fix failure to propagate nthreads and output batch size to relevant c…

…onstructors

ebwt_search.cpp

@@ -91,6 +91,7 @@ static bool strata;     // true -> don't stop at stratum boundaries
 static bool refOut;     // if true, alignments go to per-ref files
 static int partitionSz; // output a partitioning key in first field
 static int readsPerBatch; // # reads to read from input file at once
+static int outBatchSz; // # alignments to write to output file at once
 static bool noMaqRound; // true -> don't round quals to nearest 10 like maq
 static bool fileParallel; // separate threads read separate input files in parallel
 static bool useShmem;     // use shared memory to hold the index
@@ -198,6 +199,7 @@ static void resetOptions() {
 	refOut					= false; // if true, alignments go to per-ref files
 	partitionSz				= 0;     // output a partitioning key in first field
 	readsPerBatch			= 16;    // # reads to read from input file at once
+	outBatchSz				= 16;    // # alignments to wrote to output file at once
 	noMaqRound				= false; // true -> don't round quals to nearest 10 like maq
 	fileParallel			= false; // separate threads read separate input files in parallel
 	useShmem				= false; // use shared memory to hold the index
@@ -2598,8 +2600,6 @@ patsrcFromStrings(int format,
 	}
 }
 
-#define PASS_DUMP_FILES dumpAlBase, dumpUnalBase, dumpMaxBase
-
 static string argstr;
 
 template<typename TStr>
@@ -2872,58 +2872,86 @@ static void driver(const char * type,
 							ebwt.nPat(), offBase,
 							colorSeq, colorQual, printCost,
 							suppressOuts, rmap, amap,
-							fullRef, PASS_DUMP_FILES,
+							fullRef,
+							dumpAlBase,
+							dumpUnalBase,
+							dumpMaxBase,
 							format == TAB_MATE, sampleMax,
-							refnames, partitionSz);
+							refnames, nthreads,
+							outBatchSz, partitionSz);
 				} else {
 					sink = new VerboseHitSink(
 							fout, offBase,
 							colorSeq, colorQual, printCost,
 							suppressOuts, rmap, amap,
-							fullRef, PASS_DUMP_FILES,
+							fullRef,
+							dumpAlBase,
+							dumpUnalBase,
+							dumpMaxBase,
 							format == TAB_MATE, sampleMax,
-							refnames, partitionSz);
+							refnames, nthreads,
+							outBatchSz, partitionSz);
 				}
 				break;
 			case OUTPUT_SAM:
 				if(refOut) {
 					throw 1;
 				} else {
 					SAMHitSink *sam = new SAMHitSink(
-							fout, 1, rmap, amap,
-							fullRef, samNoQnameTrunc, defaultMapq,
-							PASS_DUMP_FILES,
-							format == TAB_MATE, sampleMax,
-							refnames, nthreads);
+						fout, 1, rmap, amap,
+						fullRef, samNoQnameTrunc,
+						dumpAlBase,
+						dumpUnalBase,
+						dumpMaxBase,
+						format == TAB_MATE,
+						sampleMax,
+						refnames,
+						nthreads,
+						outBatchSz);
 					if(!samNoHead) {
 						vector<string> refnames;
 						if(!samNoSQ) {
 							readEbwtRefnames(adjustedEbwtFileBase, refnames);
 						}
 						sam->appendHeaders(
-								sam->out(0), ebwt.nPat(),
-								refnames, color, samNoSQ, rmap,
-								ebwt.plen(), fullRef,
-								samNoQnameTrunc,
-								argstr.c_str(),
-								rgs.empty() ? NULL : rgs.c_str());
+							sam->out(0),
+							ebwt.nPat(),
+							refnames, color, samNoSQ, rmap,
+							ebwt.plen(), fullRef,
+							samNoQnameTrunc,
+							argstr.c_str(),
+							rgs.empty() ? NULL : rgs.c_str());
 					}
 					sink = sam;
 				}
 				break;
 			case OUTPUT_CONCISE:
 				if(refOut) {
 					sink = new ConciseHitSink(
-							ebwt.nPat(), offBase,
-							PASS_DUMP_FILES,
-							format == TAB_MATE,  sampleMax,
-							refnames, reportOpps);
+						ebwt.nPat(),
+						offBase,
+						dumpAlBase,
+						dumpUnalBase,
+						dumpMaxBase,
+						format == TAB_MATE,
+						sampleMax,
+						refnames,
+						nthreads,
+						outBatchSz,
+						reportOpps);
 				} else {
 					sink = new ConciseHitSink(
-							fout, offBase,
-							PASS_DUMP_FILES,
-							format == TAB_MATE,  sampleMax,
-							refnames, reportOpps);
+						fout,
+						offBase,
+						dumpAlBase,
+						dumpUnalBase,
+						dumpMaxBase,
+						format == TAB_MATE,
+						sampleMax,
+						refnames,
+						nthreads,
+						outBatchSz,
+						reportOpps);
 				}
 				break;
 			case OUTPUT_NONE:

