*** empty log message ***

Makefile

@@ -69,7 +69,8 @@ BUILD_LIBS =
 OTHER_CPPS = ccnt_lut.cpp hit.cpp ref_read.cpp alphabet.c shmem.cpp \
              edit.cpp ebwt.cpp
 SEARCH_CPPS = qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp \
-              log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp
+              log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp \
+              color.cpp color_dec.cpp
 SEARCH_CPPS_MAIN = $(SEARCH_CPPS) bowtie_main.cpp
 
 BUILD_CPPS =

VERSION

@@ -1 +1 @@
-0.11.3
+0.12.0

aligner.h

@@ -331,6 +331,8 @@ class UnpairedAlignerV2 : public Aligner {
 		const HitSinkPerThreadFactory& sinkPtFactory,
 		HitSinkPerThread* sinkPt,
 		vector<String<Dna5> >& os,
+		const BitPairReference* refs,
+		int snpPhred,
 		bool rangeMode,
 		bool verbose,
 		bool quiet,
@@ -339,6 +341,8 @@ class UnpairedAlignerV2 : public Aligner {
 		int *btCnt = NULL,
 		AlignerMetrics *metrics = NULL) :
 		Aligner(true, rangeMode),
+		refs_(refs),
+		snpPhred_(snpPhred),
 		doneFirst_(true),
 		firstIsFw_(true),
 		chase_(false),
@@ -412,11 +416,14 @@ class UnpairedAlignerV2 : public Aligner {
 		bool ebwtFw = ra.ebwt->fw();
 		params_->setFw(ra.fw);
 		return params_->reportHit(
-				ra.fw ? (ebwtFw? bufa_->patFw   : bufa_->patFwRev) :
-				        (ebwtFw? bufa_->patRc   : bufa_->patRcRev),
+				ra.fw ? (ebwtFw? bufa_->patFw    : bufa_->patFwRev) :
+				        (ebwtFw? bufa_->patRc    : bufa_->patRcRev),
 				ra.fw ? (ebwtFw? &bufa_->qual    : &bufa_->qualRev) :
 				        (ebwtFw? &bufa_->qualRev : &bufa_->qual),
 				&bufa_->name,
+				bufa_->color,
+				snpPhred_,
+				refs_,
 				ra.ebwt->rmap(),
 				ebwtFw,
 				ra.mms,                   // mismatch positions
@@ -507,6 +514,12 @@ class UnpairedAlignerV2 : public Aligner {
 	}
 
 protected:
+
+	// Reference sequences (needed for colorspace decoding)
+	const BitPairReference* refs_;
+
+	int snpPhred_;
+
 	// Progress state
 	bool doneFirst_;
 	bool firstIsFw_;
@@ -566,14 +579,16 @@ class PairedBWAlignerV1 : public Aligner {
 		uint32_t mixedThresh,
 		uint32_t mixedAttemptLim,
 		const BitPairReference* refs,
+		int snpPhred,
 		bool rangeMode,
 		bool verbose,
 		bool quiet,
 		int maxBts,
 		ChunkPool *pool,
 		int *btCnt) :
 		Aligner(true, rangeMode),
-		refs_(refs), patsrc_(NULL), qlen1_(0), qlen2_(0), doneFw_(true),
+		refs_(refs), snpPhred_(snpPhred),
+		patsrc_(NULL), qlen1_(0), qlen2_(0), doneFw_(true),
 		doneFwFirst_(true),
 		chase1Fw_(false), chase1Rc_(false),
 		chase2Fw_(false), chase2Rc_(false),
@@ -819,6 +834,9 @@ class PairedBWAlignerV1 : public Aligner {
 				rL.fw ? (ebwtFwL? &bufL->qual    : &bufL->qualRev) :
 				        (ebwtFwL? &bufL->qualRev : &bufL->qual),
 				&bufL->name,
+				bufL->color,
+				snpPhred_,
+				refs_,
 				rmap,
 				ebwtFwL,
 				rL.mms,                       // mismatch positions
@@ -846,6 +864,9 @@ class PairedBWAlignerV1 : public Aligner {
 				rR.fw ? (ebwtFwR? &bufR->qual    : &bufR->qualRev) :
 				        (ebwtFwR? &bufR->qualRev : &bufR->qual),
 				&bufR->name,
+				bufR->color,
+				snpPhred_,
+				refs_,
 				rmap,
 				ebwtFwR,
 				rR.mms,                       // mismatch positions
@@ -1228,6 +1249,8 @@ class PairedBWAlignerV1 : public Aligner {
 
 	const BitPairReference* refs_;
 
