*** empty log message ***

aligner.h

@@ -333,6 +333,7 @@ class UnpairedAlignerV2 : public Aligner {
 		vector<String<Dna5> >& os,
 		bool rangeMode,
 		bool verbose,
+		bool quiet,
 		int maxBts,
 		ChunkPool *pool,
 		int *btCnt = NULL,
@@ -346,6 +347,8 @@ class UnpairedAlignerV2 : public Aligner {
 		params_(params),
 		rchase_(rchase),
 		driver_(driver),
+		verbose_(verbose),
+		quiet_(quiet),
 		maxBts_(maxBts),
 		pool_(pool),
 		btCnt_(btCnt),
@@ -374,6 +377,15 @@ class UnpairedAlignerV2 : public Aligner {
 			metrics_->nextRead(patsrc->bufa().patFw);
 		}
 		pool_->reset(&patsrc->bufa().name, patsrc->patid());
+		if(patsrc->bufa().length() < 4) {
+			if(!quiet_) {
+				cerr << "Warning: Skipping read " << patsrc->bufa().name
+					 << " because it is less than 4 characters long" << endl;
+			}
+			this->done = true;
+			sinkPt_->finishRead(*patsrc_, true, true);
+			return;
+		}
 		driver_->setQuery(patsrc, NULL);
 		this->done = driver_->done;
 		doneFirst_ = false;
@@ -508,6 +520,9 @@ class UnpairedAlignerV2 : public Aligner {
 	// Range-finding state
 	TDriver* driver_;
 
+	bool verbose_; // be talkative
+	bool quiet_; // don't print informational/warning info
+
 	const int maxBts_;
 	ChunkPool *pool_;
 	int *btCnt_;
@@ -548,6 +563,7 @@ class PairedBWAlignerV1 : public Aligner {
 		const BitPairReference* refs,
 		bool rangeMode,
 		bool verbose,
+		bool quiet,
 		int maxBts,
 		ChunkPool *pool,
 		int *btCnt) :
@@ -572,6 +588,7 @@ class PairedBWAlignerV1 : public Aligner {
 		fw1_(fw1), fw2_(fw2),
 		rchase_(rchase),
 		verbose_(verbose),
+		quiet_(quiet),
 		maxBts_(maxBts),
 		pool_(pool),
 		btCnt_(btCnt),
@@ -654,6 +671,15 @@ class PairedBWAlignerV1 : public Aligner {
 		// Give all of the drivers pointers to the relevant read info
 		patsrc_ = patsrc;
 		pool_->reset(&patsrc->bufa().name, patsrc->patid());
+		if(patsrc->bufa().length() < 4 || patsrc->bufb().length() < 4) {
+			if(!quiet_) {
+				cerr << "Warning: Skipping pair " << patsrc->bufa().name
+					 << " because a mate is less than 4 characters long" << endl;
+			}
+			this->done = true;
+			sinkPt_->finishRead(*patsrc_, true, true);
+			return;
+		}
 		driver1Fw_->setQuery(patsrc, NULL);
 		driver1Rc_->setQuery(patsrc, NULL);
 		driver2Fw_->setQuery(patsrc, NULL);
@@ -1327,6 +1353,8 @@ class PairedBWAlignerV1 : public Aligner {
 
 	// true -> be talkative
 	bool verbose_;
+	// true -> suppress warnings
+	bool quiet_;
 