hit.h

@@ -156,9 +156,9 @@ class HitSink {
 		const std::string& dumpMax,
 		bool onePairFile,
 		bool sampleMax,
-		vector<string>* refnames = NULL,
-		size_t nthreads = 1,
-		int perThreadBufSize = 512) :
+		vector<string>* refnames,
+		size_t nthreads,
+		int perThreadBufSize) :
 		_outs(),
 		_deleteOuts(false),
 		_refnames(refnames),
@@ -204,7 +204,9 @@ class HitSink {
 		const std::string& dumpMax,
 		bool onePairFile,
 		bool sampleMax,
-		vector<string>* refnames = NULL) :
+		vector<string>* refnames,
+		size_t nthreads,
+		int perThreadBufSize) :
 		_outs(),
 		_deleteOuts(true),
 		_refnames(refnames),
@@ -1432,6 +1434,8 @@ class ConciseHitSink : public HitSink {
 		bool onePairFile,
 		bool sampleMax,
 		std::vector<std::string>* refnames,
+		size_t nthreads,
+		int perThreadBufSize,
 		bool reportOpps = false) :
 		HitSink(
 			out,
@@ -1440,7 +1444,9 @@ class ConciseHitSink : public HitSink {
 			dumpMax,
 			onePairFile,
 			sampleMax,
-			refnames),
+			refnames,
+			nthreads,
+			perThreadBufSize),
 		_reportOpps(reportOpps),
 		offBase_(offBase) { }
 
@@ -1457,6 +1463,8 @@ class ConciseHitSink : public HitSink {
 		bool onePairFile,
 		bool sampleMax,
 		std::vector<std::string>* refnames,
+		size_t nthreads,
+		int perThreadBufSize,
 		bool reportOpps = false) :
 		HitSink(
 			numOuts,
@@ -1465,7 +1473,9 @@ class ConciseHitSink : public HitSink {
 			dumpMax,
 			onePairFile,
 			sampleMax,
-			refnames),
+			refnames,
+			nthreads,
+			perThreadBufSize),
 		_reportOpps(reportOpps),
 		offBase_(offBase) { }
 
