Aparently some more recent version of multi eland stopped

writing the - and just uses fewer fields. when there were too
many hits.

diff --git a/htsworkflow/pipelines/eland.py b/htsworkflow/pipelines/eland.py
index 40507e63611136e1f10e300bb6f02b7812b02e23..bdbe5758eb2ef59319d13151d169c91c9aacf04d 100644 (file)
--- a/htsworkflow/pipelines/eland.py
+++ b/htsworkflow/pipelines/eland.py
@@ -129,7 +129,7 @@ class ElandLane(object):
             else:
                 # when there are too many hit, eland writes a - where
                 # it would have put the list of hits
-                if fields[3] == '-':
+                if len(fields) < 4 or fields[3] == '-':
                   continue
                 zero_mismatches = int(groups.group(1))
                 if zero_mismatches == 1: