[med-svn] [Git][med-team/last-align][upstream] New upstream version 1168

[Nilesh Patra]

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

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View it on GitLab: https://salsa.debian.org/med-team/last-align/-/commit/e070a325a2355129a990c43d957ba77e7bc86c10
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