 	int maxBts_;
 	ChunkPool *pool_;
@@ -1451,6 +1479,7 @@ class PairedBWAlignerV2 : public Aligner {
 		const BitPairReference* refs,
 		bool rangeMode,
 		bool verbose,
+		bool quiet,
 		int maxBts,
 		ChunkPool *pool,
 		int *btCnt) :
@@ -1477,6 +1506,8 @@ class PairedBWAlignerV2 : public Aligner {
 		rchase_(rchase),
 		driver_(driver),
 		pool_(pool),
+		verbose_(verbose),
+		quiet_(quiet),
 		maxBts_(maxBts),
 		btCnt_(btCnt)
 	{
@@ -1512,6 +1543,15 @@ class PairedBWAlignerV2 : public Aligner {
 		// Give all of the drivers pointers to the relevant read info
 		patsrc_ = patsrc;
 		pool_->reset(&patsrc->bufa().name, patsrc->patid());
+		if(patsrc->bufa().length() < 4 || patsrc->bufb().length() < 4) {
+			if(!quiet_) {
+				cerr << "Warning: Skipping pair " << patsrc->bufa().name
+					 << " because a mate is less than 4 characters long" << endl;
+			}
+			this->done = true;
+			sinkPt_->finishRead(*patsrc_, true, true);
+			return;
+		}
 		driver_->setQuery(patsrc, NULL);
 		qlen1_ = patsrc_->bufa().length();
 		qlen2_ = patsrc_->bufb().length();
@@ -1934,6 +1974,9 @@ class PairedBWAlignerV2 : public Aligner {
 	// Pool for distributing chunks of best-first path descriptor memory
 	ChunkPool *pool_;
 
+	bool verbose_;
+	bool quiet_;
+
 	int maxBts_; // maximum allowed # backtracks
 	int *btCnt_; // current backtrack count
 

aligner_0mm.h

@@ -39,6 +39,7 @@ class UnpairedExactAlignerV1Factory : public AlignerFactory {
 			bool strandFix,
 			bool rangeMode,
 			bool verbose,
+			bool quiet,
 			uint32_t seed) :
 			ebwtFw_(ebwtFw),
 			ebwtBw_(ebwtBw),
@@ -55,6 +56,7 @@ class UnpairedExactAlignerV1Factory : public AlignerFactory {
 			strandFix_(strandFix),
 			rangeMode_(rangeMode),
 			verbose_(verbose),
+			quiet_(quiet),
 			seed_(seed)
 	{
 		assert(ebwtFw.isInMemory());
@@ -107,7 +109,7 @@ class UnpairedExactAlignerV1Factory : public AlignerFactory {
 		return new UnpairedAlignerV2<EbwtRangeSource>(
 			params, dr, rchase,
 			sink_, sinkPtFactory_, sinkPt, os_, rangeMode_, verbose_,
-			INT_MAX, pool_, NULL, NULL);
+			quiet_, INT_MAX, pool_, NULL, NULL);
 	}
 
 private:
@@ -127,6 +129,7 @@ class UnpairedExactAlignerV1Factory : public AlignerFactory {
 	bool strandFix_;
 	bool rangeMode_;
 	bool verbose_;
+	bool quiet_;
 	uint32_t seed_;
 };
 
@@ -166,6 +169,7 @@ class PairedExactAlignerV1Factory : public AlignerFactory {
 			bool qualOrder,
 			bool rangeMode,
 			bool verbose,
+			bool quiet,
 			uint32_t seed) :
 			ebwtFw_(ebwtFw),
 			doFw_(doFw),
@@ -192,6 +196,7 @@ class PairedExactAlignerV1Factory : public AlignerFactory {
 			strandFix_(strandFix),
 			rangeMode_(rangeMode),
 			verbose_(verbose),
+			quiet_(quiet),
 			seed_(seed)
 	{
 		assert(ebwtFw.isInMemory());
@@ -312,7 +317,7 @@ class PairedExactAlignerV1Factory : public AlignerFactory {
 				refAligner,
 				rchase, sink_, sinkPtFactory_, sinkPt, mate1fw_, mate2fw_,
 				peInner_, peOuter_, dontReconcile_, symCeil_, mixedThresh_,
-				mixedAttemptLim_, refs_, rangeMode_, verbose_,
+				mixedAttemptLim_, refs_, rangeMode_, verbose_, quiet_,
 				INT_MAX, pool_, NULL);
 			return al;
 		} else {
@@ -328,7 +333,7 @@ class PairedExactAlignerV1Factory : public AlignerFactory {
 				rchase, sink_, sinkPtFactory_, sinkPt,
 				sinkPtSe1, sinkPtSe2, mate1fw_, mate2fw_,
 				peInner_, peOuter_,
-				mixedAttemptLim_, refs_, rangeMode_, verbose_,
+				mixedAttemptLim_, refs_, rangeMode_, verbose_, quiet_,
 				INT_MAX, pool_, NULL);
 			delete drVec;
 			return al;
@@ -363,6 +368,7 @@ class PairedExactAlignerV1Factory : public AlignerFactory {
 	const bool strandFix_;
 	const bool rangeMode_;
 	const bool verbose_;
+	const bool quiet_;
 	const uint32_t seed_;
 };
 

