From 55ada80500ce79b0980b1639b0ffdf0191adf9af Mon Sep 17 00:00:00 2001
From: mercierc <mercierc@C26881>
Date: Fri, 15 Jul 2022 16:02:21 +1200
Subject: [PATCH] import: made ngsfilter file parsing more resilient and
 switching to version 3.0.1b19

---
 python/obitools3/parsers/ngsfilter.pyx | 25 +++++++++++++------------
 python/obitools3/version.py            |  2 +-
 2 files changed, 14 insertions(+), 13 deletions(-)

diff --git a/python/obitools3/parsers/ngsfilter.pyx b/python/obitools3/parsers/ngsfilter.pyx
index 1077e11..a0f46c4 100644
--- a/python/obitools3/parsers/ngsfilter.pyx
+++ b/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,
diff --git a/python/obitools3/version.py b/python/obitools3/version.py
index d64bb53..2725823 100755
--- a/python/obitools3/version.py
+++ b/python/obitools3/version.py
@@ -1,5 +1,5 @@
 major = 3
 minor = 0
-serial= '1b18'
+serial= '1b19'
 
 version ="%d.%d.%s" % (major,minor,serial)