| /dports/biology/bbmap/bbmap/current/align2/ |
| H A D | AbstractMapThread.java | 1103 …ad r, final byte[] basesP, final byte[] basesM, final int maxSwScore, final int maxImperfectScore){ in findTipDeletions() argument
1117 if(!ss.semiperfect && ss.slowScore<maxImperfectScore){ in findTipDeletions()
1118 boolean changed=findTipDeletions(ss, bases, maxImperfectScore, findRight, findLeft); in findTipDeletions()
1135 …final boolean findTipDeletions(SiteScore ss, final byte[] bases, final int maxImperfectScore, bool… in findTipDeletions() argument
1136 if(ss.slowScore>=maxImperfectScore /*&& ss.stop()-ss.start()<=basesP.length-1*/){return false;} in findTipDeletions()
1186 final int maxImperfectScore=msa.maxImperfectScore(basesP.length); in rescue() local
1202 final boolean findTipDeletions=FIND_TIP_DELETIONS && bestLooseScore<maxImperfectScore; in rescue()
1254 slowRescue(bases, ss, maxLooseSwScore, maxImperfectScore, findRight, findLeft); in rescue()
1274 … void slowRescue(final byte[] bases, SiteScore ss, final int maxScore, final int maxImperfectScore, in slowRescue() argument
1280 if(swscoreNoIndel<maxImperfectScore && MAX_INDEL>0){ in slowRescue()
[all …]
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| H A D | MSA.java | 550 public abstract int maxImperfectScore(int numBases); in maxImperfectScore() method in MSA
552 public abstract int maxImperfectScore(byte[] baseScores); in maxImperfectScore() method in MSA
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| H A D | BBMapThread5.java | 418 maxImperfectSwScore=msa.maxImperfectScore(r.length()); in processRead()
921 final int maxImperfectSwScore1=msa.maxImperfectScore(len1); in processReadPair()
923 final int maxImperfectSwScore2=msa.maxImperfectScore(len2); in processReadPair()
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| H A D | BBMapThreadPacBio.java | 419 maxImperfectSwScore=msa.maxImperfectScore(r.length()); in processRead()
926 final int maxImperfectSwScore1=msa.maxImperfectScore(len1); in processReadPair()
928 final int maxImperfectSwScore2=msa.maxImperfectScore(len2); in processReadPair()
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| H A D | BBMapThread.java | 425 maxImperfectSwScore=msa.maxImperfectScore(r.length()); in processRead()
988 final int maxImperfectSwScore1=msa.maxImperfectScore(len1); in processReadPair()
990 final int maxImperfectSwScore2=msa.maxImperfectScore(len2); in processReadPair()
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| H A D | BBMapThreadAcc.java | 464 maxImperfectSwScore=msa.maxImperfectScore(r.length()); in processRead()
1022 final int maxImperfectSwScore1=msa.maxImperfectScore(len1); in processReadPair()
1024 final int maxImperfectSwScore2=msa.maxImperfectScore(len2); in processReadPair()
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| H A D | BBMapThreadPacBioSkimmer.java | 768 maxImperfectSwScore=msa.maxImperfectScore(r.length()); in processRead()
1291 final int maxImperfectSwScore1=msa.maxImperfectScore(len1); in processReadPair()
1293 final int maxImperfectSwScore2=msa.maxImperfectScore(len2); in processReadPair()
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| H A D | MultiStateAligner11tsJNI.java | 1291 public final int maxImperfectScore(int numBases){
1299 public final int maxImperfectScore(byte[] baseScores){
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| H A D | MultiStateAligner11ts.java | 2258 public final int maxImperfectScore(int numBases){
2272 public final int maxImperfectScore(byte[] baseScores){
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| H A D | MultiStateAligner9XFlat.java | 2092 public final int maxImperfectScore(int numBases){
2106 public final int maxImperfectScore(byte[] baseScores){
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| H A D | MultiStateAligner9ts.java | 2131 public final int maxImperfectScore(int numBases){
2145 public final int maxImperfectScore(byte[] baseScores){
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| H A D | MultiStateAligner9Flat.java | 2176 public final int maxImperfectScore(int numBases){
2190 public final int maxImperfectScore(byte[] baseScores){
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| H A D | MultiStateAligner9PacBio.java | 2176 public final int maxImperfectScore(int numBases){
2190 public final int maxImperfectScore(byte[] baseScores){
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| H A D | TranslateColorspaceRead.java | 96 final int maxI=msa.maxImperfectScore(r.length()); in realignByReversingRef()
312 final int maxI=msa.maxImperfectScore(bases.length); in realign_new()
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| H A D | MultiStateAligner10ts.java | 3298 public final int maxImperfectScore(int numBases){
3312 public final int maxImperfectScore(byte[] baseScores){
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| /dports/biology/bbmap/bbmap/current/aligner/ |
| H A D | MultiStateAligner9PacBioAdapter.java | 1273 public static final int maxImperfectScore(int numBases){
1286 public static final int maxImperfectScore(byte[] baseScores){
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| H A D | MultiStateAligner9PacBioAdapter2.java | 1456 public static final int maxImperfectScore(int numBases){
1469 public static final int maxImperfectScore(byte[] baseScores){
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| H A D | MultiStateAligner9PacBioAdapter3.java | 1279 public static final int maxImperfectScore(int numBases){ in maxImperfectScore() method
1292 public static final int maxImperfectScore(byte[] baseScores){
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| H A D | MultiStateAligner9PacBioAdapter_WithBarriers.java | 2258 public static final int maxImperfectScore(int numBases){
2271 public static final int maxImperfectScore(byte[] baseScores){
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| /dports/biology/bbmap/bbmap/current/pacbio/ |
| H A D | RemoveAdapters3.java | 266 maxImperfectSwScore=msa.maxImperfectScore(query1.length); in ProcessThread()
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| H A D | RemoveAdapters2.java | 289 maxImperfectSwScore=msa.maxImperfectScore(query1.length); in ProcessThread()
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| /dports/biology/bbmap/bbmap/current/icecream/ |
| H A D | IceCreamFinder.java | 140 maxImperfectSwScore=aligner.MultiStateAligner9PacBioAdapter.maxImperfectScore(alen); in IceCreamFinder()
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