aligner_1mm.h

@@ -39,6 +39,7 @@ class Unpaired1mmAlignerV1Factory : public AlignerFactory {
 			bool strandFix,
 			bool rangeMode,
 			bool verbose,
+			bool quiet,
 			uint32_t seed) :
 			ebwtFw_(ebwtFw),
 			ebwtBw_(ebwtBw),
@@ -56,6 +57,7 @@ class Unpaired1mmAlignerV1Factory : public AlignerFactory {
 			strandFix_(strandFix),
 			rangeMode_(rangeMode),
 			verbose_(verbose),
+			quiet_(quiet),
 			seed_(seed)
 	{
 		assert(ebwtFw.isInMemory());
@@ -144,7 +146,7 @@ class Unpaired1mmAlignerV1Factory : public AlignerFactory {
 		return new UnpairedAlignerV2<EbwtRangeSource>(
 			params, dr, rchase,
 			sink_, sinkPtFactory_, sinkPt, os_, rangeMode_, verbose_,
-			INT_MAX, pool_, NULL, NULL);
+			quiet_, INT_MAX, pool_, NULL, NULL);
 	}
 
 private:
@@ -164,6 +166,7 @@ class Unpaired1mmAlignerV1Factory : public AlignerFactory {
 	bool strandFix_;
 	bool rangeMode_;
 	bool verbose_;
+	bool quiet_;
 	uint32_t seed_;
 };
 
@@ -203,6 +206,7 @@ class Paired1mmAlignerV1Factory : public AlignerFactory {
 			bool strandFix,
 			bool rangeMode,
 			bool verbose,
+			bool quiet,
 			uint32_t seed) :
 			ebwtFw_(ebwtFw),
 			ebwtBw_(ebwtBw),
@@ -230,6 +234,7 @@ class Paired1mmAlignerV1Factory : public AlignerFactory {
 			strandFix_(strandFix),
 			rangeMode_(rangeMode),
 			verbose_(verbose),
+			quiet_(quiet),
 			seed_(seed)
 	{
 		assert(ebwtBw != NULL);
@@ -424,7 +429,7 @@ class Paired1mmAlignerV1Factory : public AlignerFactory {
 				refAligner, rchase,
 				sink_, sinkPtFactory_, sinkPt, mate1fw_, mate2fw_,
 				peInner_, peOuter_, dontReconcile_, symCeil_, mixedThresh_,
-				mixedAttemptLim_, refs_, rangeMode_, verbose_,
+				mixedAttemptLim_, refs_, rangeMode_, verbose_, quiet_,
 				INT_MAX, pool_, NULL);
 			delete dr1FwVec;
 			delete dr1RcVec;
@@ -440,7 +445,7 @@ class Paired1mmAlignerV1Factory : public AlignerFactory {
 				sinkPt, sinkPtSe1, sinkPtSe2,
 				mate1fw_, mate2fw_,
 				peInner_, peOuter_,
-				mixedAttemptLim_, refs_, rangeMode_, verbose_,
+				mixedAttemptLim_, refs_, rangeMode_, verbose_, quiet_,
 				INT_MAX, pool_, NULL);
 			delete dr1FwVec;
 			return al;
@@ -475,6 +480,7 @@ class Paired1mmAlignerV1Factory : public AlignerFactory {
 	const bool strandFix_;
 	const bool rangeMode_;
 	const bool verbose_;
+	const bool quiet_;
 	const uint32_t seed_;
 };
 

