Accept to deal with sequence in lower case
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@217 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
122
.cproject
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122
.cproject
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<?xml version="1.0" encoding="UTF-8"?>
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<?fileVersion 4.0.0?>
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<cproject>
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<storageModule moduleId="org.eclipse.cdt.core.settings">
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<cconfiguration id="cdt.managedbuild.toolchain.gnu.macosx.base.985481067">
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<storageModule buildSystemId="org.eclipse.cdt.managedbuilder.core.configurationDataProvider" id="cdt.managedbuild.toolchain.gnu.macosx.base.985481067" moduleId="org.eclipse.cdt.core.settings" name="MacOSX GCC">
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<externalSettings/>
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<extensions>
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<extension id="org.eclipse.cdt.core.MachO" point="org.eclipse.cdt.core.BinaryParser"/>
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<extension id="org.eclipse.cdt.core.GASErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
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<extension id="org.eclipse.cdt.core.GLDErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
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<extension id="org.eclipse.cdt.core.GCCErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
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<extension id="org.eclipse.cdt.core.MakeErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
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</extensions>
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</storageModule>
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<storageModule moduleId="cdtBuildSystem" version="4.0.0">
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<configuration artifactName="ecoPCR" buildProperties="" id="cdt.managedbuild.toolchain.gnu.macosx.base.985481067" name="MacOSX GCC" parent="org.eclipse.cdt.build.core.emptycfg">
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<folderInfo id="cdt.managedbuild.toolchain.gnu.macosx.base.985481067.141857048" name="/" resourcePath="">
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<toolChain id="cdt.managedbuild.toolchain.gnu.macosx.base.1673936174" name="cdt.managedbuild.toolchain.gnu.macosx.base" superClass="cdt.managedbuild.toolchain.gnu.macosx.base">
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<targetPlatform archList="all" binaryParser="org.eclipse.cdt.core.MachO" id="cdt.managedbuild.target.gnu.platform.macosx.base.584997877" name="Debug Platform" osList="macosx" superClass="cdt.managedbuild.target.gnu.platform.macosx.base"/>
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<builder id="cdt.managedbuild.target.gnu.builder.macosx.base.328283627" managedBuildOn="false" name="Gnu Make Builder.MacOSX GCC" superClass="cdt.managedbuild.target.gnu.builder.macosx.base"/>
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<tool id="cdt.managedbuild.tool.macosx.c.linker.macosx.base.627652869" name="MacOS X C Linker" superClass="cdt.managedbuild.tool.macosx.c.linker.macosx.base"/>
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<tool id="cdt.managedbuild.tool.macosx.cpp.linker.macosx.base.815782479" name="MacOS X C++ Linker" superClass="cdt.managedbuild.tool.macosx.cpp.linker.macosx.base"/>
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<tool id="cdt.managedbuild.tool.gnu.assembler.macosx.base.536333148" name="GCC Assembler" superClass="cdt.managedbuild.tool.gnu.assembler.macosx.base"/>
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<tool id="cdt.managedbuild.tool.gnu.archiver.macosx.base.202459766" name="GCC Archiver" superClass="cdt.managedbuild.tool.gnu.archiver.macosx.base"/>
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<tool id="cdt.managedbuild.tool.gnu.cpp.compiler.macosx.base.1142106025" name="GCC C++ Compiler" superClass="cdt.managedbuild.tool.gnu.cpp.compiler.macosx.base"/>
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<tool id="cdt.managedbuild.tool.gnu.c.compiler.macosx.base.845498516" name="GCC C Compiler" superClass="cdt.managedbuild.tool.gnu.c.compiler.macosx.base"/>
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</toolChain>
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</folderInfo>
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</configuration>
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</storageModule>
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<storageModule moduleId="scannerConfiguration">
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<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="org.eclipse.cdt.make.core.GCCStandardMakePerProjectProfile"/>
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<profile id="org.eclipse.cdt.make.core.GCCStandardMakePerProjectProfile">
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<buildOutputProvider>
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<openAction enabled="true" filePath=""/>
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<parser enabled="true"/>
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</buildOutputProvider>
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<scannerInfoProvider id="specsFile">
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<runAction arguments="-E -P -v -dD ${plugin_state_location}/${specs_file}" command="gcc" useDefault="true"/>
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<parser enabled="true"/>
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</scannerInfoProvider>
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</profile>
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<profile id="org.eclipse.cdt.make.core.GCCStandardMakePerFileProfile">
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<buildOutputProvider>
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<openAction enabled="true" filePath=""/>
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<parser enabled="true"/>
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</buildOutputProvider>
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<scannerInfoProvider id="makefileGenerator">
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<runAction arguments="-f ${project_name}_scd.mk" command="make" useDefault="true"/>
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<parser enabled="true"/>
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</scannerInfoProvider>
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</profile>
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<profile id="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfile">
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<buildOutputProvider>
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<openAction enabled="false" filePath=""/>
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<parser enabled="false"/>
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</buildOutputProvider>
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<scannerInfoProvider id="specsFile">
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<runAction arguments="-E -P -v -dD ${plugin_state_location}/${specs_file}" command="gcc" useDefault="true"/>
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<parser enabled="true"/>
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</scannerInfoProvider>
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</profile>
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<profile id="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfileCPP">
