Switch to version 3.0.0b40

not export the first line of data and switch to version 3.0.0b39

python/obitools3/commands/ngsfilter.pyx

@@ -24,10 +24,6 @@ from cpython.exc cimport PyErr_CheckSignals
 from io import BufferedWriter
 
 
-#REVERSE_SEQ_COLUMN_NAME = b"REVERSE_SEQUENCE"      # used by alignpairedend tool
-#REVERSE_QUALITY_COLUMN_NAME = b"REVERSE_QUALITY"   # used by alignpairedend tool
-
-
 __title__="Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers"
 
 

python/obitools3/format/tab.pyx

@@ -23,9 +23,8 @@ cdef class TabFormat:
         if self.first_line:
             self.tags = [k for k in data.keys()]
         
-        for k in self.tags:
+        if self.header and self.first_line:
-            
+            for k in self.tags:
-            if self.header and self.first_line:
                 if isinstance(data.view[k], Column_multi_elts):
                     keys = data.view[k].keys()
                     keys.sort()
@@ -33,27 +32,36 @@ cdef class TabFormat:
                         line.append(tobytes(k)+b':'+tobytes(k2))
                 else:
                     line.append(tobytes(k))
-            else:
+            r = self.sep.join(value for value in line)
-                value = data[k]
+            r += b'\n'
-                if isinstance(data.view[k], Column_multi_elts):
+            line = []
-                    keys = data.view[k].keys()
+                    
-                    keys.sort()
+        for k in self.tags:
-                    if value is None:  # all keys at None
+            value = data[k]
-                        for k2 in keys: # TODO could be much more efficient
+            if isinstance(data.view[k], Column_multi_elts):
-                            line.append(self.NAString)
+                keys = data.view[k].keys()
-                    else:
+                keys.sort()
-                        for k2 in keys: # TODO could be much more efficient
+                if value is None:  # all keys at None
-                            if value[k2] is not None:
+                    for k2 in keys: # TODO could be much more efficient
-                                line.append(str2bytes(str(bytes2str_object(value[k2]))))  # genius programming
-                            else:
-                                line.append(self.NAString)
-                else:
-                    if value is not None:
-                        line.append(str2bytes(str(bytes2str_object(value))))
-                    else:
                         line.append(self.NAString)
+                else:
+                    for k2 in keys: # TODO could be much more efficient
+                        if value[k2] is not None:
+                            line.append(str2bytes(str(bytes2str_object(value[k2]))))  # genius programming
+                        else:
+                            line.append(self.NAString)
+            else:
+                if value is not None:
+                    line.append(str2bytes(str(bytes2str_object(value))))
+                else:
+                    line.append(self.NAString)
+                  	      	
+        if self.header and self.first_line:
+            r += self.sep.join(value for value in line)
+        else:
+            r = self.sep.join(value for value in line)
 
         if self.first_line:
             self.first_line = False
 
-        return self.sep.join(value for value in line)
+        return r

python/obitools3/version.py

@@ -1,5 +1,5 @@
 major = 3
 minor = 0
-serial= '0b38'
+serial= '0b40'
 
 version ="%d.%d.%s" % (major,minor,serial)

src/obisig.h

@@ -25,7 +25,7 @@
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  *
  */
-bool volatile keep_running;
+extern bool volatile keep_running;
 void sig_handler(int signum);