Switch to version 3.0.1b20

version 3.0.1b19

python/obitools3/commands/alignpairedend.pyx

@@ -234,6 +234,10 @@ def run(config):
 
         consensus = o_view[i]
         
+        if two_views:
+            consensus[b"R1_parent"] = forward[i].id
+            consensus[b"R2_parent"] = reverse[i].id
+               
         if not two_views:
             seqF = entries[i]
         else:

python/obitools3/commands/ngsfilter.pyx

@@ -265,6 +265,10 @@ cdef tuple annotate(sequences, infos, no_tags, verbose=False):
     not_aligned = len(sequences) > 1
     sequences[0] = sequences[0].clone()
     
+    if not_aligned:
+        sequences[0][b"R1_parent"] = sequences[0].id
+        sequences[0][b"R2_parent"] = sequences[1].id
+
     if not_aligned:
         sequences[1] = sequences[1].clone()
         sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq             # used by alignpairedend tool

python/obitools3/parsers/ngsfilter.pyx

@@ -48,13 +48,14 @@ def ngsfilterIterator(lineiterator,
         all_lines.insert(0, firstline)
         
     # Insert header for column names
-    column_names = [b"experiment", b"sample", b"forward_tag", b"reverse_tag", b"forward_primer", b"reverse_primer",b"additional_info"]
+    column_names = [b"experiment", b"sample", b"forward_tag", b"reverse_tag", b"forward_primer", b"reverse_primer"] #,b"additional_info"]
     header = out_sep.join(column_names)
     
     new_lines.append(header)
         
     for line in all_lines:
         split_line = line.split(maxsplit=5)
+        if split_line:
             tags = split_line.pop(2)
             tags = tags.split(b":")
             for t_idx in range(len(tags)):
@@ -64,7 +65,7 @@ def ngsfilterIterator(lineiterator,
                 tags.append(tags[0])
             split_line.insert(2, tags[0])
             split_line.insert(3, tags[1])
-        new_lines.append(out_sep.join(split_line[0:7]))
+            new_lines.append(out_sep.join(split_line[0:6]))
         
     return tabIterator(iter(new_lines),
                        header = True,

python/obitools3/version.py

@@ -1,5 +1,5 @@
 major = 3
 minor = 0
-serial= '1b18'
+serial= '1b20'
 
 version ="%d.%d.%s" % (major,minor,serial)

src/.gitignore

@@ -3,3 +3,4 @@
 /cmake_install.cmake
 /libcobitools3.dylib
 /Makefile
+/build/