    		totallength+=database[i]->SQ_length;
+    		getrusage(RUSAGE_SELF,&usage);
+    		if (options->statistics)
+    		{
+    			asprintf(&logfilename,"ecoprimer_%d.log",getpid());
+    			logfile = fopen(logfilename,"a");
+    			seconde = timeval_subtract(&(usage.ru_utime),&(start.ru_utime)) +
+    			          timeval_subtract(&(usage.ru_stime),&(start.ru_stime));
+    			fprintf(logfile,"%d\t%llu\t%llu\t%8.3f\t%8.3e\n",i,
+    					(long long unsigned)totallength,
+					strictprimers->size*(sizeof(int64_t)+sizeof(int32_t)),
+    					seconde,seconde/(double)totallength);
+    			fclose(logfile);
     		}
-    		else
-    			strictprimers = initCountTable(strictprimers,options->primer_length,
-                                                             options->circular,
-                                                             options->doublestrand,
-                                               database[i]);
-
     	}
     	else
     		strictprimers->outseqcount++;
 
-    	fprintf(stderr,"  Indexed sequences %5d/%5d  : considered words %-10d  \r",(int32_t)i+1,(int32_t)seqdbsize,strictprimers->size);
+    	fprintf(stderr,"  Indexed sequences %5d/%5d  : considered words %-10llu  \r",
+				(int32_t)i+1,(int32_t)seqdbsize,
+				(long long unsigned)strictprimers->size);
 
 //    	DEBUG_LOG("First  word : %s ==> %d",ecoUnhashWord(strictprimers->words[0],18),strictprimers->incount[0])
 //    	DEBUG_LOG("Second word : %s ==> %d",ecoUnhashWord(strictprimers->words[1],18),strictprimers->incount[1])
@@ -139,6 +248,39 @@ pwordcount_t lookforStrictPrimer(pecodnadb_t database, uint32_t seqdbsize,
 										sizeof(word_t)*strictprimers->size,
 										"Cannot reallocate strict primer table");
 
+    if (neededWords){
+    	ECOFREE(neededWords,"Clean needed word table");
+	}
+	//TR: Somehow for some primers strictcount value is extremely large hence invalid
+	//we need to remove these primers from the list
+	j = strictprimers->size+1;
+	for (i=0; i<strictprimers->size; i++)
+	{
+		if (strictprimers->strictcount[i] > seqdbsize)
+		{
+			if (j == (strictprimers->size+1))
+				j = i;
+		}
+		
+		if (j < i && strictprimers->strictcount[i] <= seqdbsize)
+		{
+			strictprimers->words[j] = strictprimers->words[i];
+			strictprimers->strictcount[j] = strictprimers->strictcount[i];
+			j++;
+		}
+	}
+	
+	if (j < strictprimers->size)
+	{
+		strictprimers->size = j;
+		strictprimers->strictcount = ECOREALLOC(strictprimers->strictcount,
+												sizeof(uint32_t)*strictprimers->size,
+												"Cannot reallocate strict primer count table");
+		strictprimers->words   = ECOREALLOC(strictprimers->words,
+											sizeof(word_t)*strictprimers->size,
+											"Cannot reallocate strict primer table");		
+	}
+	
 	return strictprimers;
 }
 

src/libecoprimer/taxstats.c

@@ -0,0 +1,378 @@
+/*
+ * taxstats.c
+ *
+ *  Created on: 12 mars 2009
+ *      Author: coissac
+ */
+
+#include <search.h>
+//void tdestroy (void *root, void (*free_node)(void *nodep));
+
+#include  "ecoprimer.h"
+
+static int cmptaxon(const void *t1, const void* t2);
+
+void **tree_root = NULL;
+int delete_passes = 0; 
+
+void delete_twalkaction (const void *node, VISIT order, int level)
+{
+	switch (order)
+	{
+	case preorder:
+		delete_passes++;
+		break;
+	case postorder:
+		delete_passes++;
+		break;
+	case endorder:
+		delete_passes++;
+		break;
+	case leaf:
+		if (tree_root)
+			tdelete (node, tree_root,cmptaxon);
+		delete_passes++;
+		break;
+	}
+}
+
+void free_tree_nodes (void *tree)
+{
+	while (1)
+	{
+		delete_passes = 0;
+		twalk (tree, delete_twalkaction);
+		if (delete_passes <= 1) break;
+	}
+}
+
+static int cmptaxon(const void *t1, const void* t2)
+{
+	const size_t taxid1=(size_t)t1;
+	const size_t taxid2=(size_t)t2;
+
+	// fprintf(stderr,"==> counted taxid1 : %d\n",taxid1);
+	// fprintf(stderr,"==> counted taxid2 : %d\n",taxid2);
+
+	if (taxid1 < taxid2)
+		return -1;
+	if (taxid1 > taxid2)
+		return +1;
+	return 0;
+}
+
+int32_t counttaxon(int32_t taxid)
+{
+	static void* taxontree=NULL;
+	static int32_t taxoncount=0;
+
+	// fprintf(stderr,"counted taxid : %d taxontree %p\n",taxid,taxontree);
+
+	if (taxid==-1)
+	{
+		if (taxontree)
+		{
+			tree_root = (void **)&taxontree;
+			//free_tree_nodes (taxontree);
+			ECOFREE(taxontree,"Free taxon tree");
+			tree_root = NULL;
+		}
+		taxontree=NULL;
+		taxoncount=0;
+		return 0;
+	}
+
+
+	if ((taxid > 0) && ((!taxontree) || (!tfind((void*)((size_t)taxid),&taxontree,cmptaxon))))
+	{
+		tsearch((void*)((size_t)taxid),&taxontree,cmptaxon);
+		taxoncount++;
+	}
+	return taxoncount;
+}
+
+int32_t getrankdbstats(pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *taxonomy,
+					   poptions_t options)
+{
+
+	uint32_t i;
+	ecotx_t  *taxon;
+	ecotx_t  *tmptaxon;
+
+	counttaxon(-1);
+	options->intaxa = 0;
+
+    for (i=0;i<seqdbsize;i++)
+	{
+    	taxon = &(taxonomy->taxons->taxon[seqdb[i]->taxid]);
+	    seqdb[i]->isexample=isExampleTaxon(taxonomy,seqdb[i]->taxid,options);
+
+		tmptaxon = eco_findtaxonatrank(taxon,
+									   options->taxonrankidx);
+
+	    // fprintf(stderr,"Taxid : %d %p\n",taxon->taxid,tmptaxon);
+
+		if (tmptaxon)
+		{
+			// fprintf(stderr,"orig : %d trans : %d\n",taxon->taxid,
+			// 		                                tmptaxon->taxid);
+
+			seqdb[i]->ranktaxonid=tmptaxon->taxid;
+			if (seqdb[i]->isexample)
+				options->intaxa = counttaxon(tmptaxon->taxid);
+		}
+		else
+			seqdb[i]->ranktaxonid=-1;
+	}
+
+	counttaxon(-1);
+	options->outtaxa = 0;
+
+    for (i=0;i<seqdbsize;i++)
+		{
+			if (seqdb[i]->ranktaxonid>=0 && !seqdb[i]->isexample)
+				options->outtaxa = counttaxon(seqdb[i]->ranktaxonid);
+		}
+
+    return options->outtaxa + options->intaxa;
+}
+
+
+float taxonomycoverage(ppair_t pair, poptions_t options, pecodnadb_t seqdb,uint32_t seqdbsize)
+{
+	int32_t seqcount;
+	int32_t i;
+	int32_t incount=0;
+	int32_t outcount=0;
+	uint32_t j;
+
+
+	memset (pair->coveredSeqs, 0, seqdbsize*sizeof (int));
+	seqcount=pair->pcr.ampcount;
+
+	counttaxon(-1);
+	for (i=0; i < seqcount; i++)
+		if (pair->pcr.amplifias[i].sequence->isexample
+				&& pair->pcr.amplifias[i].sequence->ranktaxonid > 0 )
+		{
+			incount = counttaxon(pair->pcr.amplifias[i].sequence->ranktaxonid);
+
+			for (j=0; j<seqdbsize; j++)
+				if (pair->pcr.amplifias[i].sequence == seqdb[j])
+					{pair->coveredSeqs[j] = 1; break;}
+		}
+
+	counttaxon(-1);
+	for (i=0; i < seqcount; i++)
+		if (!pair->pcr.amplifias[i].sequence->isexample
+				&& pair->pcr.amplifias[i].sequence->ranktaxonid)
+			outcount = counttaxon(pair->pcr.amplifias[i].sequence->ranktaxonid);
+
+
+	pair->intaxa=incount;
+	pair->outtaxa=outcount;
+	pair->bc=(float)incount/options->intaxa;
+	return pair->bc;
+}
+
+/*
+static int cmpamp(const void *ampf1, const void* ampf2)
+{
+	int i;
+	int j = 0;
+	int incr = 1;
+	char cd1;
+	char cd2;
+	int chd = 0;
+	int len = 0;
+
+	pamptotaxon_t pampf1 = (pamptotaxon_t) ampf1;
+	pamptotaxon_t pampf2 = (pamptotaxon_t) ampf2;
+
+
+	if (pampf1->strand != pampf2->strand)
+	{
+		incr = -1;
+		j = pampf1->length - 1;
+		
+		if (pampf2->strand)
+		{
+			pampf1 = (pamptotaxon_t) ampf2;
+			pampf2 = (pamptotaxon_t) ampf1;
+			chd = 1;
+		}
+		//j = pampf2->length - 1; should have been here and pampf2 instead of pampf1?
+	}
+
+	len = (pampf1->length <= pampf2->length)? pampf1->length: pampf2->length;
+
+	for (i = 0; i < len; i++, j += incr)
+	{
+		cd1 = pampf1->amplifia[i];
+		if (incr == -1)
+			cd2 = ecoComplementChar(pampf2->amplifia[j]);
+		else
+			cd2 = pampf2->amplifia[j];
+
+		if (cd1 < cd2) return chd ? 1: -1;
+		if (cd2 < cd1) return chd ? -1: 1;
+	}
+
+	if (pampf1->length > pampf2->length) return chd ? -1: 1;
+	if (pampf2->length > pampf1->length) return chd ? 1: -1;
+
+	return 0;
+}*/
+
+
+static int cmpamp(const void *ampf1, const void* ampf2)
+{
+	int i;
+	char cd1;
+	char cd2;
+	int len = 0;
+	const char *ch1;
+	const char *ch2;
+	int incr1;
+	int incr2;
+
+	pamptotaxon_t pampf1 = (pamptotaxon_t) ampf1;
+	pamptotaxon_t pampf2 = (pamptotaxon_t) ampf2;
+
+	ch1 = pampf1->amplifia;
+	ch2 = pampf2->amplifia;
+	
+	incr1 = 1;
+	incr2 = 1;
+	
+	if (!pampf1->strand)
+		incr1 = -1;
+	if (!pampf2->strand)
+		incr2 = -1;
+	
+	len = (pampf1->length <= pampf2->length)? pampf1->length: pampf2->length;
+	for (i = 0; i < len; i++)
+	{
+		cd1 = *ch1;
+		if (incr1 == -1)
+			cd1 = ecoComplementChar(*ch1);
+		
+		cd2 = *ch2;
+		if (incr2 == -1)
+			cd2 = ecoComplementChar(*ch2);
+		
+		if (cd1 < cd2) return -1;
+		if (cd2 < cd1) return 1;
+		
+		ch1 += incr1;
+		ch2 += incr2;
+	}
+	
+	if (pampf1->length > pampf2->length) return 1;
+	if (pampf2->length > pampf1->length) return -1;
+
+	return 0;
+}
+
+void twalkaction (const void *node, VISIT order, int level)
+{
+	int32_t *taxid = (int32_t*)node;
+	//const size_t taxid=(size_t)node;
+	//printf ("\t%d:%p, ", *taxid, node);
+	counttaxon(*taxid);
+}
+
+int32_t gtxid;
+void twalkaction2 (const void *node, VISIT order, int level)
+{
+	int32_t *pt = (int32_t *) node;
+	gtxid = *pt;
+}
+
+void taxonomyspecificity (ppair_t pair, pecodnadb_t seqdb,uint32_t seqdbsize)
+{
+	uint32_t i, j;
+	uint32_t ampfindex = 0;
+	int32_t taxid;
+	uint32_t wellidentifiedcount;
+	
+	void *ampftree = NULL;
+	pamptotaxon_t pcurrentampf;
+	pamptotaxon_t *ptmp;
+
+	pamptotaxon_t ampfwithtaxtree = ECOMALLOC(sizeof(amptotaxon_t) * pair->pcr.ampcount,"Cannot allocate amplifia tree");
+
+	for (i = 0; i < pair->pcr.ampcount; i++)
+	{
+		/*populate taxon ids tree against each unique amplifia
+		i.e set of taxon ids for each amplifia*/
+		if (pair->pcr.amplifias[i].sequence->isexample)
+		{
+			ampfwithtaxtree[ampfindex].amplifia = pair->pcr.amplifias[i].amplifia;
+			ampfwithtaxtree[ampfindex].strand = pair->pcr.amplifias[i].strand;
+			ampfwithtaxtree[ampfindex].length = pair->pcr.amplifias[i].length;
+			pcurrentampf = &ampfwithtaxtree[ampfindex];
+			taxid = pair->pcr.amplifias[i].sequence->ranktaxonid;
+			ptmp = tfind((const void*)pcurrentampf, &ampftree, cmpamp);
+			if (ptmp == NULL)
+			{
+				pcurrentampf = &ampfwithtaxtree[ampfindex];
+				tsearch((void*)pcurrentampf,&ampftree,cmpamp);
+				ampfindex++;
+			}
+			else
+				pcurrentampf = *ptmp;
+
+			if (tfind((void*)((size_t)taxid), &(pcurrentampf->taxontree), cmptaxon) == NULL)
+			{
+				pcurrentampf->taxoncount++;
+				tsearch((void*)((size_t)taxid),&(pcurrentampf->taxontree),cmptaxon);
+			}
+		}
+	}
+
+	memset (pair->wellIdentifiedSeqs, 0, seqdbsize*sizeof (int));
+	//counttaxon(-1);
+	for (i = 0; i < ampfindex; i++)
+	{
+		if (ampfwithtaxtree[i].taxoncount > 1)
+		{
+			//printf ("\nampfwithtaxtree[i].taxoncount: %d\n", ampfwithtaxtree[i].taxoncount);
+			//twalk(ampfwithtaxtree[i].taxontree, twalkaction);
+		}
+		//TR 5/9/10 - added code for well identified seqs
+		else if(ampfwithtaxtree[i].taxoncount == 1) /*well identified*/
+		{
+			gtxid = -1;
+			twalk(ampfwithtaxtree[i].taxontree, twalkaction2);
+			
+			if (gtxid != -1)
+			{
+				for (j = 0; j < seqdbsize; j++)
+					if (seqdb[j]->ranktaxonid == gtxid 
+							&& seqdb[j]->isexample
+							&&(pair->p1->directCount[j] > 0 
+							|| pair->p1->reverseCount[j] > 0)
+							&& (pair->p2->directCount[j] > 0 
+							|| pair->p2->reverseCount[j] > 0))
+					{
+						pair->wellIdentifiedSeqs[j] = 1;
+					}
+			}
+		}
+	}
+	//printf ("\n");
+	counttaxon(-1);
+	wellidentifiedcount = 0;
+	for (j = 0; j < seqdbsize; j++)
+		if (pair->wellIdentifiedSeqs[j] == 1)
+			counttaxon(seqdb[j]->ranktaxonid);
+	wellidentifiedcount = counttaxon(-2);
+	//pair->notwellidentifiedtaxa = counttaxon(-2);
+	pair->notwellidentifiedtaxa = (pair->intaxa-wellidentifiedcount); //counttaxon(-2);
+	//pair->bs = ((float)pair->intaxa - (float)pair->notwellidentifiedtaxa) / pair->intaxa;
+	pair->bs = ((float)wellidentifiedcount) / (float)pair->intaxa;
+	
+	ECOFREE (ampfwithtaxtree, "Free amplifia table");
+
+}

