1.0beta.22: Paired read matcher doesn't drop reads where both mates a…

…re unaligned in the input
amplab · Nov 4, 2015 · ee3efdd · ee3efdd
1 parent c45c723
commit ee3efdd
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/SNAPLib/CommandProcessor.cpp b/SNAPLib/CommandProcessor.cpp
@@ -35,7 +35,7 @@ Pulled from the main program and expanded to handle daemon mode
 #include "Error.h"
 #include "Compat.h"
 
-const char *SNAP_VERSION = "1.0beta.21";
+const char *SNAP_VERSION = "1.0beta.22";
 
 static void usage()
 {

diff --git a/SNAPLib/PairedReadMatcher.cpp b/SNAPLib/PairedReadMatcher.cpp
@@ -246,7 +246,7 @@ PairedReadMatcher::getNextReadPair(
         }
 
         if (quicklyDropUnpairedReads) {
-            if (localRead.getOriginalPNEXT() == 0 || localRead.getOriginalRNEXTLength() == 1 && localRead.getOriginalRNEXT()[0] == '*') {
+            if (((localRead.getOriginalSAMFlags() & SAM_NEXT_UNMAPPED) == 0) && (localRead.getOriginalPNEXT() == 0 || localRead.getOriginalRNEXTLength() == 1 && localRead.getOriginalRNEXT()[0] == '*')) {
                 nReadsQuicklyDropped++;
                 skipped--;
                 continue;