Nilesh Patra pushed to branch upstream at Debian Med / last-align
Commits: e070a325 by Nilesh Patra at 2020-12-19T16:19:02+05:30 New upstream version 1168 - - - - - 4 changed files: - ChangeLog.txt - src/Alignment.cc - src/lastal.cc - src/version.hh Changes: ===================================== ChangeLog.txt ===================================== @@ -1,9 +1,16 @@ +2020-12-15 Martin C. Frith <Martin C. Frith> + + * src/Alignment.cc, src/lastal.cc, test/last-test.out, test/last- + test.sh: + New frameshifts: fix print precision of score + [abed5cbf2f29] [tip] + 2020-12-11 Martin C. Frith <Martin C. Frith> * src/GeneticCode.cc, src/GeneticCode.hh, src/lastal.cc, test/last- test.out, test/last-test.sh: Better rep-masking for codons & new frameshifts - [c1fbf7da4f68] [tip] + [c1fbf7da4f68] * src/GappedXdropAlignerFrame.cc, src/GeneticCode.cc, src/GeneticCode.hh, src/lastal.cc: ===================================== src/Alignment.cc ===================================== @@ -51,12 +51,7 @@ void Alignment::makeXdrop( Aligners &aligners, bool isGreedy, const Alphabet& alph, AlignmentExtras& extras, double gamma, int outputType ){ score = seed.score; - - if (gap.isNewFrameshifts()) { - extras.fullScore = -1; // means that "score" is (non-integer) fullScore - } else if (outputType > 3) { - extras.fullScore = seed.score; - } + if (outputType > 3 && !gap.isNewFrameshifts()) extras.fullScore = seed.score; if( outputType == 7 ){ assert( seed.size > 0 ); // makes things easier to understand ===================================== src/lastal.cc ===================================== @@ -808,8 +808,7 @@ void alignFinish( LastAligner& aligner, const AlignmentPot& gappedAlns, } centroid.setPssm(dis.p, queryLen, args.temperature, matrices.oneQualExp, dis.b, dis.j); - } - else{ + } else { centroid.setScoreMatrix( dis.m, args.temperature ); } centroid.setOutputType( args.outputType ); @@ -817,12 +816,12 @@ void alignFinish( LastAligner& aligner, const AlignmentPot& gappedAlns, for( size_t i = 0; i < gappedAlns.size(); ++i ){ const Alignment& aln = gappedAlns.items[i]; + AlignmentExtras extras; + if (isFullScoreThreshold()) extras.fullScore = -1; // score is fullScore if( args.outputType < 4 ){ - writeAlignment( aligner, aln, queryNum, querySeq ); - } - else{ // calculate match probabilities: + writeAlignment(aligner, aln, queryNum, querySeq, extras); + } else { // calculate match probabilities: Alignment probAln; - AlignmentExtras extras; probAln.seed = aln.seed; probAln.makeXdrop(aligner.engines, args.isGreedy, dis.a, dis.b, args.globality, dis.m, @@ -830,8 +829,8 @@ void alignFinish( LastAligner& aligner, const AlignmentPot& gappedAlns, dis.r, matrices.stats.lambda(), gapCosts, dis.d, frameSize, dis.p, dis.t, dis.i, dis.j, alph, extras, args.gamma, args.outputType); - assert( aln.score != -INF ); - writeAlignment( aligner, probAln, queryNum, querySeq, extras ); + assert(aln.score != -INF); + writeAlignment(aligner, probAln, queryNum, querySeq, extras); } } } @@ -1128,7 +1127,7 @@ void readIndex( const std::string& baseName, indexT seqCount ) { if( numOfIndexes > 1 ){ suffixArrays[x].fromFiles(baseName + char('a' + x), isCaseSensitiveSeeds, alph.encode, alph.letters); - }else{ + } else { suffixArrays[x].fromFiles(baseName, isCaseSensitiveSeeds, alph.encode, alph.letters); } @@ -1221,8 +1220,7 @@ void writeHeader( countT refSequences, countT refLetters, std::ostream& out ){ if( args.outputType == 0 ){ // we just want hit counts out << "# length\tcount\n" << "#\n"; - } - else{ // we want alignments + } else { // we want alignments if( args.inputFormat != sequenceFormat::pssm || !args.matrixFile.empty() ){ // we're not reading PSSMs, or we bothered to specify a matrix file scoreMatrix.writeCommented( out ); @@ -1382,7 +1380,7 @@ void lastal( int argc, char** argv ){ args.isKeepLowercase, args.maskLowercase > 1)) { if( query.isFinished() ){ ++sequenceCount; - }else{ + } else { // this enables downstream parsers to read one batch at a time: out << "# batch " << queryBatchCount++ << "\n"; scanAllVolumes( volumes, out ); ===================================== src/version.hh ===================================== @@ -1 +1 @@ -"1167" +"1168" View it on GitLab: https://salsa.debian.org/med-team/last-align/-/commit/e070a325a2355129a990c43d957ba77e7bc86c10 -- View it on GitLab: https://salsa.debian.org/med-team/last-align/-/commit/e070a325a2355129a990c43d957ba77e7bc86c10 You're receiving this email because of your account on salsa.debian.org.
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