Fixed a bug that caused output of unmapped mates for single end align…

…ments even with --outSAMunmapped None .
deepbiomed9 · Jan 29, 2016 · c708ab0 · c708ab0
1 parent 3077a62
commit c708ab0
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diff --git a/CHANGES.md b/CHANGES.md
@@ -1,3 +1,6 @@
+* Fixed a bug that caused output of unmapped mates for single end alignments even with --outSAMunmapped None .
+
+
 STAR 2.5.1b 2016/01/22
 ======================
 

diff --git a/bin/Linux_x86_64/STAR b/bin/Linux_x86_64/STAR
diff --git a/bin/Linux_x86_64/STARlong b/bin/Linux_x86_64/STARlong
diff --git a/bin/Linux_x86_64_static/STAR b/bin/Linux_x86_64_static/STAR
diff --git a/bin/Linux_x86_64_static/STARlong b/bin/Linux_x86_64_static/STARlong
diff --git a/source/ReadAlign_outputAlignments.cpp b/source/ReadAlign_outputAlignments.cpp
@@ -161,7 +161,7 @@ void ReadAlign::outputAlignments() {
                 unmapType=4;
             };
 
-            if (unmapType==4)
+            if (unmapType==4 && P->outSAMunmapped.yes)
             {//output unmapped end for single-end alignments
                 if (P->outSAMbool && !P->outSAMunmapped.keepPairs && outSAMfilterYes)
                 {

diff --git a/source/VERSION b/source/VERSION
@@ -1 +1 @@
-#define STAR_VERSION "STAR_2.5.1b"
+#define STAR_VERSION "STAR_2.5.1b_modified"
diff --git a/source/parametersDefault.xxd b/source/parametersDefault.xxd