1.0beta.20: fix infinite loop in alignment adjustment code

wholebiome · Sep 21, 2015 · 3b222a2 · 3b222a2
1 parent bf4a24b
commit 3b222a2
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Showing 2 changed files with 8 additions and 3 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.19";
+const char *SNAP_VERSION = "1.0beta.20";
 
 static void usage()
 {

diff --git a/SNAPLib/ReadWriter.cpp b/SNAPLib/ReadWriter.cpp
@@ -173,9 +173,13 @@ SimpleReadWriter::writeReads(
             int cumulativeAddFrontClipping = 0;
             finalLocations[whichResult] = results[whichResult].location;
 
+            unsigned nAdjustments = 0;
+
             while (!format->writeRead(context, &lvc, buffer + used, size - used, &usedBuffer[whichResult], read->getIdLength(), read, results[whichResult].status,
                 results[whichResult].mapq, finalLocations[whichResult], results[whichResult].direction, (whichResult > 0) || !firstIsPrimary, &addFrontClipping)) {
 
+                nAdjustments++;
+
                 if (0 == addFrontClipping) {
                     blewBuffer = true;
                     break;
@@ -186,9 +190,10 @@ SimpleReadWriter::writeReads(
                     : genome->getContigAtLocation(results[whichResult].location);
                 const Genome::Contig *newContig = results[whichResult].status == NotFound ? NULL
                     : genome->getContigAtLocation(results[whichResult].location + addFrontClipping);
-                if (newContig == NULL || newContig != originalContig || finalLocations[whichResult] + addFrontClipping > originalContig->beginningLocation + originalContig->length - genome->getChromosomePadding()) {
+                if (newContig == NULL || newContig != originalContig || finalLocations[whichResult] + addFrontClipping > originalContig->beginningLocation + originalContig->length - genome->getChromosomePadding() ||
+                    nAdjustments > read->getDataLength()) {
                     //
-                    // Altering this would push us over a contig boundary.  Just give up on the read.
+                    // Altering this would push us over a contig boundary, or we're stuck in a loop.  Just give up on the read.
                     //
                     results[whichResult].status = NotFound;
                     results[whichResult].location = InvalidGenomeLocation;