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<buildOutputProvider>
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<openAction enabled="false" filePath=""/>
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<parser enabled="false"/>
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</buildOutputProvider>
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<scannerInfoProvider id="specsFile">
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<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.cpp" command="g++" useDefault="true"/>
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<parser enabled="true"/>
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</scannerInfoProvider>
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</profile>
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<profile id="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfileC">
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<buildOutputProvider>
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<openAction enabled="false" filePath=""/>
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<parser enabled="false"/>
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</buildOutputProvider>
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<scannerInfoProvider id="specsFile">
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<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.c" command="gcc" useDefault="true"/>
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<parser enabled="true"/>
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</scannerInfoProvider>
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</profile>
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<profile id="org.eclipse.cdt.managedbuilder.core.GCCWinManagedMakePerProjectProfile">
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<buildOutputProvider>
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<openAction enabled="false" filePath=""/>
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<parser enabled="false"/>
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</buildOutputProvider>
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<scannerInfoProvider id="specsFile">
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<runAction arguments="-E -P -v -dD ${plugin_state_location}/${specs_file}" command="gcc" useDefault="true"/>
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<parser enabled="true"/>
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</scannerInfoProvider>
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</profile>
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<profile id="org.eclipse.cdt.managedbuilder.core.GCCWinManagedMakePerProjectProfileCPP">
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<buildOutputProvider>
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<openAction enabled="false" filePath=""/>
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<parser enabled="false"/>
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</buildOutputProvider>
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<scannerInfoProvider id="specsFile">
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<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.cpp" command="g++" useDefault="true"/>
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<parser enabled="true"/>
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</scannerInfoProvider>
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</profile>
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<profile id="org.eclipse.cdt.managedbuilder.core.GCCWinManagedMakePerProjectProfileC">
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<buildOutputProvider>
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<openAction enabled="false" filePath=""/>
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<parser enabled="false"/>
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</buildOutputProvider>
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<scannerInfoProvider id="specsFile">
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<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.c" command="gcc" useDefault="true"/>
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<parser enabled="true"/>
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</scannerInfoProvider>
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</profile>
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</storageModule>
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<storageModule moduleId="org.eclipse.cdt.core.externalSettings"/>
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</cconfiguration>
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</storageModule>
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<storageModule moduleId="cdtBuildSystem" version="4.0.0">
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<project id="ecoPCR.null.1320766773" name="ecoPCR"/>
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</storageModule>
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</cproject>
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83
.project
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83
.project
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<?xml version="1.0" encoding="UTF-8"?>
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<projectDescription>
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<name>ecoPCR</name>
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<comment></comment>
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<projects>
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</projects>
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<buildSpec>
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<buildCommand>
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<name>org.python.pydev.PyDevBuilder</name>
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<arguments>
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</arguments>
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</buildCommand>
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<buildCommand>
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<name>org.eclipse.cdt.managedbuilder.core.genmakebuilder</name>
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<triggers>clean,full,incremental,</triggers>
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<arguments>
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<dictionary>
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<key>org.eclipse.cdt.make.core.fullBuildTarget</key>
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<value>all</value>
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</dictionary>
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<dictionary>
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<key>?name?</key>
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<value></value>
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</dictionary>
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<dictionary>
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<key>org.eclipse.cdt.make.core.enableAutoBuild</key>
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<value>false</value>
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</dictionary>
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<dictionary>
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<key>org.eclipse.cdt.make.core.enableFullBuild</key>
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<value>true</value>
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</dictionary>
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<dictionary>
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<key>org.eclipse.cdt.make.core.enableCleanBuild</key>