src/libthermo/Makefile

@@ -0,0 +1,23 @@
+
+SOURCES = nnparams.c \
+		  thermostats.c
+
+SRCS=$(SOURCES)
+         
+OBJECTS= $(patsubst %.c,%.o,$(SOURCES))
+
+LIBFILE= libthermo.a
+RANLIB= ranlib
+
+
+include ../global.mk
+
+
+all: $(LIBFILE)
+
+clean:
+	rm -rf $(OBJECTS) $(LIBFILE)
+
+$(LIBFILE): $(OBJECTS)
+	ar -cr $@ $?
+	$(RANLIB) $@

src/libthermo/nnparams.c

@@ -0,0 +1,609 @@
+/*
+ *  nnparams.cpp
+ *  PHunterLib
+ *
+ *  Nearest Neighbor Model / Parameters
+ *
+ *  Created by Tiayyba Riaz on 7/2/09.
+ *
+ */
+
+#include <memory.h>
+#include <math.h>
+#include <stdio.h>
+#include <string.h>
+#include"nnparams.h"
+
+
+double forbidden_entropy;
+
+char bpencoder[] = {	1,							// A
+		                   	0,                          // b
+		                   	2,                          // C
+		                   	0,0,0,                      // d, e, f
+		                   	3,                          // G
+		                   	0,0,0,0,0,0,0,0,0,0,0,0,    // h,i,j,k,l,m,n,o,p,q,r,s
+		                   	4,0,                        // T,U
+		                   	0,0,0,0,0};                 // v,w,x,y,z
+
+
+double nparam_GetInitialEntropy(PNNParams nparm)
+{
+	return 	-5.9f+nparm->rlogc;
+}
+
+
+//Retrieve Enthalpy for given NN-Pair from parameter table
+double nparam_GetEnthalpy(PNNParams nparm, char x0, char x1, char y0, char y1)
+{
+	return ndH(x0,x1,y0,y1); //xx, yx are already numbers
+}
+
+
+//Retrieve Entropy for given NN-Pair from parameter table
+double nparam_GetEntropy(PNNParams nparm, char x0, char x1, char y0, char y1)
+{
+	//xx and yx are already numbers
+	char nx0=x0;//nparam_convertNum(x0);
+	char nx1=x1;//nparam_convertNum(x1);
+	char ny0=y0;//nparam_convertNum(y0);
+	char ny1=y1;//nparam_convertNum(y1);
+	double answer = ndS(nx0,nx1,ny0,ny1);
+	/*Salt correction Santalucia*/
+	if (nparm->saltMethod == SALT_METHOD_SANTALUCIA) {
+		if(nx0!=5 && 1<= nx1 && nx1<=4) {
+			answer += 0.5*nparm->kfac;
+		}
+		if(ny1!=5 && 1<= ny0 && ny0<=4) {
+			answer += 0.5*nparm->kfac;
+		}
+	}
+	/*Salt correction Owczarzy*/
+	if (nparm->saltMethod == SALT_METHOD_OWCZARZY) {
+		double logk = log(nparm->kplus);
+		answer += ndH(nx0,nx1,ny0,ny1)*((4.29 * nparm->gcContent-3.95)*0.00001*logk+ 0.0000094*logk*logk);
+	}
+	return answer;
+}
+
+/* PURPOSE:    Return melting temperature TM for given entropy and enthalpy
+*              Assuming a one-state transition and using the formula
+*                TM = dH / (dS + R ln(Ct/4))
+*              entropy = dS + R ln Ct/4 (must already be included!)
+*              enthaklpy = dH
+*              where
+*                dH = enthalpy
+*                dS = entropy
+*                R  = Boltzmann factor
+*                Ct = Strand Concentration
+*
+*  PARAMETERS:
+*	entrypy and enthalpy
+*
+*  RETURN VALUE:
+* 	temperature
+*/
+
+double nparam_CalcTM(double entropy,double enthalpy)
+{
+	double tm = 0;               // absolute zero - return if model fails!
+    if (enthalpy>=forbidden_enthalpy)   //||(entropy==-cfact))
+		return 0;
+	if (entropy<0)         // avoid division by zero and model errors!
+	{
+	  tm = enthalpy/entropy;// - kfac; //LKFEB
+		if (tm<0)
+			return 0;
+	}
+	return tm;
+}
+
+
+void nparam_InitParams(PNNParams nparm, double c1, double c2, double kp, int sm)
+{
+	nparm->Ct1 = c1;
+	nparm->Ct2 = c2;
+	nparm->kplus = kp;
+	int maxCT = 1;
+	if(nparm->Ct2 > nparm->Ct1)
+	{
+		maxCT = 2;
+	}
+	double ctFactor;
+ 	if(nparm->Ct1 == nparm->Ct2)
+	{
+		ctFactor = nparm->Ct1/2;
+	}
+	else if (maxCT == 1)
+	{
+		ctFactor = nparm->Ct1-nparm->Ct2/2;
+	}
+	else
+	{
+		ctFactor = nparm->Ct2-nparm->Ct1/2;
+	}
+	nparm->rlogc = R * log(ctFactor);
+	forbidden_entropy = nparm->rlogc;
+	nparm->kfac = 0.368 * log (nparm->kplus);
+	nparm->saltMethod = sm;
+	int x,y,a,b;  // variables used as counters...
+
+	// Set all parameters to zero!
+	memset(nparm->dH,0,sizeof(nparm->dH));
+	memset(nparm->dS,0,sizeof(nparm->dS));
+
+	// Set all X-/Y-, -X/Y- and X-/-Y so, that TM will be VERY small!
+	for (x=1;x<=4;x++)
+	{
+		for (y=1;y<=4;y++)
+		{
+			ndH(0,x,y,0)=forbidden_enthalpy;
+			ndS(0,x,y,0)=forbidden_entropy;
+			ndH(x,0,0,y)=forbidden_enthalpy;
+			ndS(x,0,0,y)=forbidden_entropy;
+			ndH(x,0,y,0)=forbidden_enthalpy;
+			ndS(x,0,y,0)=forbidden_entropy;
+			// forbid X-/Y$ and X$/Y- etc., i.e. terminal must not be paired with gap!
+			ndH(x,5,y,0)=forbidden_enthalpy;
+			ndS(x,5,y,0)=forbidden_entropy;
+			ndH(x,0,y,5)=forbidden_enthalpy;
+			ndS(x,0,y,5)=forbidden_entropy;
+			ndH(5,x,0,y)=forbidden_enthalpy;
+			ndS(5,x,0,y)=forbidden_entropy;
+			ndH(0,x,5,y)=forbidden_enthalpy;
+			ndS(0,x,5,y)=forbidden_entropy;
+			// forbid X$/-Y etc.
+			ndH(x,5,0,y)=forbidden_enthalpy;
+			ndS(x,5,0,y)=forbidden_entropy;
+			ndH(x,0,5,y)=forbidden_enthalpy;
+			ndS(x,0,5,y)=forbidden_entropy;
+			ndH(5,x,y,0)=forbidden_enthalpy;
+			ndS(5,x,y,0)=forbidden_entropy;
+			ndH(0,x,y,5)=forbidden_enthalpy;
+			ndS(0,x,y,5)=forbidden_entropy;
+
+		}
+		// also, forbid x-/-- and --/x-, i.e. no two inner gaps paired
+		ndH(x,0,0,0)=forbidden_enthalpy;
+		ndS(x,0,0,0)=forbidden_entropy;
+		ndH(0,0,x,0)=forbidden_enthalpy;
+		ndS(0,0,x,0)=forbidden_entropy;
+		// x-/-$
+		ndH(x,0,0,5)=forbidden_enthalpy;
+		ndS(x,0,0,5)=forbidden_entropy;
+		ndH(5,0,0,x)=forbidden_enthalpy;
+		ndS(5,0,0,x)=forbidden_entropy;
+		ndH(0,5,x,0)=forbidden_enthalpy;
+		ndS(x,0,0,5)=forbidden_entropy;
+		ndH(0,x,5,0)=forbidden_enthalpy;
+		ndS(0,x,5,0)=forbidden_entropy;
+	}
+	// forbid --/--
+	ndH(0,0,0,0)=forbidden_enthalpy;
+	ndS(0,0,0,0)=forbidden_entropy;
+
+	ndH(5,0,0,0)=forbidden_enthalpy;
+	ndS(5,0,0,0)=forbidden_entropy;
+	ndH(0,0,5,0)=forbidden_enthalpy;