+	int snpPhred_;
+
 	PatternSourcePerThread *patsrc_;
 	uint32_t qlen1_;
 	uint32_t qlen2_;
@@ -1408,14 +1431,17 @@ class PairedBWAlignerV2 : public Aligner {
 		uint32_t maxInsert,
 		uint32_t mixedAttemptLim,
 		const BitPairReference* refs,
+		int snpPhred,
 		bool rangeMode,
 		bool verbose,
 		bool quiet,
 		int maxBts,
 		ChunkPool *pool,
 		int *btCnt) :
 		Aligner(true, rangeMode),
-		refs_(refs), patsrc_(NULL),
+		refs_(refs),
+		snpPhred_(snpPhred),
+		patsrc_(NULL),
 		qlen1_(0), qlen2_(0),
 		chase_(false),
 		donePe_(false),
@@ -1643,6 +1669,9 @@ class PairedBWAlignerV2 : public Aligner {
 				rL.fw ? (ebwtFwL? &bufL->qual    : &bufL->qualRev) :
 				        (ebwtFwL? &bufL->qualRev : &bufL->qual),
 				&bufL->name,
+				bufL->color,
+				snpPhred_,
+				refs_,
 				rmap,
 				ebwtFwL,
 				rL.mms,                       // mismatch positions
@@ -1670,6 +1699,9 @@ class PairedBWAlignerV2 : public Aligner {
 				rR.fw ? (ebwtFwR? &bufR->qual    : &bufR->qualRev) :
 				        (ebwtFwR? &bufR->qualRev : &bufR->qual),
 				&bufR->name,
+				bufR->color,
+				snpPhred_,
+				refs_,
 				rmap,
 				ebwtFwR,
 				rR.mms,                       // mismatch positions
@@ -1709,6 +1741,9 @@ class PairedBWAlignerV2 : public Aligner {
 			r.fw ? (ebwtFw? &buf->qual    : &buf->qualRev) :
 			       (ebwtFw? &buf->qualRev : &buf->qual),
 			&buf->name,
+			buf->color,
+			snpPhred_,
+			refs_,
 			r.ebwt->rmap(),
 			ebwtFw,
 			r.mms,                   // mismatch positions
@@ -1871,6 +1906,9 @@ class PairedBWAlignerV2 : public Aligner {
 	}
 
 	const BitPairReference* refs_;
+
+	int snpPhred_;
+
 	PatternSourcePerThread *patsrc_;
 	uint32_t qlen1_, qlen2_;
 	bool chase_;

aligner_0mm.h

@@ -25,6 +25,7 @@ class UnpairedExactAlignerV1Factory : public AlignerFactory {
 	UnpairedExactAlignerV1Factory(
 			Ebwt<String<Dna> >& ebwtFw,
 			Ebwt<String<Dna> >* ebwtBw,
+			int snpPhred,
 			bool doFw,
 			bool doRc,
 			HitSink& sink,
@@ -33,6 +34,7 @@ class UnpairedExactAlignerV1Factory : public AlignerFactory {
 			RangeCache* cacheBw,
 			uint32_t cacheLimit,
 			ChunkPool *pool,
+			BitPairReference* refs,
 			vector<String<Dna5> >& os,
 			bool maqPenalty,
 			bool qualOrder,
@@ -43,13 +45,15 @@ class UnpairedExactAlignerV1Factory : public AlignerFactory {
 			uint32_t seed) :
 			ebwtFw_(ebwtFw),
 			ebwtBw_(ebwtBw),
+			snpPhred_(snpPhred),
 			doFw_(doFw), doRc_(doRc),
 			sink_(sink),
 			sinkPtFactory_(sinkPtFactory),
 			cacheFw_(cacheFw),
 			cacheBw_(cacheBw),
 			cacheLimit_(cacheLimit),
 			pool_(pool),
+			refs_(refs),
 			os_(os),
 			maqPenalty_(maqPenalty),
 			qualOrder_(qualOrder),
@@ -68,7 +72,7 @@ class UnpairedExactAlignerV1Factory : public AlignerFactory {
 	virtual Aligner* create() const {
 		HitSinkPerThread* sinkPt = sinkPtFactory_.create();
 		EbwtSearchParams<String<Dna> >* params =
-			new EbwtSearchParams<String<Dna> >(*sinkPt, os_, true, true, true, rangeMode_);
+			new EbwtSearchParams<String<Dna> >(*sinkPt, os_, true, true);
 
 		const int halfAndHalf = 0;
 		const bool seeded = false;
@@ -108,13 +112,14 @@ class UnpairedExactAlignerV1Factory : public AlignerFactory {
 
 		return new UnpairedAlignerV2<EbwtRangeSource>(
 			params, dr, rchase,
-			sink_, sinkPtFactory_, sinkPt, os_, rangeMode_, verbose_, quiet_,
-			INT_MAX, pool_, NULL, NULL);
+			sink_, sinkPtFactory_, sinkPt, os_, refs_, snpPhred_,
+			rangeMode_, verbose_, quiet_, INT_MAX, pool_, NULL, NULL);
 	}
 
