Nilesh Patra pushed to branch master at Debian Med / last-align
Commits:
68e69904 by Nilesh Patra at 2020-12-19T16:18:11+05:30
Add myself to uploaders
- - - - -
7e19ec01 by Nilesh Patra at 2020-12-19T16:19:01+05:30
routine-update: New upstream version
- - - - -
e070a325 by Nilesh Patra at 2020-12-19T16:19:02+05:30
New upstream version 1168
- - - - -
42e9b079 by Nilesh Patra at 2020-12-19T16:19:04+05:30
Update upstream source from tag 'upstream/1168'
Update to upstream version '1168'
with Debian dir 1ca25d700028731e7b63a0288aba7786594c3602
- - - - -
bdbe013d by Nilesh Patra at 2020-12-19T16:19:45+05:30
routine-update: Ready to upload to unstable
- - - - -
6 changed files:
- ChangeLog.txt
- debian/changelog
- debian/control
- 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:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+last-align (1168-1) unstable; urgency=medium
+
+ * New upstream version
+
+ -- Nilesh Patra <[email protected]> Sat, 19 Dec 2020 16:19:45 +0530
+
last-align (1167-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -1,7 +1,8 @@
Source: last-align
Maintainer: Debian Med Packaging Team
<[email protected]>
Uploaders: Charles Plessy <[email protected]>,
- Andreas Tille <[email protected]>
+ Andreas Tille <[email protected]>,
+ Nilesh Patra <[email protected]>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
=====================================
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/-/compare/e4dd67552cc8676aac4146d838288851e1c243cb...bdbe013d86b97d323468dc44bef2bfafaa6767dc
--
View it on GitLab:
https://salsa.debian.org/med-team/last-align/-/compare/e4dd67552cc8676aac4146d838288851e1c243cb...bdbe013d86b97d323468dc44bef2bfafaa6767dc
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