+	ndS(0,0,5,0)=forbidden_entropy;
+	ndH(0,5,5,0)=forbidden_enthalpy;
+	ndS(0,5,5,0)=forbidden_entropy;
+
+	// Interior loops (double Mismatches)
+    #define iloop_entropy -0.97f
+    #define iloop_enthalpy 0.0f
+	for (x=1; x<=4; x++)
+		for (y=1; y<=4; y++)
+			for (a=1; a<=4; a++)
+				for (b=1; b<=4; b++)
+					// AT and CG pair, and as A=1, C=2, G=3, T=4 this means
+					// we have Watson-Crick pairs if (x+a==5) and (y+b)==5.
+					if (!((x+a==5)||(y+b==5)))
+					{
+						// No watson-crick-pair, i.e. double mismatch!
+						// set enthalpy/entropy to loop expansion!
+						ndH(x,y,a,b) = iloop_enthalpy;
+						ndS(x,y,a,b) = iloop_entropy;
+					}
+
+	// xy/-- and --/xy (Bulge Loops of size > 1)
+    #define bloop_entropy -1.3f
+    #define bloop_enthalpy 0.0f
+	for (x=1; x<=4; x++)
+		for (y=1; y<=4; y++)
+		{
+			ndH(x,y,0,0) = bloop_enthalpy;
+			ndS(x,y,0,0) = bloop_entropy;
+			ndH(0,0,x,y) = bloop_enthalpy;
+			ndS(0,0,x,y) = bloop_entropy;
+		}
+
+    // x-/ya abd xa/y- as well as -x/ay and ax/-y
+	// bulge opening and closing parameters with
+	// adjacent matches / mismatches
+	// obulge_mism and cbulge_mism chosen so high to avoid
+	//     AAAAAAAAA
+	//     T--G----T
+	// being better than
+	//     AAAAAAAAA
+	//     TG------T
+    #define obulge_match_H (-2.66f * 1000)
+    #define obulge_match_S -14.22f
+    #define cbulge_match_H (-2.66f * 1000)
+    #define cbulge_match_S -14.22f
+    #define obulge_mism_H (0.0f * 1000)
+    #define obulge_mism_S -6.45f
+    #define cbulge_mism_H 0.0f
+    #define cbulge_mism_S -6.45f
+	for (x=1; x<=4; x++)
+		for (y=1; y<=4; y++)
+			for (a=1; a<=4; a++)
+			{
+				if (x+y==5)  // other base pair matches!
+				{
+					ndH(x,0,y,a)=obulge_match_H;  // bulge opening
+					ndS(x,0,y,a)=obulge_match_S;
+					ndH(x,a,y,0)=obulge_match_H;
+					ndS(x,a,y,0)=obulge_match_S;
+					ndH(0,x,a,y)=cbulge_match_H;  // bulge closing
+					ndS(0,x,a,y)=cbulge_match_S;
+					ndH(a,x,0,y)=cbulge_match_H;
+					ndS(a,x,0,y)=cbulge_match_S;
+				}
+				else
+				{           // mismatch in other base pair!
+					ndH(x,0,y,a)=obulge_mism_H;   // bulge opening
+					ndS(x,0,y,a)=obulge_mism_S;
+					ndH(x,a,y,0)=obulge_mism_H;
+					ndS(x,a,y,0)=obulge_mism_S;
+					ndH(0,x,a,y)=cbulge_mism_H;   // bulge closing
+					ndS(0,x,a,y)=cbulge_mism_S;
+					ndH(a,x,0,y)=cbulge_mism_H;
+					ndS(a,x,0,y)=cbulge_mism_S;
+				}
+			}
+
+	// Watson-Crick pairs (note that only ten are unique, as obviously
+	// 5'-AG-3'/3'-TC-5'  =  5'-CT-3'/3'-GA-5' etc.
+	ndH(1,1,4,4)=-7.6f*1000;  ndS(1,1,4,4)=-21.3f;   // AA/TT 04
+	ndH(1,2,4,3)=-8.4f*1000;  ndS(1,2,4,3)=-22.4f;   // AC/TG adapted GT/CA
+	ndH(1,3,4,2)=-7.8f*1000;  ndS(1,3,4,2)=-21.0f;   // AG/TC adapted CT/GA
+	ndH(1,4,4,1)=-7.2f*1000;  ndS(1,4,4,1)=-20.4f;   // AT/TA 04
+	ndH(2,1,3,4)=-8.5f*1000;  ndS(2,1,3,4)=-22.7f;   // CA/GT 04
+	ndH(2,2,3,3)=-8.0f*1000;  ndS(2,2,3,3)=-19.9f;   // CC/GG adapted GG/CC
+	ndH(2,3,3,2)=-10.6f*1000; ndS(2,3,3,2)=-27.2f;   // CG/GC 04
+	ndH(2,4,3,1)=-7.8f*1000;  ndS(2,4,3,1)=-21.0f;   // CT/GA 04
+	ndH(3,1,2,4)=-8.2f*1000;  ndS(3,1,2,4)=-22.2f;   // GA/CT 04
+	ndH(3,2,2,3)=-9.8f*1000;  ndS(3,2,2,3)=-24.4f;   // GC/CG 04
+	ndH(3,3,2,2)=-8.0f*1000;  ndS(3,3,2,2)=-19.9f;   // GG/CC 04
+	ndH(3,4,2,1)=-8.4f*1000;  ndS(3,4,2,1)=-22.4f;   // GT/CA 04
+	ndH(4,1,1,4)=-7.2f*1000;  ndS(4,1,1,4)=-21.3f;   // TA/AT 04
+	ndH(4,2,1,3)=-8.2f*1000;  ndS(4,2,1,3)=-22.2f;   // TC/AG adapted GA/CT
+	ndH(4,3,1,2)=-8.5f*1000;  ndS(4,3,1,2)=-22.7f;   // TG/AC adapted CA/GT
+	ndH(4,4,1,1)=-7.6f*1000;  ndS(4,4,1,1)=-21.3f;   // TT/AA adapted AA/TT
+
+    // A-C Mismatches (Values for pH 7.0)
+	ndH(1,1,2,4)=7.6f*1000;   ndS(1,1,2,4)=20.2f;    // AA/CT
+	ndH(1,1,4,2)=2.3f*1000;   ndS(1,1,4,2)=4.6f;     // AA/TC
+	ndH(1,2,2,3)=-0.7f*1000;  ndS(1,2,2,3)=-3.8f;    // AC/CG
+	ndH(1,2,4,1)=5.3f*1000;   ndS(1,2,4,1)=14.6f;    // AC/TA
+	ndH(1,3,2,2)=0.6f*1000;   ndS(1,3,2,2)=-0.6f;    // AG/CC
+	ndH(1,4,2,1)=5.3f*1000;   ndS(1,4,2,1)=14.6f;    // AT/CA
+	ndH(2,1,1,4)=3.4f*1000;   ndS(2,1,1,4)=8.0f;     // CA/AT
+	ndH(2,1,3,2)=1.9f*1000;   ndS(2,1,3,2)=3.7f;     // CA/GC
+	ndH(2,2,1,3)=5.2f*1000;   ndS(2,2,1,3)=14.2f;    // CC/AG
+	ndH(2,2,3,1)=0.6f*1000;   ndS(2,2,3,1)=-0.6f;    // CC/GA
+	ndH(2,3,1,2)=1.9f*1000;   ndS(2,3,1,2)=3.7f;     // CG/AC
+	ndH(2,4,1,1)=2.3f*1000;   ndS(2,4,1,1)=4.6f;     // CT/AA
+	ndH(3,1,2,2)=5.2f*1000;   ndS(3,1,2,2)=14.2f;    // GA/CC
+	ndH(3,2,2,1)=-0.7f*1000;  ndS(3,2,2,1)=-3.8f;    // GC/CA
+	ndH(4,1,1,2)=3.4f*1000;   ndS(4,1,1,2)=8.0f;     // TA/AC
+	ndH(4,2,1,1)=7.6f*1000;   ndS(4,2,1,1)=20.2f;    // TC/AA
+
+	// C-T Mismatches
+	ndH(1,2,4,4)=0.7f*1000;   ndS(1,2,4,4)=0.2f;     // AC/TT
+	ndH(1,4,4,2)=-1.2f*1000;  ndS(1,4,4,2)=-6.2f;    // AT/TC
+	ndH(2,1,4,4)=1.0f*1000;   ndS(2,1,4,4)=0.7f;     // CA/TT
+	ndH(2,2,3,4)=-0.8f*1000;  ndS(2,2,3,4)=-4.5f;    // CC/GT
+	ndH(2,2,4,3)=5.2f*1000;   ndS(2,2,4,3)=13.5f;    // CC/TG
+	ndH(2,3,4,2)=-1.5f*1000;  ndS(2,3,4,2)=-6.1f;    // CG/TC
+	ndH(2,4,3,2)=-1.5f*1000;  ndS(2,4,3,2)=-6.1f;    // CT/GC
+	ndH(2,4,4,1)=-1.2f*1000;  ndS(2,4,4,1)=-6.2f;    // CT/TA
+	ndH(3,2,2,4)=2.3f*1000;   ndS(3,2,2,4)=5.4f;     // GC/CT
+	ndH(3,4,2,2)=5.2f*1000;   ndS(3,4,2,2)=13.5f;    // GT/CC
+	ndH(4,1,2,4)=1.2f*1000;   ndS(4,1,2,4)=0.7f;     // TA/CT
+	ndH(4,2,2,3)=2.3f*1000;   ndS(4,2,2,3)=5.4f;     // TC/CG
+	ndH(4,2,1,4)=1.2f*1000;   ndS(4,2,1,4)=0.7f;     // TC/AT
+	ndH(4,3,2,2)=-0.8f*1000;  ndS(4,3,2,2)=-4.5f;    // TG/CC
+	ndH(4,4,2,1)=0.7f*1000;   ndS(4,4,2,1)=0.2f;     // TT/CA
+	ndH(4,4,1,2)=1.0f*1000;   ndS(4,4,1,2)=0.7f;     // TT/AC
+
+	// G-A Mismatches
+	ndH(1,1,3,4)=3.0f*1000;   ndS(1,1,3,4)=7.4f;     // AA/GT
