Stop Chromsweeep cache scan when DB is after query; allow BAM unmapped reads/chrom in genome file.

src/utils/GenomeFile/NewGenomeFile.cpp

@@ -23,12 +23,20 @@ NewGenomeFile::NewGenomeFile(const QuickString &genomeFilename)
 NewGenomeFile::NewGenomeFile(const BamTools::RefVector &refVector)
 : _maxId(-1)
 {
-    for (size_t i = 0; i < refVector.size(); ++i) {
+	size_t i = 0;
+    for (; i < refVector.size(); ++i) {
         QuickString chrom = refVector[i].RefName;
         CHRPOS length = refVector[i].RefLength;
         _maxId++;
         _chromSizeIds[chrom] = pair<CHRPOS, CHRPOS>(length, _maxId);
+		_chromList.push_back(chrom);
     }
+	// Special: BAM files can have unmapped reads, which show as no chromosome, or an empty chrom string.
+	// Add in an empty chrom so these don't error.
+	_maxId++;
+	_chromSizeIds[""] = pair<CHRPOS, int>(0, _maxId);
+	_chromList.push_back("");
+
 }
 
 // Destructor
@@ -69,6 +77,13 @@ void NewGenomeFile::loadGenomeFileIntoMap() {
 		cerr << "Error: The genome file " << _genomeFileName << " has no valid entries. Exiting." << endl;
 		exit(1);
 	}
+	// Special: BAM files can have unmapped reads, which show as no chromosome, or an empty chrom string.
+	// Add in an empty chrom so these don't error.
+	_maxId++;
+	_chromSizeIds[""] = pair<CHRPOS, int>(0, _maxId);
+	_chromList.push_back("");
+
+
 	_startOffsets.push_back(_genomeLength); //insert the final length as the last element
 	//to help with the lower_bound call in the projectOnGenome method.
 	genFile.close();

src/utils/GenomeFile/NewGenomeFile.h

@@ -38,7 +38,7 @@ public:
     CHRPOS getChromSize(const QuickString &chrom);  // return the size of a chromosome
     CHRPOS getChromId(const QuickString &chrom); // return chromosome's sort order
     const vector<QuickString> &getChromList() const { return _chromList; }  // return a list of chrom names
-    CHRPOS getNumberOfChroms() const { return _chromList.size(); }
+    CHRPOS getNumberOfChroms() const { return _chromList.size() -1; }//the -1 excludes the blank chrom added for unmapped reads
     const QuickString &getGenomeFileName() const { return _genomeFileName; }
 
 

src/utils/NewChromsweep/NewChromsweep.cpp

@@ -99,7 +99,7 @@ void NewChromSweep::scanCache(int dbIdx, RecordKeyVector &retList) {
         if (_currQueryRec->sameChrom(cacheRec) && !(_currQueryRec->after(cacheRec))) {
             if (intersects(_currQueryRec, cacheRec)) {
                 retList.push_back(cacheRec);
-            }
+            } else break; // cacheRec is after the query rec, stop scanning.
             cacheIter = _caches[dbIdx].next();
         }
         else {

test/intersect/performanceTest.sh

@@ -23,7 +23,7 @@ if true; then
   echo "generating data..."
   mkdir perfData
   cd perfData
-  ../$BT random -l 1000 -n 20000000 -g ../human.hg19.genome | sort -k1,1 -k2,2n > a10M.bed 
+  ../$BT random -l 1000 -n 10000000 -g ../human.hg19.genome | sort -k1,1 -k2,2n > a10M.bed 
   ../$BT random -l 1000 -n 10000000 -g ../human.hg19.genome | sort -k1,1 -k2,2n > b10M.bed 
   cp a10M.bed a10M_gzipped.bed
   gzip a10M_gzipped.bed