2.0.5: fix bug where -f would result in reads being unaligned

SNAPLib/AlignerOptions.cpp

@@ -154,7 +154,7 @@ AlignerOptions::usage()
             "  -x   explore some hits of overly popular seeds (useful for filtering)\n"
             "  -S   suppress additional processing (sorted BAM output only)\n"
             "       i=index, d=duplicate marking\n"
-            "  -f   stop on first match within edit distance limit (filtering mode)\n"
+            "  -f   stop on first match within edit distance limit (filtering mode, single-end only)\n"
             "  -F   filter output (a=aligned only, s=single hit only (MAPQ >= %d), u=unaligned only, l=long enough to align (see -mrl))\n"
             "  -E   an alternate (and fully general) way to specify filter options.  Emit only these types s = single hit (MAPQ >= %d), m = multiple hit (MAPQ < %d),\n"
             "       x = not long enough to align, u = unaligned, b = filter must apply to both ends of a paired-end read.  Combine the letters after\n"

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;
                 }
 

SNAPLib/CommandProcessor.cpp

@@ -36,7 +36,7 @@ Revision History:
 #include "Compat.h"
 #include "HitDepth.h"
 
-const char *SNAP_VERSION = "2.0.4";
+const char *SNAP_VERSION = "2.0.5";
 
 static void usage()
 {