+	ndH(1,1,4,3)=-0.6f*1000;  ndS(1,1,4,3)=-2.3f;    // AA/TG
+	ndH(1,2,3,3)=0.5f*1000;   ndS(1,2,3,3)=3.2f;     // AC/GG
+	ndH(1,3,3,2)=-4.0f*1000;  ndS(1,3,3,2)=-13.2f;   // AG/GC
+	ndH(1,3,4,1)=-0.7f*1000;  ndS(1,3,4,1)=-2.3f;    // AG/TA
+	ndH(1,4,3,1)=-0.7f*1000;  ndS(1,4,3,1)=-2.3f;    // AT/GA
+	ndH(2,1,3,3)=-0.7f*1000;  ndS(2,1,3,3)=-2.3f;    // CA/GG
+	ndH(2,3,3,1)=-4.0f*1000;  ndS(2,3,3,1)=-13.2f;   // CG/GA
+	ndH(3,1,1,4)=0.7f*1000;   ndS(3,1,1,4)=0.7f;     // GA/AT
+	ndH(3,1,2,3)=-0.6f*1000;  ndS(3,1,2,3)=-1.0f;    // GA/CG
+	ndH(3,2,1,3)=-0.6f*1000;  ndS(3,2,1,3)=-1.0f;    // GC/AG
+	ndH(3,3,1,2)=-0.7f*1000;  ndS(3,3,1,2)=-2.3f;    // GG/AC
+	ndH(3,3,2,1)=0.5f*1000;   ndS(3,3,2,1)=3.2f;     // GG/CA
+	ndH(3,4,1,1)=-0.6f*1000;  ndS(3,4,1,1)=-2.3f;    // GT/AA
+	ndH(4,1,1,3)=0.7f*1000;   ndS(4,1,1,3)=0.7f;     // TA/AG
+	ndH(4,3,1,1)=3.0f*1000;   ndS(4,3,1,1)=7.4f;     // TG/AA
+
+	// G-T Mismatches
+	ndH(1,3,4,4)=1.0f*1000;   ndS(1,3,4,4)=0.9f;     // AG/TT
+	ndH(1,4,4,3)=-2.5f*1000;  ndS(1,4,4,3)=-8.3f;    // AT/TG
+	ndH(2,3,3,4)=-4.1f*1000;  ndS(2,3,3,4)=-11.7f;   // CG/GT
+	ndH(2,4,3,3)=-2.8f*1000;  ndS(2,4,3,3)=-8.0f;    // CT/GG
+	ndH(3,1,4,4)=-1.3f*1000;  ndS(3,1,4,4)=-5.3f;    // GA/TT
+	ndH(3,2,4,3)=-4.4f*1000;  ndS(3,2,4,3)=-12.3f;   // GC/TG
+	ndH(3,3,2,4)=3.3f*1000;   ndS(3,3,2,4)=10.4f;    // GG/CT
+	ndH(3,3,4,2)=-2.8f*1000;  ndS(3,3,4,2)=-8.0f;    // GG/TC
+//	ndH(3,3,4,4)=5.8f*1000;   ndS(3,3,4,4)=16.3f;    // GG/TT
+	ndH(3,4,2,3)=-4.4f*1000;  ndS(3,4,2,3)=-12.3f;   // GT/CG
+	ndH(3,4,4,1)=-2.5f*1000;  ndS(3,4,4,1)=-8.3f;    // GT/TA
+//	ndH(3,4,4,3)=4.1f*1000;   ndS(3,4,4,3)=9.5f;     // GT/TG
+	ndH(4,1,3,4)=-0.1f*1000;  ndS(4,1,3,4)=-1.7f;    // TA/GT
+	ndH(4,2,3,3)=3.3f*1000;   ndS(4,2,3,3)=10.4f;    // TC/GG
+	ndH(4,3,1,4)=-0.1f*1000;  ndS(4,3,1,4)=-1.7f;    // TG/AT
+	ndH(4,3,3,2)=-4.1f*1000;  ndS(4,3,3,2)=-11.7f;   // TG/GC
+//	ndH(4,3,3,4)=-1.4f*1000;  ndS(4,3,3,4)=-6.2f;    // TG/GT
+	ndH(4,4,1,3)=-1.3f*1000;  ndS(4,4,1,3)=-5.3f;    // TT/AG
+	ndH(4,4,3,1)=1.0f*1000;   ndS(4,4,3,1)=0.9f;     // TT/GA
+//	ndH(4,4,3,3)=5.8f*1000;   ndS(4,4,3,3)=16.3f;    // TT/GG
+
+	// A-A Mismatches
+	ndH(1,1,1,4)=4.7f*1000;   ndS(1,1,1,4)=12.9f;    // AA/AT
+	ndH(1,1,4,1)=1.2f*1000;   ndS(1,1,4,1)=1.7f;     // AA/TA
+	ndH(1,2,1,3)=-2.9f*1000;  ndS(1,2,1,3)=-9.8f;    // AC/AG
+	ndH(1,3,1,2)=-0.9f*1000;  ndS(1,3,1,2)=-4.2f;    // AG/AC
+	ndH(1,4,1,1)=1.2f*1000;   ndS(1,4,1,1)=1.7f;     // AT/AA
+	ndH(2,1,3,1)=-0.9f*1000;  ndS(2,1,3,1)=-4.2f;    // CA/GA
+    ndH(3,1,2,1)=-2.9f*1000;  ndS(3,1,2,1)=-9.8f;    // GA/CA
+	ndH(4,1,1,1)=4.7f*1000;   ndS(4,1,1,1)=12.9f;    // TA/AA
+
+	// C-C Mismatches
+	ndH(1,2,4,2)=0.0f*1000;   ndS(1,2,4,2)=-4.4f;    // AC/TC
+	ndH(2,1,2,4)=6.1f*1000;   ndS(2,1,2,4)=16.4f;    // CA/CT
+	ndH(2,2,2,3)=3.6f*1000;   ndS(2,2,2,3)=8.9f;     // CC/CG
+	ndH(2,2,3,2)=-1.5f*1000;  ndS(2,2,3,2)=-7.2f;    // CC/GC
+	ndH(2,3,2,2)=-1.5f*1000;  ndS(2,3,2,2)=-7.2f;    // CG/CC
+	ndH(2,4,2,1)=0.0f*1000;   ndS(2,4,2,1)=-4.4f;    // CT/CA
+	ndH(3,2,2,2)=3.6f*1000;   ndS(3,2,2,2)=8.9f;     // GC/CC
+	ndH(4,2,1,2)=6.1f*1000;   ndS(4,2,1,2)=16.4f;    // TC/AC
+
+	// G-G Mismatches
+	ndH(1,3,4,3)=-3.1f*1000;  ndS(1,3,4,3)=-9.5f;    // AG/TG
+	ndH(2,3,3,3)=-4.9f*1000;  ndS(2,3,3,3)=-15.3f;   // CG/GG
+	ndH(3,1,3,4)=1.6f*1000;   ndS(3,1,3,4)=3.6f;     // GA/GT
+	ndH(3,2,3,3)=-6.0f*1000;  ndS(3,2,3,3)=-15.8f;   // GC/GG
+	ndH(3,3,2,3)=-6.0f*1000;  ndS(3,3,2,3)=-15.8f;   // GG/CG
+	ndH(3,3,3,2)=-4.9f*1000;  ndS(3,3,3,2)=-15.3f;   // GG/GC
+	ndH(3,4,3,1)=-3.1f*1000;  ndS(3,4,3,1)=-9.5f;    // GT/GA
+	ndH(4,3,1,3)=1.6f*1000;   ndS(4,3,1,3)=3.6f;     // TG/AG
+
+	// T-T Mismatches
+	ndH(1,4,4,4)=-2.7f*1000;  ndS(1,4,4,4)=-10.8f;   // AT/TT
+	ndH(2,4,3,4)=-5.0f*1000;  ndS(2,4,3,4)=-15.8f;   // CT/GT
+	ndH(3,4,2,4)=-2.2f*1000;  ndS(3,4,2,4)=-8.4f;    // GT/CT
+	ndH(4,1,4,4)=0.2f*1000;   ndS(4,1,4,4)=-1.5f;    // TA/TT
+	ndH(4,2,4,3)=-2.2f*1000;  ndS(4,2,4,3)=-8.4f;    // TC/TG
+	ndH(4,3,4,2)=-5.0f*1000;  ndS(4,3,4,2)=-15.8f;   // TG/TC
+	ndH(4,4,1,4)=0.2f*1000;   ndS(4,4,1,4)=-1.5f;    // TT/AT
+	ndH(4,4,4,1)=-2.7f*1000;  ndS(4,4,4,1)=-10.8f;   // TT/TA
+
+	// Dangling Ends
+	ndH(5,1,1,4)=-0.7f*1000;  ndS(5,1,1,4)=-0.8f;    // $A/AT
+	ndH(5,1,2,4)=4.4f*1000;   ndS(5,1,2,4)=14.9f;    // $A/CT
+	ndH(5,1,3,4)=-1.6f*1000;  ndS(5,1,3,4)=-3.6f;    // $A/GT
+	ndH(5,1,4,4)=2.9f*1000;   ndS(5,1,4,4)=10.4f;    // $A/TT
+	ndH(5,2,1,3)=-2.1f*1000;  ndS(5,2,1,3)=-3.9f;    // $C/AG
+	ndH(5,2,2,3)=-0.2f*1000;  ndS(5,2,2,3)=-0.1f;    // $C/CG
+	ndH(5,2,3,3)=-3.9f*1000;  ndS(5,2,3,3)=-11.2f;   // $C/GG
+	ndH(5,2,4,3)=-4.4f*1000;  ndS(5,2,4,3)=-13.1f;   // $C/TG
+	ndH(5,3,1,2)=-5.9f*1000;  ndS(5,3,1,2)=-16.5f;   // $G/AC
+	ndH(5,3,2,2)=-2.6f*1000;  ndS(5,3,2,2)=-7.4f;    // $G/CC
+	ndH(5,3,3,2)=-3.2f*1000;  ndS(5,3,3,2)=-10.4f;   // $G/GC
+	ndH(5,3,4,2)=-5.2f*1000;  ndS(5,3,4,2)=-15.0f;   // $G/TC
+	ndH(5,4,1,1)=-0.5f*1000;  ndS(5,4,1,1)=-1.1f;    // $T/AA
+	ndH(5,4,2,1)=4.7f*1000;   ndS(5,4,2,1)=14.2f;    // $T/CA
+	ndH(5,4,3,1)=-4.1f*1000;  ndS(5,4,3,1)=-13.1f;   // $T/GA
+	ndH(5,4,4,1)=-3.8f*1000;  ndS(5,4,4,1)=-12.6f;   // $T/TA
+	ndH(1,5,4,1)=-2.9f*1000;  ndS(1,5,4,1)=-7.6f;    // A$/TA
+	ndH(1,5,4,2)=-4.1f*1000;  ndS(1,5,4,2)=-13.0f;   // A$/TC
+	ndH(1,5,4,3)=-4.2f*1000;  ndS(1,5,4,3)=-15.0f;   // A$/TG
+	ndH(1,5,4,4)=-0.2f*1000;  ndS(1,5,4,4)=-0.5f;    // A$/TT
+	ndH(1,1,5,4)=0.2f*1000;   ndS(1,1,5,4)=2.3f;     // AA/$T
+	ndH(1,1,4,5)=-0.5f*1000;  ndS(1,1,4,5)=-1.1f;    // AA/T$
+	ndH(1,2,5,3)=-6.3f*1000;  ndS(1,2,5,3)=-17.1f;   // AC/$G
+	ndH(1,2,4,5)=4.7f*1000;   ndS(1,2,4,5)=14.2f;    // AC/T$
+	ndH(1,3,5,2)=-3.7f*1000;  ndS(1,3,5,2)=-10.0f;   // AG/$C
