/dports/biology/bbmap/bbmap/current/aligner/ |
H A D | SingleStateAlignerFlat2Amino.java | 101 …assert(refStartLoc>=0) : "Check that values are in-bounds before calling this function: "+refStart… in fillUnlimited() 104 final int refOffset=refStartLoc-1; in fillUnlimited() 192 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; in traceback() 202 byte r=ref[refStartLoc+col-1]; in traceback() 266 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; in tracebackIdentity() 274 byte r=ref[refStartLoc+col-1]; in tracebackIdentity() 336 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; in tracebackIdentityAmino() 344 byte r=ref[refStartLoc+col-1]; in tracebackIdentityAmino() 433 assert(refStartLoc<=refEndLoc); in score() 441 final byte r=ref[refStartLoc+col-1]; in score() [all …]
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H A D | SingleStateAlignerFlat.java | 117 …assert(refStartLoc>=0) : "Check that values are in-bounds before calling this function: "+refStart… in fillUnlimited() 120 final int refOffset=refStartLoc-1; in fillUnlimited() 193 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 203 byte r=ref[refStartLoc+col-1]; 265 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 273 byte r=ref[refStartLoc+col-1]; 362 assert(refStartLoc<=refEndLoc); 366 final int bestRefStop=refStartLoc+col-1; 395 final int bestRefStart=refStartLoc+col; 415 int a=Tools.max(0, refStartLoc); [all …]
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H A D | SingleStateAlignerFlat2.java | 102 …assert(refStartLoc>=0) : "Check that values are in-bounds before calling this function: "+refStart… in fillUnlimited() 105 final int refOffset=refStartLoc-1; in fillUnlimited() 195 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; in traceback() 205 byte r=ref[refStartLoc+col-1]; in traceback() 268 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; in tracebackIdentity() 276 byte r=ref[refStartLoc+col-1]; in tracebackIdentity() 365 assert(refStartLoc<=refEndLoc); in score() 369 final int bestRefStop=refStartLoc+col-1; in score() 373 final byte r=ref[refStartLoc+col-1]; in score() 398 final int bestRefStart=refStartLoc+col; in score() [all …]
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H A D | SingleStateAlignerFlat3.java | 102 …assert(refStartLoc>=0) : "Check that values are in-bounds before calling this function: "+refStart… in fillUnlimited() 105 final int refOffset=refStartLoc-1; in fillUnlimited() 194 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; in traceback() 204 byte r=ref[refStartLoc+col-1]; in traceback() 266 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; in tracebackIdentity() 274 byte r=ref[refStartLoc+col-1]; in tracebackIdentity() 363 assert(refStartLoc<=refEndLoc); in score() 367 final int bestRefStop=refStartLoc+col-1; in score() 371 final byte r=ref[refStartLoc+col-1]; in score() 396 final int bestRefStart=refStartLoc+col; in score() [all …]
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H A D | SingleStateAlignerFlat2_1D.java | 88 …assert(refStartLoc>=0) : "Check that values are in-bounds before calling this function: "+refStart… in fillUnlimited() 91 final int refOffset=refStartLoc-1; in fillUnlimited() 180 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; in traceback() 190 byte r=ref[refStartLoc+col-1]; in traceback() 252 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; in tracebackIdentity() 260 byte r=ref[refStartLoc+col-1]; in tracebackIdentity() 345 assert(refStartLoc<=refEndLoc); in score() 349 final int bestRefStop=refStartLoc+col-1; in score() 353 final byte r=ref[refStartLoc+col-1]; in score() 378 final int bestRefStart=refStartLoc+col; in score() [all …]
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H A D | SingleStateAlignerFlatFloat.java | 104 …assert(refStartLoc>=0) : "Check that values are in-bounds before calling this function: "+refStart… in fillUnlimited() 107 final int refOffset=refStartLoc-1; in fillUnlimited() 230 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; in traceback() 240 int rpos=refStartLoc+col-1; in traceback() 305 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; in tracebackIdentity() 313 int rpos=refStartLoc+col-1; in tracebackIdentity() 404 assert(refStartLoc<=refEndLoc); in score() 408 final int bestRefStop=refStartLoc+col-1; in score() 412 int rpos=refStartLoc+col-1; in score() 439 final int bestRefStart=refStartLoc+col; in score() [all …]