@@ -1553,6 +1563,8 @@ class VerboseHitSink : public HitSink {
 		bool onePairFile,
 		bool sampleMax,
 		std::vector<std::string>* refnames,
+		size_t nthreads,
+		int perThreadBufSize,
 		int partition = 0) :
 		HitSink(
 			out,
@@ -1561,7 +1573,9 @@ class VerboseHitSink : public HitSink {
 			dumpMax,
 			onePairFile,
 			sampleMax,
-			refnames),
+			refnames,
+			nthreads,
+			perThreadBufSize),
 		partition_(partition),
 		offBase_(offBase),
 		colorSeq_(colorSeq),
@@ -1592,6 +1606,8 @@ class VerboseHitSink : public HitSink {
 		bool onePairFile,
 		bool sampleMax,
 		std::vector<std::string>* refnames,
+		size_t nthreads,
+		int perThreadBufSize,
 		int partition = 0) :
 		HitSink(
 			numOuts,
@@ -1600,7 +1616,9 @@ class VerboseHitSink : public HitSink {
 			dumpMax,
 			onePairFile,
 			sampleMax,
-			refnames),
+			refnames,
+			nthreads,
+			perThreadBufSize),
 		partition_(partition),
 		offBase_(offBase),
 		colorSeq_(colorSeq),
@@ -1664,7 +1682,7 @@ class VerboseHitSink : public HitSink {
  */
 class StubHitSink : public HitSink {
 public:
-	StubHitSink() : HitSink(new OutFileBuf(".tmp"), "", "", "", false, false, NULL) { }
+	StubHitSink() : HitSink(new OutFileBuf(".tmp"), "", "", "", false, false, NULL, 1, 1) { }
 	
 	virtual void append(BTString& o, const Hit& h, int mapq, int xms) { }
 };

sam.h

@@ -47,14 +47,14 @@ class SAMHitSink : public HitSink {
 		AnnotationMap *amap,
 		bool fullRef,
 		bool noQnameTrunc,
-		int defaultMapq,
 		const std::string& dumpAl,
 		const std::string& dumpUnal,
 		const std::string& dumpMax,
 		bool onePairFile,
 		bool sampleMax,
 		std::vector<std::string>* refnames,
-		int nthreads) :
+		size_t nthreads,
+		int perThreadBufSize) :
 		HitSink(
 			out,
 			dumpAl,
@@ -63,9 +63,12 @@ class SAMHitSink : public HitSink {
 			onePairFile,
 			sampleMax,
 			refnames,
-			nthreads),
-		offBase_(offBase), defaultMapq_(defaultMapq),
-		rmap_(rmap), amap_(amap), fullRef_(fullRef),
+			nthreads,
+			perThreadBufSize),
+		offBase_(offBase),
+		rmap_(rmap),
+		amap_(amap),
+		fullRef_(fullRef),
 		noQnameTrunc_(noQnameTrunc) { }
 
 	/**
@@ -78,23 +81,28 @@ class SAMHitSink : public HitSink {
 		ReferenceMap *rmap,
 		AnnotationMap *amap,
 		bool fullRef,
-		int defaultMapq,
 		const std::string& dumpAl,
 		const std::string& dumpUnal,
 		const std::string& dumpMax,
 		bool onePairFile,
 		bool sampleMax,
-		std::vector<std::string>* refnames) :
+		std::vector<std::string>* refnames,
+		size_t nthreads,
+		int perThreadBufSize) :
 		HitSink(
 			numOuts,
 			dumpAl,
 			dumpUnal,
 			dumpMax,
 			onePairFile,
 			sampleMax,
-			refnames),
-		offBase_(offBase), defaultMapq_(defaultMapq),
-		rmap_(rmap), amap_(amap), fullRef_(fullRef) { }
+			refnames,
+			nthreads,
+			perThreadBufSize),
+		offBase_(offBase),
+		rmap_(rmap),
+		amap_(amap),
+		fullRef_(fullRef) { }
 
 	/**
 	 * Append a verbose, readable hit to the output stream
@@ -151,8 +159,6 @@ class SAMHitSink : public HitSink {
 	int  offBase_;        /// Add this to reference offsets before outputting.
 	                      /// (An easy way to make things 1-based instead of
 	                      /// 0-based)
-	int  defaultMapq_;    /// Default mapping quality to report when one is
-	                      /// not specified
 	ReferenceMap *rmap_;  /// mapping to reference coordinate system.
 	AnnotationMap *amap_; ///
 	bool fullRef_;        /// print full reference name, not just up to whitespace