import: made ngsfilter file parsing more resilient and switching to

version 3.0.1b19

python/obitools3/parsers/ngsfilter.pyx

@@ -48,24 +48,25 @@ 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)
-        tags = split_line.pop(2)
-        tags = tags.split(b":")
-        for t_idx in range(len(tags)):
-            if tags[t_idx]==b"-" or tags[t_idx]==b"None" or tags[t_idx]==b"":
-                tags[t_idx] = nastring
-        if len(tags) == 1:          # Forward and reverse tags are the same
-            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]))
-    
+        if split_line:
+            tags = split_line.pop(2)
+            tags = tags.split(b":")
+            for t_idx in range(len(tags)):
+                if tags[t_idx]==b"-" or tags[t_idx]==b"None" or tags[t_idx]==b"":
+                    tags[t_idx] = nastring
+            if len(tags) == 1:          # Forward and reverse tags are the same
+                tags.append(tags[0])
+            split_line.insert(2, tags[0])
+            split_line.insert(3, tags[1])
+            new_lines.append(out_sep.join(split_line[0:6]))
+        
     return tabIterator(iter(new_lines),
                        header = True,
                        sep = out_sep,

python/obitools3/version.py

@@ -1,5 +1,5 @@
 major = 3
 minor = 0
-serial= '1b18'
+serial= '1b19'
 
 version ="%d.%d.%s" % (major,minor,serial)