the SAM field MQ should be all caps

GMOD · Oct 10, 2012 · beba766 · beba766
1 parent 461f4d5
commit beba766
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/src/JBrowse/Store/SeqFeature/BAM/Feature.js b/src/JBrowse/Store/SeqFeature/BAM/Feature.js
@@ -48,7 +48,7 @@ return declare( null,
         // trying to determine orientation from 'XS' optional field
         data.strand = data.sam_XS == '-' ? -1 : 1;
 
-        data.score = data.sam_MQ;
+        data.score = data.sam_MQ || data.sam_mq;
         data.type = 'match';
         data.source = store.source;
         data.seq_id = data.sam_segment;

diff --git a/src/JBrowse/Store/SeqFeature/BAM/File.js b/src/JBrowse/Store/SeqFeature/BAM/File.js
@@ -286,7 +286,7 @@ var BamFile = declare( null,
             record.quals = qseq;
 
             record.pos = pos;
-            record.mq = mq;
+            record.MQ = mq;
             record.readName = readName;
             record.segment = this.indexToChr[refID];