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Aparently some more recent version of multi eland stopped
author
Diane Trout
<diane@caltech.edu>
Fri, 13 Feb 2009 01:59:42 +0000
(
01:59
+0000)
committer
Diane Trout
<diane@caltech.edu>
Fri, 13 Feb 2009 01:59:42 +0000
(
01:59
+0000)
writing the - and just uses fewer fields. when there were too
many hits.
htsworkflow/pipelines/eland.py
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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
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:
continue
zero_mismatches = int(groups.group(1))
if zero_mismatches == 1: