Merge branch 'affineGap' of https://github.com/amplab/snap into affin…

…eGap

SNAPLib/AlignerContext.cpp

@@ -220,7 +220,7 @@ AlignerContext::initialize()
              WriteStatusMessage("%llds.  %u bases, seed size %d\n",
                     loadTime / 1000, index->getGenome()->getCountOfBases(), index->getSeedLength());
 
-			 if (index->getMajorVersion() < 5 || index->getMajorVersion() == 5 && index->getMinorVersion() == 0) {
+			 if (index->getMajorVersion() < 5 || (index->getMajorVersion() == 5 && index->getMinorVersion() == 0)) {
 				 WriteErrorMessage("WARNING: The version of the index you're using was built with an earlier version of SNAP and will result in Ns in the reference NOT matching Ns in reads.\n         If you do not want this behavior, rebuild the index.\n");
 			 }
          } else {
@@ -473,7 +473,7 @@ AlignerContext::printStats()
         (stats->filtered > 0) ? numPctAndPad(filtered, stats->filtered, 100.0 * stats->filtered / stats->totalReads, 23, strBufLen) : "",
         (stats->extraAlignments > 0) ? FormatUIntWithCommas(stats->extraAlignments, extraAlignments, strBufLen, 18) : "",
 		isPaired() ? pctAndPad(pctPairs,  100.0 * stats->alignedAsPairs / stats->totalReads, 7, strBufLen, true) : "",
-		FormatUIntWithCommas((unsigned _int64)(1000 * stats->totalReads / max(alignTime, (_int64)1)), readsPerSecond, strBufLen),	// Aligntime is in ms
+		FormatUIntWithCommas((_uint64)(1000 * stats->totalReads / max(alignTime, (_int64)1)), readsPerSecond, strBufLen),	// Aligntime is in ms
 		FormatUIntWithCommas((alignTime + 500) / 1000, alignTimeString, strBufLen, 20),
         options->profile ? pctAndPad(pctRead, (double)stats->millisReading / (double)totalTime, 5, strBufLen, false) : "",
         options->profile ? pctAndPad(pctAlign, (double)stats->millisAligning / (double)totalTime, 6, strBufLen, false) : "",

SNAPLib/AlignerOptions.cpp

@@ -912,8 +912,8 @@ AlignerOptions::usage()
                 WriteErrorMessage("Must specify the desired extra search depth after -D\n");
             }
         } else if (strlen(argv[n]) >= 2 && '-' == argv[n][0] && 'C' == argv[n][1]) {
-            if (strlen(argv[n]) != 4 || '-' != argv[n][2] && '+' != argv[n][2] ||
-                '-' != argv[n][3] && '+' != argv[n][3]) {
+            if (strlen(argv[n]) != 4 || ('-' != argv[n][2] && '+' != argv[n][2]) ||
+                ('-' != argv[n][3] && '+' != argv[n][3])) {
 
                 WriteErrorMessage("Invalid -C argument.\n\n");
                 return false;

SNAPLib/BaseAligner.cpp

@@ -1142,7 +1142,7 @@ Return Value:
                 // cause us to lose confidence in the alignment, since they're probably both pretty good).
                 //
                 if (anyNearbyCandidatesAlreadyScored) {
-                    if (elementToScore->bestScore < score || elementToScore->bestScore == score && matchProbability <= elementToScore->matchProbabilityForBestScore) {
+                    if (elementToScore->bestScore < score || (elementToScore->bestScore == score && matchProbability <= elementToScore->matchProbabilityForBestScore)) {
                     // if (matchProbability <= elementToScore->matchProbabilityForBestScore) {
 						//
                         // This is a no better mapping than something nearby that we already tried.  Just ignore it.
@@ -1192,7 +1192,7 @@ Return Value:
                         //
                         nearbyElement = NULL;
                     } else {
-                        if (nearbyElement->bestScore < score || nearbyElement->bestScore == score && nearbyElement->matchProbabilityForBestScore >= matchProbability) {
+                        if (nearbyElement->bestScore < score || (nearbyElement->bestScore == score && nearbyElement->matchProbabilityForBestScore >= matchProbability)) {
                            //
                             // Again, this is no better than something nearby we already tried.  Give up.
                             //

SNAPLib/Compat.h

@@ -81,6 +81,7 @@ int getpagesize();
 #include <xmmintrin.h>  // This is currently (in Dec 2013) broken on Mac OS X 10.9 (Apple clang-500.2.79)
 #else
 #define _mm_prefetch(...) {}
+#include <emmintrin.h> // For vector types like __m128i
 #endif
 
 typedef int64_t _int64;