+	ndH(1,3,4,5)=-4.1f*1000;  ndS(1,3,4,5)=-13.1f;   // AG/T$
+	ndH(1,4,5,1)=-2.9f*1000;  ndS(1,4,5,1)=-7.6f;    // AT/$A
+	ndH(1,4,4,5)=-3.8f*1000;  ndS(1,4,4,5)=-12.6f;   // AT/T$
+	ndH(2,5,3,1)=-3.7f*1000;  ndS(2,5,3,1)=-10.0f;   // C$/GA
+	ndH(2,5,3,2)=-4.0f*1000;  ndS(2,5,3,2)=-11.9f;   // C$/GC
+	ndH(2,5,3,3)=-3.9f*1000;  ndS(2,5,3,3)=-10.9f;   // C$/GG
+	ndH(2,5,3,4)=-4.9f*1000;  ndS(2,5,3,4)=-13.8f;   // C$/GT
+	ndH(2,1,5,4)=0.6f*1000;   ndS(2,1,5,4)=3.3f;     // CA/$T
+	ndH(2,1,3,5)=-5.9f*1000;  ndS(2,1,3,5)=-16.5f;   // CA/G$
+	ndH(2,2,5,3)=-4.4f*1000;  ndS(2,2,5,3)=-12.6f;   // CC/$G
+	ndH(2,2,3,5)=-2.6f*1000;  ndS(2,2,3,5)=-7.4f;    // CC/G$
+	ndH(2,3,5,2)=-4.0f*1000;  ndS(2,3,5,2)=-11.9f;   // CG/$C
+	ndH(2,3,3,5)=-3.2f*1000;  ndS(2,3,3,5)=-10.4f;   // CG/G$
+	ndH(2,4,5,1)=-4.1f*1000;  ndS(2,4,5,1)=-13.0f;   // CT/$A
+	ndH(2,4,3,5)=-5.2f*1000;  ndS(2,4,3,5)=-15.0f;   // CT/G$
+	ndH(3,5,2,1)=-6.3f*1000;  ndS(3,5,2,1)=-17.1f;   // G$/CA
+	ndH(3,5,2,2)=-4.4f*1000;  ndS(3,5,2,2)=-12.6f;   // G$/CC
+	ndH(3,5,2,3)=-5.1f*1000;  ndS(3,5,2,3)=-14.0f;   // G$/CG
+	ndH(3,5,2,4)=-4.0f*1000;  ndS(3,5,2,4)=-10.9f;   // G$/CT
+	ndH(3,1,5,4)=-1.1f*1000;  ndS(3,1,5,4)=-1.6f;    // GA/$T
+	ndH(3,1,2,5)=-2.1f*1000;  ndS(3,1,2,5)=-3.9f;    // GA/C$
+	ndH(3,2,5,3)=-5.1f*1000;  ndS(3,2,5,3)=-14.0f;   // GC/$G
+	ndH(3,2,2,5)=-0.2f*1000;  ndS(3,2,2,5)=-0.1f;    // GC/C$
+	ndH(3,3,5,2)=-3.9f*1000;  ndS(3,3,5,2)=-10.9f;   // GG/$C
+	ndH(3,3,2,5)=-3.9f*1000;  ndS(3,3,2,5)=-11.2f;   // GG/C$
+	ndH(3,4,5,1)=-4.2f*1000;  ndS(3,4,5,1)=-15.0f;   // GT/$A
+	ndH(3,4,2,5)=-4.4f*1000;  ndS(3,4,2,5)=-13.1f;   // GT/C$
+	ndH(4,5,1,1)=0.2f*1000;   ndS(4,5,1,1)=2.3f;     // T$/AA
+	ndH(4,5,1,2)=0.6f*1000;   ndS(4,5,1,2)=3.3f;     // T$/AC
+	ndH(4,5,1,3)=-1.1f*1000;  ndS(4,5,1,3)=-1.6f;    // T$/AG
+	ndH(4,5,1,4)=-6.9f*1000;  ndS(4,5,1,4)=-20.0f;   // T$/AT
+	ndH(4,1,5,4)=-6.9f*1000;  ndS(4,1,5,4)=-20.0f;   // TA/$T
+	ndH(4,1,1,5)=-0.7f*1000;  ndS(4,1,1,5)=-0.7f;    // TA/A$
+	ndH(4,2,5,3)=-4.0f*1000;  ndS(4,2,5,3)=-10.9f;   // TC/$G
+	ndH(4,2,1,5)=4.4f*1000;   ndS(4,2,1,5)=14.9f;    // TC/A$
+	ndH(4,3,5,2)=-4.9f*1000;  ndS(4,3,5,2)=-13.8f;   // TG/$C
+	ndH(4,3,1,5)=-1.6f*1000;  ndS(4,3,1,5)=-3.6f;    // TG/A$
+	ndH(4,4,5,1)=-0.2f*1000;  ndS(4,4,5,1)=-0.5f;    // TT/$A
+	ndH(4,4,1,5)=2.9f*1000;   ndS(4,4,1,5)=10.4f;    // TT/A$
+
+	return;
+}
+
+int nparam_CountGCContent(char * seq ) {
+	int lseq = strlen(seq);
+	int k;
+	double count = 0;
+	for( k=0;k<lseq;k++) {
+		if (seq[k] == 'G' || seq[k] == 'C' ) {
+			count+=1;
+		}
+	}
+	return count;
+}
+
+void nparam_CleanSeq (const char* inseq, char* outseq, int len)
+{
+	int seqlen = strlen (inseq);
+	int i, j;
+
+	if (len != 0)
+		seqlen = len;
+
+	outseq[0]='x';
+
+	for (i = 0, j = 0; i < seqlen && outseq[0]; i++,j++)
+	{
+		switch (inseq[i])
+		{
+		case 'a':
+		case '\0':
+		case 'A':
+			outseq[j] = 'A'; break;
+		case 'c':
+		case '\1':
+		case 'C':
+			outseq[j] = 'C'; break;
+		case 'g':
+		case '\2':
+		case 'G':
+			outseq[j] = 'G'; break;
+		case 't':
+		case '\3':
+		case 'T':
+			outseq[j] = 'T'; break;
+		default:
+			outseq[0]=0;
+		}
+	}
+	outseq[j] = '\0';
+}
+
+//Calculate TM for given sequence against its complement
+double nparam_CalcSelfTM(PNNParams nparm, const char* seq, size_t len)
+{
+	double thedH = 0;
+	//double thedS = nparam_GetInitialEntropy(nparm);
+	double thedS = -5.9f+nparm->rlogc;
+	double mtemp;
+	char c1;
+	char c2;
+	char c3;
+	char c4;
+	unsigned int i;
+	char nseq[50];
+	const char *useq = seq;
+
+	nparam_CleanSeq (seq, nseq, len);
+	useq = nseq;
+
+	for ( i=1;i<len;i++)
+	{
+		c1 = GETREVCODE(useq[i-1]); //nparam_getComplement(seq[i-1],1);
+		c2 = GETREVCODE(useq[i]); //nparam_getComplement(seq[i],1);
+		c3 = GETNUMCODE(useq[i-1]);
+		c4 = GETNUMCODE(useq[i]);
+
+
+		thedH += nparm->dH[(uint8_t) c3][(uint8_t)c4][(uint8_t)c1][(uint8_t)c2];//nparam_GetEnthalpy(nparm, c3,c4,c1,c2);
+		thedS += nparam_GetEntropy(nparm, c3,c4,c1,c2);
+	}
+	//printf("------------------\n");
+	mtemp = nparam_CalcTM(thedS,thedH);
+		//fprintf(stderr,"Enthalpy: %f, entropy: %f, seq: %s  rloc=%f\n", thedH, thedS, useq, nparm->rlogc);
+		//exit (0);
+	return mtemp;
+}
+
+double nparam_CalcTwoTM(PNNParams nparm, const char* seq1, const char* seq2, size_t len)
+{
+	double thedH = 0;
+	//double thedS = nparam_GetInitialEntropy(nparm);
+	double thedS = -5.9f+nparm->rlogc;
+	double mtemp;
+	char c1;
+	char c2;
+	char c3;
+	char c4;
+	unsigned int i;
+	char nseq1[50];
+	char nseq2[50];
+	char *useq1;
+	char *useq2;
+
+	nparam_CleanSeq (seq1, nseq1, len);
+	useq1 = nseq1;
+
+	nparam_CleanSeq (seq2, nseq2, len);
+	useq2 = nseq2;
+
+	//fprintf (stderr,"Primer : %s\n",useq);
+	for ( i=1;i<len;i++)
+	{
+		c1 = GETREVCODE(useq2[i-1]); //nparam_getComplement(seq[i-1],1);
+		c2 = GETREVCODE(useq2[i]);   //nparam_getComplement(seq[i],1);
+		c3 = GETNUMCODE(useq1[i-1]);
+		c4 = GETNUMCODE(useq1[i]);
+
+		//fprintf (stderr,"Primer : %s %f %f %d %d, %d %d %f\n",useq,thedH,thedS,(int)c3,(int)c4,(int)c1,(int)c2,nparam_GetEnthalpy(nparm, c3,c4,c1,c2));
+
+		thedH += nparm->dH[(uint8_t)c3][(uint8_t)c4][(uint8_t)c1][(uint8_t)c2];//nparam_GetEnthalpy(nparm, c3,c4,c1,c2);
+		thedS += nparam_GetEntropy(nparm, c3,c4,c1,c2);
+	}
+	//fprintf(stderr,"------------------\n");
+	mtemp = nparam_CalcTM(thedS,thedH);
+	//if (mtemp == 0)
+	//{
+	//	fprintf(stderr,"Enthalpy: %f, entropy: %f, seq: %s\n", thedH, thedS, useq);
+		//exit (0);
+	//}
+	return mtemp;
+}
+
+double calculateMeltingTemperatureBasic (char * seq) {
+	int gccount;
+	double temp;
+	int seqlen;
+
+	seqlen = strlen (seq);
+	gccount = nparam_CountGCContent (seq);
+	temp = 64.9 + 41*(gccount - 16.4)/seqlen;
+	return temp;
+}