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<value>true</value>
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</dictionary>
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<dictionary>
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<key>org.eclipse.cdt.make.core.cleanBuildTarget</key>
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<value>clean</value>
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</dictionary>
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<dictionary>
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<key>org.eclipse.cdt.make.core.append_environment</key>
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<value>true</value>
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</dictionary>
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<dictionary>
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<key>org.eclipse.cdt.make.core.contents</key>
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<value>org.eclipse.cdt.make.core.activeConfigSettings</value>
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</dictionary>
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<dictionary>
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<key>org.eclipse.cdt.make.core.useDefaultBuildCmd</key>
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<value>true</value>
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</dictionary>
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<dictionary>
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<key>org.eclipse.cdt.make.core.buildArguments</key>
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<value></value>
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</dictionary>
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<dictionary>
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<key>org.eclipse.cdt.make.core.buildCommand</key>
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<value>make</value>
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</dictionary>
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<dictionary>
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<key>org.eclipse.cdt.make.core.autoBuildTarget</key>
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<value>all</value>
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</dictionary>
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<dictionary>
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<key>org.eclipse.cdt.make.core.stopOnError</key>
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<value>true</value>
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</dictionary>
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</arguments>
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</buildCommand>
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<buildCommand>
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<name>org.eclipse.cdt.managedbuilder.core.ScannerConfigBuilder</name>
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<arguments>
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</arguments>
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</buildCommand>
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</buildSpec>
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<natures>
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<nature>org.eclipse.cdt.core.cnature</nature>
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<nature>org.eclipse.cdt.managedbuilder.core.ScannerConfigNature</nature>
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<nature>org.eclipse.cdt.managedbuilder.core.managedBuildNature</nature>
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<nature>org.python.pydev.pythonNature</nature>
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</natures>
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</projectDescription>
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7
.pydevproject
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7
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<?xml version="1.0" encoding="UTF-8"?>
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<?eclipse-pydev version="1.0"?>
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<pydev_project>
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<pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.4</pydev_property>
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<pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Default</pydev_property>
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</pydev_project>
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BIN
src/ecoPCR.gz
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BIN
src/ecoPCR.gz
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BIN
src/ecofind.gz
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BIN
src/ecofind.gz
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BIN
src/ecogrep
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BIN
src/ecogrep
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BIN
src/ecogrep.gz
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BIN
src/ecogrep.gz
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BIN
src/ecoisundertaxon
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BIN
src/ecoisundertaxon
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@ -4,6 +4,7 @@
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#include <zlib.h>
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#include <zlib.h>
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#include <string.h>
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#include <string.h>
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#include <stdio.h>
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#include <stdio.h>
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#include <ctype.h>
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static FILE *open_seqfile(const char *prefix,int32_t index);
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static FILE *open_seqfile(const char *prefix,int32_t index);
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@ -97,6 +98,8 @@ ecoseq_t *readnext_ecoseq(FILE *f)
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int32_t comp_status;
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int32_t comp_status;
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unsigned long int seqlength;
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unsigned long int seqlength;
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int32_t rs;
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int32_t rs;
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char *c;
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int32_t i;
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raw = read_ecorecord(f,&rs);
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raw = read_ecorecord(f,&rs);
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@ -139,6 +142,10 @@ ecoseq_t *readnext_ecoseq(FILE *f)
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if (comp_status != Z_OK)
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if (comp_status != Z_OK)
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ECOERROR(ECO_IO_ERROR,"I cannot uncompress sequence data");
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ECOERROR(ECO_IO_ERROR,"I cannot uncompress sequence data");
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for (c=seq->SQ,i=0;i<seqlength;c++,i++)
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*c=toupper(*c);
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return seq;
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return seq;
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}
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}
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Reference in New Issue
Block a user