 private:
 	Ebwt<String<Dna> >& ebwtFw_;
 	Ebwt<String<Dna> >* ebwtBw_;
+	int snpPhred_;
 	bool doFw_;
 	bool doRc_;
 	HitSink& sink_;
@@ -123,6 +128,7 @@ class UnpairedExactAlignerV1Factory : public AlignerFactory {
 	RangeCache *cacheBw_;
 	const uint32_t cacheLimit_;
 	ChunkPool *pool_;
+	BitPairReference* refs_;
 	vector<String<Dna5> >& os_;
 	bool maqPenalty_;
 	bool qualOrder_;
@@ -144,6 +150,8 @@ class PairedExactAlignerV1Factory : public AlignerFactory {
 	PairedExactAlignerV1Factory(
 			Ebwt<String<Dna> >& ebwtFw,
 			Ebwt<String<Dna> >* ebwtBw,
+			bool color,
+			int snpPhred,
 			bool doFw,
 			bool doRc,
 			bool v1,
@@ -172,6 +180,8 @@ class PairedExactAlignerV1Factory : public AlignerFactory {
 			bool quiet,
 			uint32_t seed) :
 			ebwtFw_(ebwtFw),
+			color_(color),
+			snpPhred_(snpPhred),
 			doFw_(doFw),
 			doRc_(doRc),
 			v1_(v1),
@@ -209,15 +219,15 @@ class PairedExactAlignerV1Factory : public AlignerFactory {
 		HitSinkPerThread* sinkPt = sinkPtFactory_.createMult(2);
 		HitSinkPerThread* sinkPtSe1 = NULL, * sinkPtSe2 = NULL;
 		EbwtSearchParams<String<Dna> >* params =
-			new EbwtSearchParams<String<Dna> >(*sinkPt, os_, true, true, true, rangeMode_);
+			new EbwtSearchParams<String<Dna> >(*sinkPt, os_, true, true);
 		EbwtSearchParams<String<Dna> >* paramsSe1 = NULL, * paramsSe2 = NULL;
 		if(reportSe_) {
 			sinkPtSe1 = sinkPtFactory_.create();
 			sinkPtSe2 = sinkPtFactory_.create();
 			paramsSe1 =
-				new EbwtSearchParams<String<Dna> >(*sinkPtSe1, os_, true, true, true, rangeMode_);
+				new EbwtSearchParams<String<Dna> >(*sinkPtSe1, os_, true, true);
 			paramsSe2 =
-				new EbwtSearchParams<String<Dna> >(*sinkPtSe2, os_, true, true, true, rangeMode_);
+				new EbwtSearchParams<String<Dna> >(*sinkPtSe2, os_, true, true);
 		}
 
 		const int halfAndHalf = 0;
@@ -301,7 +311,8 @@ class PairedExactAlignerV1Factory : public AlignerFactory {
 				os_, verbose_, quiet_, false, pool_, NULL);
 		}
 
-		RefAligner<String<Dna5> >* refAligner = new ExactRefAligner<String<Dna5> >(verbose_, quiet_);
+		RefAligner<String<Dna5> >* refAligner
+			= new ExactRefAligner<String<Dna5> >(color_, verbose_, quiet_);
 
 		// Set up a RangeChaser
 		RangeChaser<String<Dna> > *rchase =
@@ -317,8 +328,8 @@ class PairedExactAlignerV1Factory : public AlignerFactory {
 				refAligner,
 				rchase, sink_, sinkPtFactory_, sinkPt, mate1fw_, mate2fw_,
 				peInner_, peOuter_, dontReconcile_, symCeil_, mixedThresh_,
-				mixedAttemptLim_, refs_, rangeMode_, verbose_, quiet_,
-				INT_MAX, pool_, NULL);
+				mixedAttemptLim_, refs_, snpPhred_, rangeMode_, verbose_,
+				quiet_, INT_MAX, pool_, NULL);
 			return al;
 		} else {
 			TRangeSrcDrPtrVec *drVec = new TRangeSrcDrPtrVec();
@@ -333,8 +344,8 @@ class PairedExactAlignerV1Factory : public AlignerFactory {
 				rchase, sink_, sinkPtFactory_, sinkPt,
 				sinkPtSe1, sinkPtSe2, mate1fw_, mate2fw_,
 				peInner_, peOuter_,
-				mixedAttemptLim_, refs_, rangeMode_, verbose_, quiet_,
-				INT_MAX, pool_, NULL);
+				mixedAttemptLim_, refs_, snpPhred_, rangeMode_,
+				verbose_, quiet_, INT_MAX, pool_, NULL);
 			delete drVec;
 			return al;
 		}
@@ -343,6 +354,8 @@ class PairedExactAlignerV1Factory : public AlignerFactory {
 private:
 	Ebwt<String<Dna> >& ebwtFw_;
 	Ebwt<String<Dna> >* ebwtBw_;
+	bool color_;
+	int snpPhred_;
 	bool doFw_;
 	bool doRc_;
 	bool v1_;