src/libthermo/nnparams.h

@@ -0,0 +1,67 @@
+/*
+ *  nnparams.h
+ *  PHunterLib
+ *
+ * Nearest Neighbor Model Parameters
+ *
+ *  Created by Tiayyba Riaz on 02/07/09.
+ *
+ */
+
+#ifndef NNPARAMS_H_
+#define NNPARAMS_H_
+
+#include <math.h>
+#include <string.h>
+#include <stdint.h>
+
+//#include "../libecoprimer/ecoprimer.h"
+
+// following defines to simplify coding...
+#define ndH(a,b,c,d) nparm->dH[(uint8_t) a][(uint8_t) b][(uint8_t) c][(uint8_t) d]
+#define ndS(a,b,c,d) nparm->dS[(uint8_t) a][(uint8_t) b][(uint8_t) c][(uint8_t) d]
+#define forbidden_enthalpy 1000000000000000000.0f
+#define	R 1.987f
+#define	SALT_METHOD_SANTALUCIA 1
+#define	SALT_METHOD_OWCZARZY 2
+
+#define DEF_CONC_PRIMERS 0.0000008
+#define DEF_CONC_SEQUENCES 0
+#define DEF_SALT 0.05
+
+#define GETNUMCODE(a) bpencoder[a - 'A']
+#define GETREVCODE(a) 5-bpencoder[a - 'A']
+
+
+extern double forbidden_entropy;
+
+extern char bpencoder[];                 // v,w,x,y,z
+
+
+typedef struct CNNParams_st
+{
+	double Ct1;
+	double Ct2;
+	double rlogc;
+	double kplus;
+	double kfac;
+	int saltMethod;
+	double gcContent;
+	double new_TM;
+	double dH[6][6][6][6];  // A-C-G-T + gap + initiation (dangling end, $ sign)
+	double dS[6][6][6][6];
+}CNNParams, * PNNParams;
+
+void nparam_InitParams(PNNParams nparm, double c1, double c2, double kp, int sm);
+int nparam_CountGCContent(char * seq );
+double nparam_GetEntropy(PNNParams nparm, char x0, char x1, char y0, char y1);
+double nparam_GetEnthalpy(PNNParams nparm, char x0, char x1, char y0, char y1);
+double nparam_CalcTM(double entropy,double enthalpy);
+double nparam_CalcSelfTM(PNNParams nparm, const char* seq, size_t len);
+double nparam_CalcTwoTM(PNNParams nparm, const char* seq1, const char* seq2, size_t len);
+
+double nparam_GetInitialEntropy(PNNParams nparm) ;
+double calculateMeltingTemperatureBasic (char * seq);
+//void getThermoProperties (ppair_t* pairs, size_t count, poptions_t options);
+
+#endif

src/libthermo/thermostats.c

@@ -0,0 +1,113 @@
+#include <stdio.h>
+#include <string.h>
+#include <ctype.h>
+#include <stdlib.h>
+#include "thermostats.h"
+
+word_t extractSite(char* sequence, size_t begin, size_t length, bool_t strand)
+{
+	char *c;
+	char *start;
+	uint32_t l;
+	word_t site = 0;
+
+	start=sequence+begin;
+	if (!strand)
+		start+=length-1;
+
+
+	for (c=start,
+	     l=0;
+		 l<length;
+		 l++,
+		 c+=(strand)? 1:-1)
+		site = (site << 2) | ((strand)? (*c):(~*c)&3);
+
+	return site;
+}
+
+void getThermoProperties (ppair_t* pairs, size_t count, poptions_t options)
+{
+	size_t i, j;
+	uint32_t   bp1,bp2;
+	word_t w1;
+	word_t w2;
+	bool_t strand;
+
+	char *sq;
+	char prmrd[50];
+	char prmrr[50];
+	double mtemp;
+
+	for (i = 0; i < count; i++)
+	{
+		w1 = pairs[i]->p1->word;
+		w2 = pairs[i]->p2->word;
+
+		if (!pairs[i]->asdirect1)
+			w1=ecoComplementWord(w1,options->primer_length);
+
+		if (!pairs[i]->asdirect2)
+			w2=ecoComplementWord(w2,options->primer_length);
+
+		strncpy(prmrd,ecoUnhashWord(w1, options->primer_length),options->primer_length);
+		strncpy(prmrr,ecoUnhashWord(w2, options->primer_length),options->primer_length);
+		prmrd[options->primer_length]=0;
+		prmrr[options->primer_length]=0;
+		pairs[i]->p1temp = nparam_CalcSelfTM (options->pnparm, prmrd, options->primer_length) - 273.0;
+		pairs[i]->p2temp = nparam_CalcSelfTM (options->pnparm, prmrr, options->primer_length) - 273.0;
+		pairs[i]->p1mintemp = 100;
+		pairs[i]->p2mintemp = 100;
+
+		for (j = 0; j < pairs[i]->pcr.ampcount; j++)
+			if (pairs[i]->pcr.amplifias[j].sequence->isexample)
+		{
+
+			sq = pairs[i]->pcr.amplifias[j].sequence->SQ;
+			strand = pairs[i]->pcr.amplifias[j].strand;
+			bp1 = pairs[i]->pcr.amplifias[j].begin - options->primer_length;
+			bp2 = pairs[i]->pcr.amplifias[j].end + 1;
+
+			if (!strand)
+			{
+				uint32_t tmp;
+				tmp=bp1;
+				bp1=bp2;
+				bp2=tmp;
+			}
+
+//			printf("%s : %s, %c",prmrd,
+//					               ecoUnhashWord(extractSite(sq,bp1,options->primer_length,strand),options->primer_length),
+//					               "rd"[strand]);
+		    mtemp = nparam_CalcTwoTM(options->pnparm,
+		    		                 prmrd,
+		    		                 ecoUnhashWord(extractSite(sq,bp1,options->primer_length,strand),options->primer_length),
+		    		                 options->primer_length) - 273.0;
+//		    printf(" %4.2f  %4.2f\n",pairs[i]->p1temp,mtemp);
+		    if (mtemp < pairs[i]->p1mintemp)
+				    		pairs[i]->p1mintemp = mtemp;
+
+//			printf("%s : %s, %c\n",prmrr,ecoUnhashWord(extractSite(sq,bp2,options->primer_length,!strand),options->primer_length),
+//					"rd"[strand]);
+//
+	    	mtemp = nparam_CalcTwoTM(options->pnparm,
+	    			                 prmrr,
+	    			                 ecoUnhashWord(extractSite(sq,bp2,options->primer_length,!strand),options->primer_length),
+	    			                 options->primer_length) - 273.0;
+	    	if (mtemp < pairs[i]->p2mintemp)
+	    		pairs[i]->p2mintemp = mtemp;
+		}
+
+		if (w2 < w1)
+		{
+			mtemp = pairs[i]->p1temp;
+			pairs[i]->p1temp = pairs[i]->p2temp;
+			pairs[i]->p2temp = mtemp;
+
+			mtemp = pairs[i]->p1mintemp;
+			pairs[i]->p1mintemp = pairs[i]->p2mintemp;
+			pairs[i]->p2mintemp = mtemp;
+		}
+
+	}
+}

src/libthermo/thermostats.h

@@ -0,0 +1,9 @@
+#ifndef THERMOSTATS_H_
+#define THERMOSTATS_H_
+
+#include "../libecoprimer/ecoprimer.h"
+
+void getThermoProperties (ppair_t* pairs, size_t count, poptions_t options);
+word_t extractSite(char* sequence, size_t begin, size_t length, bool_t strand);
+
+#endif