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H A D | SingleStateAlignerPacBioAdapter.java | 70 return fillLimitedX(read, ref, refStartLoc, refEndLoc, minScore); in fillLimited() 85 columns=refEndLoc-refStartLoc+1; in fillUnlimited() 95 …assert(refStartLoc>=0) : "Check that values are in-bounds before calling this function: "+refStart… in fillUnlimited() 98 final int refOffset=refStartLoc-1; in fillUnlimited() 171 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 255 assert(refStartLoc<=refEndLoc); 259 final int bestRefStop=refStartLoc+col-1; 282 final int bestRefStart=refStartLoc+col; 288 int padLeft=Tools.max(0, refStartLoc-bestRefStart); 301 int a=Tools.max(0, refStartLoc); [all …]
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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 | MultiStateAligner9PacBioAdapter_WithBarriers.java | 130 columns=refEndLoc-refStartLoc+1; in fillLimitedX() 576 columns=refEndLoc-refStartLoc+1; in fillUnlimited() 593 …assert(refStartLoc>=0) : "Check that values are in-bounds before calling this function: "+refStart… in fillUnlimited() 829 columns=refEndLoc-refStartLoc+1; 1047 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 1080 byte r=ref[refStartLoc+col-1]; 1105 byte r=ref[refStartLoc+col-1]; 1244 assert(refStartLoc<=refEndLoc); 1327 int a=Tools.max(0, refStartLoc); 1471 assert(refStartLoc<=gaps[0]) : refStartLoc+", "+refEndLoc+", "+Arrays.toString(gaps); [all …]
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H A D | MultiStateAligner9PacBioAdapter2.java | 163 …assert(refStartLoc>=0) : "Check that values are in-bounds before calling this function: "+refStart… in fillLimitedX() 253 final byte ref1=ref[refStartLoc+col-1]; in fillLimitedX() 587 …assert(refStartLoc>=0) : "Check that values are in-bounds before calling this function: "+refStart… in fillUnlimited() 805 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 836 byte r=ref[refStartLoc+col-1]; 861 byte r=ref[refStartLoc+col-1]; 920 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 947 byte r=ref[refStartLoc+col-1]; 1042 assert(refStartLoc<=refEndLoc); 1107 final int bestRefStart=refStartLoc+col; [all …]
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H A D | MultiStateAligner9PacBioAdapter.java | 93 columns=refEndLoc-refStartLoc+1; in fillLimitedX() 107 …assert(refStartLoc>=0) : "Check that values are in-bounds before calling this function: "+refStart… in fillLimitedX() 197 final byte ref1=ref[refStartLoc+col-1]; in fillLimitedX() 501 columns=refEndLoc-refStartLoc+1; in fillUnlimited() 515 …assert(refStartLoc>=0) : "Check that values are in-bounds before calling this function: "+refStart… in fillUnlimited() 723 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 754 byte r=ref[refStartLoc+col-1]; 779 byte r=ref[refStartLoc+col-1]; 863 assert(refStartLoc<=refEndLoc); 928 final int bestRefStart=refStartLoc+col; [all …]
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H A D | MultiStateAligner9PacBioAdapter3.java | 89 columns=refEndLoc-refStartLoc+1; in fillLimitedX() 103 …assert(refStartLoc>=0) : "Check that values are in-bounds before calling this function: "+refStart… in fillLimitedX() 200 final byte ref1=ref[refStartLoc+col-1]; in fillLimitedX() 494 columns=refEndLoc-refStartLoc+1; in fillUnlimited() 508 …assert(refStartLoc>=0) : "Check that values are in-bounds before calling this function: "+refStart… in fillUnlimited() 729 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 760 byte r=ref[refStartLoc+col-1]; 785 byte r=ref[refStartLoc+col-1]; 869 assert(refStartLoc<=refEndLoc); in score() 934 final int bestRefStart=refStartLoc+col; in score() [all …]
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/dports/biology/bbmap/bbmap/current/align2/ |
H A D | MultiStateAligner11ts.java | 117 columns=refEndLoc-refStartLoc+1; in fillLimitedX() 140 …assert(refStartLoc>=0) : "Check that values are in-bounds before calling this function: "+refStart… in fillLimitedX() 201 byte c=ref[refStartLoc+i]; in fillLimitedX() 631 …assert(refStartLoc>=0) : "Check that values are in-bounds before calling this function: "+refStart… in fillUnlimited() 927 columns=refEndLoc-refStartLoc+1; in fillQ() 1148 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 1181 byte r=ref[refStartLoc+col-1]; 1206 byte r=ref[refStartLoc+col-1]; 1349 assert(refStartLoc<=refEndLoc); 1428 if(bestRefStart<refStartLoc){ [all …]
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H A D | MultiStateAligner9XFlat.java | 113 columns=refEndLoc-refStartLoc+1; in fillLimitedX() 136 …assert(refStartLoc>=0) : "Check that values are in-bounds before calling this function: "+refStart… in fillLimitedX() 197 byte c=ref[refStartLoc+i]; in fillLimitedX() 598 columns=refEndLoc-refStartLoc+1; in fillUnlimited() 848 columns=refEndLoc-refStartLoc+1; 1061 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 1094 byte r=ref[refStartLoc+col-1]; 1119 byte r=ref[refStartLoc+col-1]; 1262 assert(refStartLoc<=refEndLoc); 1341 if(bestRefStart<refStartLoc){ [all …]
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H A D | MultiStateAligner11tsJNI.java | 94 columns=refEndLoc-refStartLoc+1; in fillLimitedX() 159 columns=refEndLoc-refStartLoc+1; in fillQ() 164 …assert(refStartLoc>=0) : "Check that values are in-bounds before calling this function: "+refStart… in fillQ() 337 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 364 byte r=ref[refStartLoc+col-1]; 388 byte r=ref[refStartLoc+col-1]; 525 assert(refStartLoc<=refEndLoc); 528 final int bestRefStop=refStartLoc+col-1; 589 final int bestRefStart=refStartLoc+col; 600 if(bestRefStart<refStartLoc){ [all …]
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H A D | MultiStateAligner9ts.java | 109 columns=refEndLoc-refStartLoc+1; in fillLimitedX() 132 …assert(refStartLoc>=0) : "Check that values are in-bounds before calling this function: "+refStart… in fillLimitedX() 189 byte c=ref[refStartLoc+i]; in fillLimitedX() 584 columns=refEndLoc-refStartLoc+1; in fillUnlimited() 602 …assert(refStartLoc>=0) : "Check that values are in-bounds before calling this function: "+refStart… in fillUnlimited() 839 columns=refEndLoc-refStartLoc+1; 1057 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 1090 byte r=ref[refStartLoc+col-1]; 1115 byte r=ref[refStartLoc+col-1]; 1258 assert(refStartLoc<=refEndLoc); [all …]
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H A D | MultiStateAligner10ts.java | 129 columns=refEndLoc-refStartLoc+1; in fillLimitedX() 206 byte c=ref[refStartLoc+i]; in fillLimitedX() 603 columns=refEndLoc-refStartLoc+1; in fillBanded1() 681 byte c=ref[refStartLoc+i]; in fillBanded1() 1069 columns=refEndLoc-refStartLoc+1; 1133 byte c=ref[refStartLoc+i]; 1554 columns=refEndLoc-refStartLoc+1; 1808 columns=refEndLoc-refStartLoc+1; 2028 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 2227 assert(refStartLoc<=refEndLoc); [all …]
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H A D | MultiStateAligner9Flat.java | 114 columns=refEndLoc-refStartLoc+1; in fillLimitedX() 137 …assert(refStartLoc>=0) : "Check that values are in-bounds before calling this function: "+refStart… in fillLimitedX() 198 byte c=ref[refStartLoc+i]; in fillLimitedX() 604 columns=refEndLoc-refStartLoc+1; in fillUnlimited() 859 columns=refEndLoc-refStartLoc+1; 1077 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 1110 byte r=ref[refStartLoc+col-1]; 1135 byte r=ref[refStartLoc+col-1]; 1278 assert(refStartLoc<=refEndLoc); 1357 if(bestRefStart<refStartLoc){ [all …]
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H A D | MultiStateAligner9PacBio.java | 114 columns=refEndLoc-refStartLoc+1; in fillLimitedX() 137 …assert(refStartLoc>=0) : "Check that values are in-bounds before calling this function: "+refStart… in fillLimitedX() 198 byte c=ref[refStartLoc+i]; in fillLimitedX() 604 columns=refEndLoc-refStartLoc+1; in fillUnlimited() 622 …assert(refStartLoc>=0) : "Check that values are in-bounds before calling this function: "+refStart… in fillUnlimited() 859 columns=refEndLoc-refStartLoc+1; 1077 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc; 1110 byte r=ref[refStartLoc+col-1]; 1135 byte r=ref[refStartLoc+col-1]; 1278 assert(refStartLoc<=refEndLoc); [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() 57 int match=(read[row]==ref[refStartLoc+col] ? 1 : -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 …public abstract int[] fillQ(byte[] read, byte[] ref, byte[] baseScores, int refStartLoc, int refEn… in fillQ() argument 71 …public abstract byte[] traceback2(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int row… in traceback2() argument 74 …public abstract int[] score(final byte[] read, final byte[] ref, final int refStartLoc, final int … in score() argument 78 …public abstract int[] score2(final byte[] read, final byte[] ref, final int refStartLoc, final int… in score2() argument 84 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in… in fillAndScoreLimited() argument 85 int a=Tools.max(0, refStartLoc); in fillAndScoreLimited() 102 assert(false) : refStartLoc+", "+refEndLoc; in fillAndScoreLimited() 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 | 105 jint refStartLoc, in fillUnlimited() argument 117 const jint columns=refEndLoc-refStartLoc+1; in fillUnlimited() 142 const jbyte ref0=(col<2 ? (jbyte)'!' : ref[refStartLoc+col-2]); in fillUnlimited() 143 const jbyte ref1=ref[refStartLoc+col-1]; in fillUnlimited() 366 jint refStartLoc, in fillLimitedX() argument 385 const jint columns=refEndLoc-refStartLoc+1; in fillLimitedX() 430 jbyte c=ref[refStartLoc+i]; in fillLimitedX() 463 const jbyte ref0=(col<2 ? (jbyte)'!' : ref[refStartLoc+col-2]); in fillLimitedX() 464 const jbyte ref1=ref[refStartLoc+col-1]; in fillLimitedX() 712 jint refStartLoc, in Java_align2_MultiStateAligner11tsJNI_fillUnlimitedJNI() argument [all …]
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