2.0.5.dev.1: fix bug where aligned reads in single-end would show as …

…unaligned in the output when -f is specified
amplab · Feb 22, 2025 · da7a4a6 · da7a4a6
2 parents 80cf81a + 231b426
commit da7a4a6
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Showing 2 changed files with 8 additions and 1 deletion.
diff --git a/SNAPLib/BaseAligner.cpp b/SNAPLib/BaseAligner.cpp
@@ -1492,8 +1492,15 @@ Return Value:
                     // care about the best alignment. Stop now but mark the result as MultipleHits because we're not
                     // confident that it's the best one.  We don't support mapq in this secnario, because we haven't
                     // explored enough to compute it.
+
+
+                    (altAwareness ? scoresForNonAltAlignments : scoresForAllAlignments).fillInSingleAlignmentResult(primaryResult, popularSeedsSkipped);
+                    //
+                    // Force MAPQ 0 in this case, since we didn't explore the whole space and can't say.
+                    //
                     primaryResult->status = MultipleHits;
                     primaryResult->mapq = 0;
+                    firstALTResult->status = NotFound;
                     return true;
                 }
 

diff --git a/SNAPLib/CommandProcessor.cpp b/SNAPLib/CommandProcessor.cpp
@@ -36,7 +36,7 @@ Revision History:
 #include "Compat.h"
 #include "HitDepth.h"
 
-const char *SNAP_VERSION = "2.0.4.dev.1";
+const char *SNAP_VERSION = "2.0.5.dev.1";
 
 static void usage()
 {