From: Diane Trout <diane@caltech.edu>
Date: Fri, 13 Feb 2009 01:59:42 +0000 (+0000)
Subject: Aparently some more recent version of multi eland stopped
X-Git-Tag: 0.2.0.1~23
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=55f3e5b228a76e6903262cdc718ee40446aaa0b5

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 40507e6..bdbe575 100644
--- 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: