/dports/biology/bbmap/bbmap/current/aligner/ |
H A D | Aligner.java | 7 int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minScore); in fillLimited() argument 11 int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc); in fillUnlimited() argument 15 int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minScore); in fillUnlimited() argument 18 …byte[] traceback(byte[] query, byte[] ref, int refStartLoc, int refEndLoc, int row, int col, int s… in traceback() argument 22 …float tracebackIdentity(byte[] query, byte[] ref, int refStartLoc, int refEndLoc, int row, int col… in tracebackIdentity() argument 25 int[] score(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int maxRow, int maxCol, in score() argument 30 int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minScore); in fillAndScoreLimited() argument
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H A D | SingleStateAlignerFlat2Amino.java | 79 return fillUnlimited(read, ref, refStartLoc, refEndLoc, minScore); in fillLimited() 84 return fillUnlimited(read, ref, refStartLoc, refEndLoc, -999999); in fillUnlimited() 91 initialize(read.length, refEndLoc-refStartLoc+1); in fillUnlimited() 102 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… in fillUnlimited() 192 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; in traceback() local 266 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; in tracebackIdentity() local 336 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; in tracebackIdentityAmino() local 433 assert(refStartLoc<=refEndLoc); in score() 472 int padRight=Tools.max(0, bestRefStop-refEndLoc); in score() 486 int b=Tools.min(ref.length-1, refEndLoc); in fillAndScoreLimited() [all …]
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H A D | SingleStateAlignerFlat.java | 95 return fillUnlimited(read, ref, refStartLoc, refEndLoc, minScore); in fillLimited() 99 public final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc){ in fillUnlimited() argument 100 return fillUnlimited(read, ref, refStartLoc, refEndLoc, -999999); in fillUnlimited() 107 initialize(read.length, refEndLoc-refStartLoc+1); in fillUnlimited() 118 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… in fillUnlimited() 193 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 265 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 362 assert(refStartLoc<=refEndLoc); 402 int padRight=Tools.max(0, bestRefStop-refEndLoc); 416 int b=Tools.min(ref.length-1, refEndLoc); [all …]
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H A D | SingleStateAlignerFlat2.java | 80 return fillUnlimited(read, ref, refStartLoc, refEndLoc, minScore); in fillLimited() 84 public final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc){ in fillUnlimited() argument 85 return fillUnlimited(read, ref, refStartLoc, refEndLoc, -999999); in fillUnlimited() 92 initialize(read.length, refEndLoc-refStartLoc+1); in fillUnlimited() 103 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… in fillUnlimited() 195 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; in traceback() local 268 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; in tracebackIdentity() local 365 assert(refStartLoc<=refEndLoc); in score() 404 int padRight=Tools.max(0, bestRefStop-refEndLoc); in score() 418 int b=Tools.min(ref.length-1, refEndLoc); in fillAndScoreLimited() [all …]
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H A D | SingleStateAlignerFlat3.java | 80 return fillUnlimited(read, ref, refStartLoc, refEndLoc, minScore); in fillLimited() 84 public final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc){ in fillUnlimited() argument 85 return fillUnlimited(read, ref, refStartLoc, refEndLoc, -999999); in fillUnlimited() 92 initialize(read.length, refEndLoc-refStartLoc+1); in fillUnlimited() 103 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… in fillUnlimited() 194 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; in traceback() local 266 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; in tracebackIdentity() local 363 assert(refStartLoc<=refEndLoc); in score() 402 int padRight=Tools.max(0, bestRefStop-refEndLoc); in score() 416 int b=Tools.min(ref.length-1, refEndLoc); in fillAndScoreLimited() [all …]
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H A D | SingleStateAlignerPacBioAdapter.java | 69 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited() argument 70 return fillLimitedX(read, ref, refStartLoc, refEndLoc, minScore); in fillLimited() 77 return fillUnlimited(read, ref, refStartLoc, refEndLoc, minScore); in fillLimitedX() 85 columns=refEndLoc-refStartLoc+1; in fillUnlimited() 96 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… in fillUnlimited() 169 public final byte[] traceback(int refStartLoc, int refEndLoc, int row, int col, int state){ 171 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 255 assert(refStartLoc<=refEndLoc); 289 int padRight=Tools.max(0, bestRefStop-refEndLoc); 302 int b=Tools.min(ref.length-1, refEndLoc); [all …]
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H A D | SingleStateAlignerFlatFloat.java | 80 return fillUnlimited(read, ref, refStartLoc, refEndLoc, minScore); in fillLimited() 84 public final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc){ in fillUnlimited() argument 85 return fillUnlimited(read, ref, refStartLoc, refEndLoc, -999999); in fillUnlimited() 92 initialize(read.length, refEndLoc-refStartLoc+1); in fillUnlimited() 105 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… in fillUnlimited() 230 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; in traceback() local 305 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; in tracebackIdentity() local 404 assert(refStartLoc<=refEndLoc); in score() 445 int padRight=Tools.max(0, bestRefStop-refEndLoc); in score() 459 int b=Tools.min(ref.length-1, refEndLoc); in fillAndScoreLimited() [all …]
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H A D | SingleStateAlignerFlat2_1D.java | 68 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited() argument 69 return fillUnlimited(read, ref, refStartLoc, refEndLoc, minScore); in fillLimited() 73 public final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc){ in fillUnlimited() argument 74 return fillUnlimited(read, ref, refStartLoc, refEndLoc, -999999); in fillUnlimited() 81 initialize(read.length, refEndLoc-refStartLoc+1); in fillUnlimited() 89 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… in fillUnlimited() 180 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; in traceback() local 252 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; in tracebackIdentity() local 345 assert(refStartLoc<=refEndLoc); in score() 384 int padRight=Tools.max(0, bestRefStop-refEndLoc); in score() [all …]
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H A D | MultiStateAligner9PacBioAdapter_WithBarriers.java | 130 columns=refEndLoc-refStartLoc+1; in fillLimitedX() 150 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… in fillLimitedX() 576 columns=refEndLoc-refStartLoc+1; in fillUnlimited() 594 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… in fillUnlimited() 829 columns=refEndLoc-refStartLoc+1; 1047 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 1244 assert(refStartLoc<=refEndLoc); 1328 int b=Tools.min(ref.length-1, refEndLoc); 1472 assert(refEndLoc>=gaps[gaps.length-1]); 1550 assert(gref[gpos-1]==ref[refEndLoc]); [all …]
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H A D | MultiStateAligner9PacBioAdapter2.java | 149 initialize(read.length, refEndLoc-refStartLoc+1); in fillLimitedX() 165 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… in fillLimitedX() 573 initialize(read.length, refEndLoc-refStartLoc+1); in fillUnlimited() 588 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… in fillUnlimited() 805 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 920 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 1042 assert(refStartLoc<=refEndLoc); 1113 int padRight=Tools.max(0, bestRefStop-refEndLoc); 1126 initialize(read.length, refEndLoc-refStartLoc+1); 1128 int b=Tools.min(ref.length-1, refEndLoc); [all …]
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H A D | MultiStateAligner9PacBioAdapter.java | 83 return fillLimitedX(read, ref, refStartLoc, refEndLoc, minScore); in fillLimited() 93 columns=refEndLoc-refStartLoc+1; in fillLimitedX() 97 return fillUnlimited(read, ref, refStartLoc, refEndLoc, minScore); in fillLimitedX() 109 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… in fillLimitedX() 501 columns=refEndLoc-refStartLoc+1; in fillUnlimited() 516 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… in fillUnlimited() 723 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 863 assert(refStartLoc<=refEndLoc); 934 int padRight=Tools.max(0, bestRefStop-refEndLoc); 947 int b=Tools.min(ref.length-1, refEndLoc); [all …]
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H A D | MultiStateAligner9PacBioAdapter3.java | 79 return fillLimitedX(read, ref, refStartLoc, refEndLoc, minScore); in fillLimited() 89 columns=refEndLoc-refStartLoc+1; in fillLimitedX() 93 return fillUnlimited(read, ref, refStartLoc, refEndLoc); in fillLimitedX() 105 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… in fillLimitedX() 494 columns=refEndLoc-refStartLoc+1; in fillUnlimited() 509 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… in fillUnlimited() 729 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 869 assert(refStartLoc<=refEndLoc); in score() 940 int padRight=Tools.max(0, bestRefStop-refEndLoc); in score() 953 int b=Tools.min(ref.length-1, refEndLoc); in fillAndScoreLimited() [all …]
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/dports/biology/bbmap/bbmap/current/align2/ |
H A D | MultiStateAligner11tsJNI.java | 78 byte[] gref=makeGref(ref, gaps, refStartLoc, refEndLoc); in fillLimited() 94 columns=refEndLoc-refStartLoc+1; in fillLimitedX() 159 columns=refEndLoc-refStartLoc+1; in fillQ() 165 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… in fillQ() 337 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 525 assert(refStartLoc<=refEndLoc); 605 if(bestRefStop>refEndLoc){ 606 padRight=Tools.max(0, bestRefStop-refEndLoc); 632 assert(refEndLoc>=gaps[gaps.length-1]); 637 gaps[gaps.length-1]=Tools.max(gN_old, refEndLoc); [all …]
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H A D | MultiStateAligner11ts.java | 117 columns=refEndLoc-refStartLoc+1; in fillLimitedX() 142 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… in fillLimitedX() 632 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… in fillUnlimited() 927 columns=refEndLoc-refStartLoc+1; in fillQ() 933 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… in fillQ() 1148 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 1349 assert(refStartLoc<=refEndLoc); 1433 if(bestRefStop>refEndLoc){ 1434 padRight=Tools.max(0, bestRefStop-refEndLoc); 1460 assert(refEndLoc>=gaps[gaps.length-1]); [all …]
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H A D | MultiStateAligner9XFlat.java | 113 columns=refEndLoc-refStartLoc+1; in fillLimitedX() 138 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… in fillLimitedX() 598 columns=refEndLoc-refStartLoc+1; in fillUnlimited() 617 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… in fillUnlimited() 848 columns=refEndLoc-refStartLoc+1; 854 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… 1061 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 1262 assert(refStartLoc<=refEndLoc); 1346 if(bestRefStop>refEndLoc){ 1373 assert(refEndLoc>=gaps[gaps.length-1]); [all …]
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H A D | MultiStateAligner9ts.java | 109 columns=refEndLoc-refStartLoc+1; in fillLimitedX() 134 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… in fillLimitedX() 584 columns=refEndLoc-refStartLoc+1; in fillUnlimited() 603 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… in fillUnlimited() 839 columns=refEndLoc-refStartLoc+1; 845 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… 1057 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 1258 assert(refStartLoc<=refEndLoc); 1349 assert(refEndLoc>=gaps[gaps.length-1]); 1354 gaps[gaps.length-1]=Tools.max(gN_old, refEndLoc); [all …]
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H A D | MultiStateAligner9Flat.java | 114 columns=refEndLoc-refStartLoc+1; in fillLimitedX() 139 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… in fillLimitedX() 604 columns=refEndLoc-refStartLoc+1; in fillUnlimited() 623 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… in fillUnlimited() 859 columns=refEndLoc-refStartLoc+1; 865 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… 1077 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 1278 assert(refStartLoc<=refEndLoc); 1362 if(bestRefStop>refEndLoc){ 1389 assert(refEndLoc>=gaps[gaps.length-1]); [all …]
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H A D | MultiStateAligner9PacBio.java | 114 columns=refEndLoc-refStartLoc+1; in fillLimitedX() 139 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… in fillLimitedX() 604 columns=refEndLoc-refStartLoc+1; in fillUnlimited() 623 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… in fillUnlimited() 859 columns=refEndLoc-refStartLoc+1; 865 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… 1077 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 1278 assert(refStartLoc<=refEndLoc); 1362 if(bestRefStop>refEndLoc){ 1389 assert(refEndLoc>=gaps[gaps.length-1]); [all …]
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H A D | MultiStateAligner10ts.java | 129 columns=refEndLoc-refStartLoc+1; in fillLimitedX() 151 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… in fillLimitedX() 603 columns=refEndLoc-refStartLoc+1; in fillBanded1() 1069 columns=refEndLoc-refStartLoc+1; 1554 columns=refEndLoc-refStartLoc+1; 1572 …assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+re… 1808 columns=refEndLoc-refStartLoc+1; 2028 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 2227 assert(refStartLoc<=refEndLoc); 2318 assert(refEndLoc>=gaps[gaps.length-1]); [all …]
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H A D | NeedlemanWunsch.java | 49 public void fill(byte[] read, byte[] ref, int refStartLoc, int refEndLoc){ in fill() argument 51 columns=refEndLoc-refStartLoc+1; in fill() 76 public byte[] traceback(byte[] read, byte[] ref, int refStartLoc, int refEndLoc){ in traceback() argument
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H A D | MSA.java | 53 …public abstract int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int min… in fillLimited() argument 58 …public abstract int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int[]… in fillUnlimited() argument 62 …c abstract int[] fillQ(byte[] read, byte[] ref, byte[] baseScores, int refStartLoc, int refEndLoc); in fillQ() argument 71 …public abstract byte[] traceback2(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int row… in traceback2() argument 74 …stract int[] score(final byte[] read, final byte[] ref, final int refStartLoc, final int refEndLoc, in score() argument 78 …tract int[] score2(final byte[] read, final byte[] ref, final int refStartLoc, final int refEndLoc, in score2() argument 84 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in… in fillAndScoreLimited() argument 86 int b=Tools.min(ref.length-1, refEndLoc); in fillAndScoreLimited() 102 assert(false) : refStartLoc+", "+refEndLoc; in fillAndScoreLimited() local 128 …public final int[] fillAndScoreQ(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, byte[] b… in fillAndScoreQ() argument [all …]
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/dports/biology/bbmap/bbmap/jni/ |
H A D | MultiStateAligner11tsJNI.c | 106 jint refEndLoc, in fillUnlimited() argument 117 const jint columns=refEndLoc-refStartLoc+1; in fillUnlimited() 367 jint refEndLoc, in fillLimitedX() argument 385 const jint columns=refEndLoc-refStartLoc+1; in fillLimitedX() 713 jint refEndLoc, in Java_align2_MultiStateAligner11tsJNI_fillUnlimitedJNI() argument 739 …fillUnlimited(jread,jref,read_length,ref_length,refStartLoc,refEndLoc,jresult,iterationsUnlimitedP… in Java_align2_MultiStateAligner11tsJNI_fillUnlimitedJNI() 759 jint refEndLoc, in Java_align2_MultiStateAligner11tsJNI_fillLimitedXJNI() argument 796 …fillLimitedX(jread,jref,read_length,ref_length,refStartLoc,refEndLoc,minScore,jresult,iterationsLi… in Java_align2_MultiStateAligner11tsJNI_fillLimitedXJNI()
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