aligner_23mm.h

@@ -40,6 +40,7 @@ class Unpaired23mmAlignerV1Factory : public AlignerFactory {
 			bool strandFix,
 			bool rangeMode,
 			bool verbose,
+			bool quiet,
 			uint32_t seed) :
 			ebwtFw_(ebwtFw),
 			ebwtBw_(ebwtBw),
@@ -57,6 +58,7 @@ class Unpaired23mmAlignerV1Factory : public AlignerFactory {
 			strandFix_(strandFix),
 			rangeMode_(rangeMode),
 			verbose_(verbose),
+			quiet_(quiet),
 			seed_(seed)
 	{
 		assert(ebwtFw.isInMemory());
@@ -213,7 +215,7 @@ class Unpaired23mmAlignerV1Factory : public AlignerFactory {
 		return new UnpairedAlignerV2<EbwtRangeSource>(
 			params, dr, rchase,
 			sink_, sinkPtFactory_, sinkPt, os_, rangeMode_, verbose_,
-			INT_MAX, pool_, NULL, NULL);
+			quiet_, INT_MAX, pool_, NULL, NULL);
 	}
 
 private:
@@ -234,6 +236,7 @@ class Unpaired23mmAlignerV1Factory : public AlignerFactory {
 	const bool strandFix_;
 	const bool rangeMode_;
 	const bool verbose_;
+	const bool quiet_;
 	uint32_t seed_;
 };
 
@@ -275,6 +278,7 @@ class Paired23mmAlignerV1Factory : public AlignerFactory {
 			bool strandFix,
 			bool rangeMode,
 			bool verbose,
+			bool quiet,
 			uint32_t seed) :
 			ebwtFw_(ebwtFw),
 			ebwtBw_(ebwtBw),
@@ -303,6 +307,7 @@ class Paired23mmAlignerV1Factory : public AlignerFactory {
 			strandFix_(strandFix),
 			rangeMode_(rangeMode),
 			verbose_(verbose),
+			quiet_(quiet),
 			seed_(seed)
 	{
 		assert(ebwtBw != NULL);
@@ -621,7 +626,7 @@ class Paired23mmAlignerV1Factory : public AlignerFactory {
 				refAligner, rchase,
 				sink_, sinkPtFactory_, sinkPt, mate1fw_, mate2fw_,
 				peInner_, peOuter_, dontReconcile_, symCeil_, mixedThresh_,
-				mixedAttemptLim_, refs_, rangeMode_, verbose_,
+				mixedAttemptLim_, refs_, rangeMode_, verbose_, quiet_,
 				INT_MAX, pool_, NULL);
 			delete dr1FwVec;
 			delete dr1RcVec;
@@ -637,7 +642,7 @@ class Paired23mmAlignerV1Factory : public AlignerFactory {
 				sinkPt, sinkPtSe1, sinkPtSe2,
 				mate1fw_, mate2fw_,
 				peInner_, peOuter_,
-				mixedAttemptLim_, refs_, rangeMode_, verbose_,
+				mixedAttemptLim_, refs_, rangeMode_, verbose_, quiet_,
 				INT_MAX, pool_, NULL);
 			delete dr1FwVec;
 			return al;
@@ -673,6 +678,7 @@ class Paired23mmAlignerV1Factory : public AlignerFactory {
 	const bool strandFix_;
 	const bool rangeMode_;
 	const bool verbose_;
+	const bool quiet_;
 	const uint32_t seed_;
 };