tools/ecoPCRFormat.py

@@ -0,0 +1,696 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from __future__ import print_function
+import re
+import gzip
+import struct
+import sys
+import time
+import getopt
+import zlib
+
+_dbenable = False
+
+#####
+#
+#
+# Generic file function
+#
+#
+#####
+
+def universalOpen(file):
+    if isinstance(file, str):
+        if file.endswith('.gz'):
+            if sys.version_info[0] < 3:
+                rep = gzip.open(file)
+            else:
+                rep = gzip.open(file, 'rt', encoding='latin-1')
+        else:
+            rep = open(file, 'r')
+    else:
+        rep = file
+    return rep
+
+def universalTell(file):
+    if hasattr(file, 'myfileobj'):  # Python 3 gzip
+        return file.myfileobj.tell()
+    elif hasattr(file, 'fileobj'):  # Python 2 gzip
+        return file.fileobj.tell()
+    return file.tell()
+
+def fileSize(file):
+    if hasattr(file, 'myfileobj'):  # Python 3 gzip
+        f = file.myfileobj
+    elif hasattr(file, 'fileobj'):  # Python 2 gzip
+        f = file.fileobj
+    else:
+        f = file
+
+    if not hasattr(f, 'fileno'):
+        return None
+
+    pos = f.tell()
+    f.seek(0, 2)
+    length = f.tell()
+    f.seek(pos, 0)
+    return length
+
+def progressBar(pos, max_size, reset=False, delta=[]):
+    if reset:
+        del delta[:]
+    if not delta:
+        delta.append(time.time())
+        delta.append(time.time())
+
+    delta[1] = time.time()
+    elapsed = delta[1] - delta[0]
+
+    if max_size is None:
+        sys.stderr.write('\rReaded sequences : %d     ' % pos)
+        sys.stderr.flush()
+        return
+
+    percent = float(pos) / max_size * 100 if max_size > 0 else 0
+
+    if percent > 0:
+        remain = elapsed / percent * (100 - percent)
+        remain_str = time.strftime('%H:%M:%S', time.gmtime(int(remain)))
+    else:
+        remain_str = '?'
+
+    bar_length = 50
+    filled = int(percent / 2)
+    bar = '#' * filled
+    bar += '|/-\\'[pos % 4]
+    bar += ' ' * (bar_length - filled - 1)
+
+    sys.stderr.write('\r%5.1f %% |%s] remain : %s' % (percent, bar, remain_str))
+    sys.stderr.flush()
+
+#####
+#
+#
+# NCBI Dump Taxonomy reader
+#
+#
+#####
+
+class endLessIterator(object):
+    def __init__(self, endedlist):
+        self.endedlist = endedlist
+        self.index = 0
+
+    def __iter__(self):
+        return self
+
+    def next(self):  # Python 2
+        if self.index < len(self.endedlist):
+            item = self.endedlist[self.index]
+            self.index += 1
+            return item
+        else:
+            return self.endedlist[-1]
+
+    __next__ = next  # Python 3 compatibility
+
+class ColumnFile(object):
+    def __init__(self, stream, sep=None, strip=True, types=None):
+        if isinstance(stream, str):
+            self._stream = open(stream)
+        else:
+            try:
+                iter(stream)
+                self._stream = stream
+            except TypeError:
+                raise ValueError('stream must be string or an iterator')
+        self._delimiter = sep
+        self._strip = strip
+        self._types = types
+
+    @staticmethod
+    def str2bool(x):
+        val = x.strip()[0].upper()
+        if val in 'T1Y':
+            return True
+        elif val in 'F0N':
+            return False
+        raise ValueError("Invalid boolean value: %s" % x)
+
+    def __iter__(self):
+        return self
+
+    def next(self):  # Python 2
+        ligne = next(self._stream)
+        data = ligne.split(self._delimiter)
+        if self._strip:
+            data = [x.strip() for x in data]
+
+        if self._types:
+            typed_data = []
+            for i, val in enumerate(data):
+                if i < len(self._types):
+                    t = self._types[i]
+                    if t is bool:
+                        typed_data.append(self.str2bool(val))
+                    else:
+                        typed_data.append(t(val))
+                else:
+                    typed_data.append(val)
+            return typed_data
+        return data
+
+    __next__ = next  # Python 3 compatibility
+
+def bsearchTaxon(taxonomy, taxid):
+    taxCount = len(taxonomy)
+    begin = 0
+    end = taxCount
+    oldcheck = -1
+    check = int(begin + (end - begin) / 2)
+
+    while check != oldcheck and check < taxCount and taxonomy[check][0] != taxid:
+        if taxonomy[check][0] < taxid:
+            begin = check
+        else:
+            end = check
+
+        oldcheck = check
+        check = int(begin + (end - begin) / 2)
+
+    if check < taxCount and taxonomy[check][0] == taxid:
+        return check
+    return None
+
+def readNodeTable(file):
+    file = universalOpen(file)
+    nodes = ColumnFile(file,
+                      sep='|',
+                      types=(int, int, str,
+                             str, str, bool,
+                             int, bool, int,
+                             bool, bool, bool, str))
+    print("Reading taxonomy dump file...", file=sys.stderr)
+    sys.stderr.flush()
+
+    taxonomy = []
+    for n in nodes:
+        taxonomy.append([n[0], n[2], n[1]])
+
+    print("List all taxonomy rank...", file=sys.stderr)
+    sys.stderr.flush()
+
+    ranks = list(set(x[1] for x in taxonomy))
+    ranks.sort()
+    rank_dict = {rank: idx for idx, rank in enumerate(ranks)}
+
+    print("Sorting taxons...", file=sys.stderr)
+    sys.stderr.flush()
+    taxonomy.sort(key=lambda x: x[0])
+
+    print("Indexing taxonomy...", file=sys.stderr)
+    sys.stderr.flush()
+
+    index = {}
+    for i, t in enumerate(taxonomy):
+        index[t[0]] = i
+
+    print("Indexing parent and rank...", file=sys.stderr)
+    sys.stderr.flush()
+
+    for t in taxonomy:
+        t[1] = rank_dict[t[1]]
+        t[2] = index.get(t[2], None)
+
+    return taxonomy, rank_dict, index
+
+def nameIterator(file):
+    file = universalOpen(file)
+    names = ColumnFile(file,
+                      sep='|',
+                      types=(int, str, str, str))
+    for row in names:
+        if len(row) >= 4:
+            taxid, name, unique, classname = row[:4]
+            yield taxid, name, classname
+
+def mergedNodeIterator(file):
+    file = universalOpen(file)
+    merged = ColumnFile(file,
+                       sep='|',
+                       types=(int, int, str))
+    for row in merged:
+        if len(row) >= 2:
+            taxid, current = row[:2]
+            yield taxid, current
+
+def deletedNodeIterator(file):
+    file = universalOpen(file)
+    deleted = ColumnFile(file,
+                       sep='|',
+                       types=(int, str))
+    for row in deleted:
+        if row:
+            taxid = row[0]
+            yield taxid
+
+def readTaxonomyDump(taxdir):
+    taxonomy, ranks, index = readNodeTable(taxdir + '/nodes.dmp')
+
+    # Initialize scientific name as empty string for each taxon
+    for tx in taxonomy:
+        tx.append("")   # Add fourth element: scientific name (empty at start)
+
+    print("Adding scientific name...", file=sys.stderr)
+    sys.stderr.flush()
+
+    alternativeName = []
+    for taxid, name, classname in nameIterator(taxdir + '/names.dmp'):
+        idx = index.get(taxid, None)
+        if idx is not None:
+            # Clean and ensure ASCII only
+            name_clean = ''.join(c for c in name if ord(c) < 128)
+            alternativeName.append((name_clean, classname, idx))
+            if classname == 'scientific name':
+                taxonomy[idx][3] = name_clean
+
+    print("Adding taxid alias...", file=sys.stderr)
+    sys.stderr.flush()
+    for taxid, current in mergedNodeIterator(taxdir + '/merged.dmp'):
+        if current in index:
+            index[taxid] = index[current]
+
+    print("Adding deleted taxid...", file=sys.stderr)
+    sys.stderr.flush()
+    for taxid in deletedNodeIterator(taxdir + '/delnodes.dmp'):
+        index[taxid] = None
+
+    return taxonomy, ranks, alternativeName, index
+
+#####
+#
+#
+#  Genbank/EMBL sequence reader
+#
+#
+#####
+
+def entryIterator(file):
+    file = universalOpen(file)
+    rep = []
+    ligne = file.readline()
+    while ligne:
+        rep.append(ligne)
+        if ligne == '//\n':
+            yield ''.join(rep)
+            rep = []
+        ligne = file.readline()
+    if rep:
+        yield ''.join(rep)
+
+def fastaEntryIterator(file):
+    file = universalOpen(file)
+    rep = []
+    ligne = file.readline()
+    while ligne:
+        if ligne.startswith('>') and rep:
+            yield ''.join(rep)
+            rep = []
+        rep.append(ligne)
+        ligne = file.readline()
+    if rep:
+        yield ''.join(rep)
+
+_cleanSeq = re.compile(r'[\s\d]')  # More efficient
+
+def cleanSeq(seq):
+    return _cleanSeq.sub('', seq)
+
+# GenBank patterns
+_gbParseID = re.compile(r'(?<=^LOCUS {7})[^ ]+(?= )', re.MULTILINE)
+_gbParseDE = re.compile(r'(?<=^DEFINITION {2}).+?\. *$', re.MULTILINE | re.DOTALL)
+_gbParseSQ = re.compile(r'(?<=^ORIGIN).+?(?=^//$)', re.MULTILINE | re.DOTALL)
+_gbParseTX = re.compile(r'(?<= /db_xref="taxon:)[0-9]+(?=")')
+
+def genbankEntryParser(entry):
+    Id_match = _gbParseID.findall(entry)
+    Id = Id_match[0] if Id_match else "UNKNOWN_ID"
+
+    De_match = _gbParseDE.findall(entry)
+    De = ' '.join(De_match[0].split()) if De_match else ""
+
+    Sq_match = _gbParseSQ.findall(entry)
+    Sq = cleanSeq(Sq_match[0].upper()) if Sq_match else ""
+
+    Tx_match = _gbParseTX.findall(entry)
+    Tx = int(Tx_match[0]) if Tx_match else None
+
+    # Clean and ensure ASCII only
+    Id = ''.join(c for c in Id if ord(c) < 128)
+    De = ''.join(c for c in De if ord(c) < 128)
+
+    return {'id': Id, 'taxid': Tx, 'definition': De, 'sequence': Sq}
+
+# EMBL patterns
+_emblParseID = re.compile(r'(?<=^ID {3})[^ ]+(?=;)', re.MULTILINE)
+_emblParseDE = re.compile(r'(?<=^DE {3}).+?\. *$', re.MULTILINE | re.DOTALL)
+_emblParseSQ = re.compile(r'(?<=^  ).+?(?=^//$)', re.MULTILINE | re.DOTALL)
+_emblParseTX = re.compile(r'(?<= /db_xref="taxon:)[0-9]+(?=")')
+
+def emblEntryParser(entry):
+    Id_match = _emblParseID.findall(entry)
+    Id = Id_match[0] if Id_match else "UNKNOWN_ID"
+
+    De_match = _emblParseDE.findall(entry)
+    De = ' '.join(De_match[0].replace('\nDE   ', ' ').split()) if De_match else ""
+
+    Sq_match = _emblParseSQ.findall(entry)
+    Sq = cleanSeq(Sq_match[0].upper()) if Sq_match else ""
+
+    Tx_match = _emblParseTX.findall(entry)
+    Tx = int(Tx_match[0]) if Tx_match else None
+
+    # Clean and ensure ASCII only