SNAPLib/IntersectingPairedEndAligner.cpp

@@ -749,7 +749,7 @@ IntersectingPairedEndAligner::alignLandauVishkin(
                     // If we haven't yet scored this mate, or we've scored it and not gotten an answer, but had a higher score limit than we'd
                     // use now, score it.
                     //
-                    if (mate->score == ScoringMateCandidate::LocationNotYetScored || mate->score == ScoreAboveLimit && mate->scoreLimit < scoreLimit - fewerEndScore) {
+                    if (mate->score == ScoringMateCandidate::LocationNotYetScored || (mate->score == ScoreAboveLimit && mate->scoreLimit < scoreLimit - fewerEndScore)) {
 	                    scoreLocation(readWithMoreHits, setPairDirection[candidate->whichSetPair][readWithMoreHits], GenomeLocationAsInt64(mate->readWithMoreHitsGenomeLocation),
                             mate->seedOffset, scoreLimit - fewerEndScore, &mate->score, &mate->matchProbability,
                             &mate->genomeOffset, &mate->usedAffineGapScoring, &mate->basesClippedBefore, &mate->basesClippedAfter, &mate->agScore, &mate->lvIndels);
@@ -2125,7 +2125,7 @@ IntersectingPairedEndAligner::MergeAnchor::checkMerge(GenomeLocation newMoreHitL
         //
         // Within merge distance.  Keep the better score (or if they're tied the better match probability).
         //
-        if (newPairAGScore > pairAGScore || newPairAGScore == pairAGScore && newMatchProbability > matchProbability) {
+        if (newPairAGScore > pairAGScore || (newPairAGScore == pairAGScore && newMatchProbability > matchProbability)) {
 #ifdef _DEBUG
             if (_DumpAlignments) {
                 printf("Merge replacement at anchor (%llu, %llu), loc (%llu, %llu), old match prob %e, new match prob %e, old pair score %d, new pair score %d\n",

SNAPLib/LandauVishkin.cpp

@@ -257,7 +257,7 @@ int LandauVishkinWithCigar::computeEditDistance(
                         t += 8;
                     }
                 }
-                if (best > bestbest || best == bestbest && bestIndels < bestBestIndels) {
+                if (best > bestbest || (best == bestbest && bestIndels < bestBestIndels)) {
                     bestbest = best;
                     bestdelta = delta;
                     bestBestIndels = bestIndels;

SNAPLib/PairedReadMatcher.cpp

@@ -246,7 +246,7 @@ PairedReadMatcher::getNextReadPair(
         }
 
         if (quicklyDropUnpairedReads) {
-            if (((localRead.getOriginalSAMFlags() & SAM_NEXT_UNMAPPED) == 0) && (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;

SNAPLib/SAM.cpp

@@ -281,7 +281,7 @@ SAMReader::parseHeader(
             //
             // Verify that they actually match what's in our reference genome.
             //
-            if (lineBuffer + 3 >= endOfLine || ' ' != lineBuffer[3] && '\t' != lineBuffer[3]) {
+            if (lineBuffer + 3 >= endOfLine || (' ' != lineBuffer[3] && '\t' != lineBuffer[3])) {
                 WriteErrorMessage("Malformed SAM file '%s' has @SQ without a following space or tab.\n", fileName);
                 delete[] lineBuffer;
                 return false;
@@ -370,7 +370,7 @@ SAMReader::parseHeader(
             !strncmp("@CO",nextLineToProcess,3)) {
 
             if (!strncmp("@RG", nextLineToProcess, 3)) {
-                if (nextLineToProcess + 3 >= endOfBuffer || ' ' != nextLineToProcess[3] && '\t' != nextLineToProcess[3]) {
+                if (nextLineToProcess + 3 >= endOfBuffer || (' ' != nextLineToProcess[3] && '\t' != nextLineToProcess[3])) {
                     WriteErrorMessage("Malformed SAM file '%s' has @RG without a following space or tab.\n", fileName);
                     return false;
                 }
@@ -4269,4 +4269,4 @@ class SAMDupMarkSupplier : public DataWriter::FilterSupplier
 DataWriterSupplier::samMarkDuplicates(const Genome* genome)
 {
     return new SAMDupMarkSupplier(genome);
-}
+}

SNAPLib/SortedDataWriter.cpp

@@ -1231,7 +1231,7 @@ SortedDataFilterSupplier::mergeSort()
         if (i->reader == NULL) // Otheriwse, it's the last block that's in memory
         {
             i->reader = readerSupplier->getDataReader(1, MAX_READ_LENGTH * 8, 0.0,
-                min(1UL << 23, max(1UL << 17, bufferSpace / blocks.size()))); // 128kB to 8MB buffer space per block
+                __min(1UL << 23, __max(1UL << 17, bufferSpace / blocks.size()))); // 128kB to 8MB buffer space per block
             i->reader->init(tempFileName);
             i->reader->reinit(i->start, i->bytes);
         }

SNAPLib/Util.h

@@ -504,7 +504,7 @@ int cheezyLogBase2(_int64 value);
 //
 inline bool isWithin(unsigned a, unsigned b, unsigned distance)
     {
-	return a <= b && a+distance >= b || a >= b && a <= b + distance;
+	return (a <= b && a+distance >= b) || (a >= b && a <= b + distance);
 }
 
 inline int getSignBit64(_int64 value)