+    Id = ''.join(c for c in Id if ord(c) < 128)
+    De = ''.join(c for c in De if ord(c) < 128)
+
+    return {'id': Id, 'taxid': Tx, 'definition': De, 'sequence': Sq}
+
+# FASTA processing
+_fastaSplit = re.compile(r';\W*')
+
+def parseFasta(seq):
+    lines = seq.split('\n')
+    if not lines:
+        return "", "", "", {}
+
+    header = lines[0].strip()
+    if header.startswith('>'):
+        header = header[1:]
+
+    parts = header.split(None, 1)
+    seq_id = parts[0] if parts else ""
+    description = parts[1] if len(parts) > 1 else ""
+
+    fields = _fastaSplit.split(description) if description else []
+    info = {}
+    other_desc = []
+    for field in fields:
+        if '=' in field:
+            key, val = field.split('=', 1)
+            info[key.strip()] = val.strip()
+        else:
+            other_desc.append(field)
+
+    definition = ' '.join(other_desc)
+    sequence = ''.join(x.strip() for x in lines[1:]).upper()
+
+    # Clean and ensure ASCII only
+    seq_id = ''.join(c for c in seq_id if ord(c) < 128)
+    definition = ''.join(c for c in definition if ord(c) < 128)
+
+    return seq_id, sequence, definition, info
+
+def fastaEntryParser(entry):
+    seq_id, sequence, definition, info = parseFasta(entry)
+    Tx = info.get('taxid', None)
+    if Tx is not None:
+        try:
+            Tx = int(Tx)
+        except ValueError:
+            Tx = None
+    return {'id': seq_id, 'taxid': Tx, 'definition': definition, 'sequence': sequence}
+
+def sequenceIteratorFactory(entryParser, entryIterator):
+    def sequenceIterator(file):
+        for entry in entryIterator(file):
+            yield entryParser(entry)
+    return sequenceIterator
+
+#####
+#
+#
+# Binary writer (CORRECTED VERSION)
+#
+#
+#####
+
+def ecoSeqPacker(sq):
+    # Ensure sequence is ASCII uppercase
+    sequence = ''.join(c for c in sq['sequence'] if ord(c) < 128).upper()
+    seq_bytes = sequence.encode('ascii')
+    compactseq = zlib.compress(seq_bytes, 9)
+    cptseqlength = len(compactseq)
+
+    # Clean definition to pure ASCII
+    definition = ''.join(c for c in sq['definition'] if ord(c) < 128)
+    de_bytes = definition.encode('ascii')
+    delength = len(de_bytes)
+
+    # Clean ID to pure ASCII and pad to 20 bytes
+    seq_id = ''.join(c for c in sq['id'] if ord(c) < 128)
+    seq_id_bytes = seq_id.encode('ascii')
+    if len(seq_id_bytes) > 20:
+        seq_id_bytes = seq_id_bytes[:20]
+    else:
+        seq_id_bytes = seq_id_bytes.ljust(20, b'\0')
+
+    # Calculate total size (4 bytes for each integer + data lengths)
+    totalSize = 4 + 20 + 4 + 4 + 4 + delength + cptseqlength
+
+    # Pack with correct byte order and field order
+    packed = struct.pack('>I', totalSize)
+    packed += struct.pack('>I', sq['taxid'])
+    packed += seq_id_bytes
+    packed += struct.pack('>I', delength)
+    packed += struct.pack('>I', len(sequence))
+    packed += struct.pack('>I', cptseqlength)
+    packed += de_bytes
+    packed += compactseq
+
+    return packed
+
+def ecoTaxPacker(tx):
+    # Clean name to pure ASCII
+    name_clean = ''.join(c for c in tx[3] if ord(c) < 128)
+    name_bytes = name_clean.encode('ascii')
+    namelength = len(name_bytes)
+    totalSize = 4 + 4 + 4 + 4 + namelength
+
+    packed = struct.pack('>I', totalSize)
+    packed += struct.pack('>I', tx[0])  # taxid
+    packed += struct.pack('>I', tx[1])  # rank index
+    packed += struct.pack('>I', tx[2])  # parent index
+    packed += struct.pack('>I', namelength)
+    packed += name_bytes
+
+    return packed
+
+def ecoRankPacker(rank):
+    # Clean rank to pure ASCII
+    rank_clean = ''.join(c for c in rank if ord(c) < 128)
+    rank_bytes = rank_clean.encode('ascii')
+    namelength = len(rank_bytes)
+    packed = struct.pack('>I', namelength)
+    packed += rank_bytes
+    return packed
+
+def ecoNamePacker(name):
+    # Clean name and class to pure ASCII
+    name_clean = ''.join(c for c in name[0] if ord(c) < 128)
+    class_clean = ''.join(c for c in name[1] if ord(c) < 128)
+
+    name_bytes = name_clean.encode('ascii')
+    class_bytes = class_clean.encode('ascii')
+    namelength = len(name_bytes)
+    classlength = len(class_bytes)
+    totalSize = 4 + 4 + 4 + 4 + namelength + classlength
+
+    packed = struct.pack('>I', totalSize)
+    packed += struct.pack('>I', 1 if name[1] == 'scientific name' else 0)
+    packed += struct.pack('>I', namelength)
+    packed += struct.pack('>I', classlength)
+    packed += struct.pack('>I', name[2])  # taxon index
+    packed += name_bytes
+    packed += class_bytes
+
+    return packed
+
+def ecoSeqWriter(file, input_file, taxindex, parser):
+    output = open(file, 'wb')
+    input_stream = universalOpen(input_file)
+    inputsize = fileSize(input_stream)
+    entries = parser(input_stream)
+    seqcount = 0
+    skipped = []
+
+    # Write placeholder for sequence count
+    output.write(struct.pack('>I', 0))
+
+    progressBar(0, inputsize, reset=True)
+
+    for entry in entries:
+        if entry['taxid'] is not None:
+            try:
+                # Convert to integer taxid
+                taxid_int = int(entry['taxid'])
+                # Lookup in taxindex
+                entry['taxid'] = taxindex.get(taxid_int, None)
+            except (ValueError, TypeError):
+                entry['taxid'] = None
+
+            if entry['taxid'] is not None:
+                seqcount += 1
+                packed = ecoSeqPacker(entry)
+                output.write(packed)
+            else:
+                skipped.append(entry['id'])
+
+        # Update progress
+        if inputsize is not None:
+            where = universalTell(input_stream)
+            progressBar(where, inputsize)
+        else:
+            progressBar(seqcount, seqcount + 1)  # Fake progress
+
+        sys.stderr.write(" Readed sequences : %d     \r" % seqcount)
+        sys.stderr.flush()
+
+    print("\n", file=sys.stderr)
+    # Update sequence count at beginning of file
+    output.seek(0)
+    output.write(struct.pack('>I', seqcount))
+    output.close()
+
+    return skipped
+
+def ecoTaxWriter(file, taxonomy):
+    output = open(file, 'wb')
+    output.write(struct.pack('>I', len(taxonomy)))
+
+    for tx in taxonomy:
+        output.write(ecoTaxPacker(tx))
+
+    output.close()
+
+def ecoRankWriter(file, ranks):
+    output = open(file, 'wb')
+    rank_list = sorted(ranks.keys())
+    output.write(struct.pack('>I', len(rank_list)))
+
+    for rank in rank_list:
+        output.write(ecoRankPacker(rank))
+
+    output.close()
+
+def ecoNameWriter(file, names):
+    output = open(file, 'wb')
+    output.write(struct.pack('>I', len(names)))
+
+    # Sort case-insensitive
+    names.sort(key=lambda x: x[0].lower())
+
+    for name in names:
+        output.write(ecoNamePacker(name))
+
+    output.close()
+
+def ecoDBWriter(prefix, taxonomy, seqFileNames, parser):
+    ecoRankWriter(prefix + '.rdx', taxonomy[1])
+    ecoTaxWriter(prefix + '.tdx', taxonomy[0])
+    ecoNameWriter(prefix + '.ndx', taxonomy[2])
+
+    filecount = 0
+    for filename in seqFileNames:
+        filecount += 1
+        outfile = "%s_%03d.sdx" % (prefix, filecount)
+        print("\nProcessing:", filename, file=sys.stderr)
+        skipped = ecoSeqWriter(outfile, filename, taxonomy[3], parser)
+
+        if skipped:
+            print("\nSkipped entries without valid taxonomy:", file=sys.stderr)
+            for sid in skipped:
+                print(sid, file=sys.stderr)
+        else:
+            print("All entries processed successfully", file=sys.stderr)
+
+def ecoParseOptions(arguments):
+    opt = {
+        'prefix': 'ecodb',
+        'taxdir': 'taxdump',
+        'parser': sequenceIteratorFactory(genbankEntryParser, entryIterator)
+    }
+
+    try:
+        o, filenames = getopt.getopt(arguments,
+                                    'ht:T:n:gfe',
+                                    ['help',
+                                     'taxonomy=',
+                                     'taxonomy_db=',
+                                     'name=',
+                                     'genbank',
+                                     'fasta',
+                                     'embl'])
+    except getopt.GetoptError as err:
+        print(str(err), file=sys.stderr)
+        printHelp()
+        sys.exit(2)
+
+    for name, value in o:
+        if name in ('-h', '--help'):
+            printHelp()
+            sys.exit()
+        elif name in ('-t', '--taxonomy'):
+            opt['taxdir'] = value
+        elif name in ('-n', '--name'):
+            opt['prefix'] = value
+        elif name in ('-g', '--genbank'):
+            opt['parser'] = sequenceIteratorFactory(genbankEntryParser, entryIterator)
+        elif name in ('-f', '--fasta'):
+            opt['parser'] = sequenceIteratorFactory(fastaEntryParser, fastaEntryIterator)
+        elif name in ('-e', '--embl'):
+            opt['parser'] = sequenceIteratorFactory(emblEntryParser, entryIterator)
+        else:
+            raise ValueError('Unknown option: %s' % name)
+
+    return opt, filenames
+
+def printHelp():
+    print("-----------------------------------")
+    print(" ecoPCRFormat.py")
+    print("-----------------------------------")
+    print("Converts sequence databases to ecoPCR format")
+    print("Usage: ecoPCRFormat.py [options] <files>")
+    print("Options:")
+    print("  -e, --embl        Input in EMBL format")
+    print("  -f, --fasta       Input in FASTA format")
+    print("  -g, --genbank     Input in GenBank format (default)")
+    print("  -h, --help        Show this help message")
+    print("  -n NAME, --name=NAME   Database prefix (default: ecodb)")
+    print("  -t DIR, --taxonomy=DIR   Taxonomy directory (default: taxdump)")
+    print("-----------------------------------")
+
+if __name__ == '__main__':
+    try:
+        opt, filenames = ecoParseOptions(sys.argv[1:])
+
+        if not filenames:
+            print("Error: No input files specified", file=sys.stderr)
+            printHelp()
+            sys.exit(1)
+
+        print("Loading taxonomy...", file=sys.stderr)
+        taxonomy = readTaxonomyDump(opt['taxdir'])
+
+        print("Processing sequence files...", file=sys.stderr)
+        ecoDBWriter(opt['prefix'], taxonomy, filenames, opt['parser'])
+
+        print("Database creation complete", file=sys.stderr)
+
+    except Exception as e:
+        print("Error: " + str(e), file=sys.stderr)
+        import traceback
+        traceback.print_exc()
+        sys.exit(1)
+