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Searched refs:refStartLoc (Results 1 – 22 of 22) sorted by relevance

/dports/biology/bbmap/bbmap/current/aligner/
H A DSingleStateAlignerFlat2Amino.java101 …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()
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H A DSingleStateAlignerFlat.java117 …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);
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H A DSingleStateAlignerFlat2.java102 …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()
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H A DSingleStateAlignerFlat3.java102 …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()
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H A DSingleStateAlignerFlat2_1D.java88 …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()
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H A DSingleStateAlignerFlatFloat.java104 …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()
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H A DSingleStateAlignerPacBioAdapter.java70 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);
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H A DAligner.java7 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
H A DMultiStateAligner9PacBioAdapter_WithBarriers.java130 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);
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H A DMultiStateAligner9PacBioAdapter2.java163 …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;
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H A DMultiStateAligner9PacBioAdapter.java93 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;
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H A DMultiStateAligner9PacBioAdapter3.java89 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()
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/dports/biology/bbmap/bbmap/current/align2/
H A DMultiStateAligner11ts.java117 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){
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H A DMultiStateAligner9XFlat.java113 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){
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H A DMultiStateAligner11tsJNI.java94 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){
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H A DMultiStateAligner9ts.java109 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);
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H A DMultiStateAligner10ts.java129 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);
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H A DMultiStateAligner9Flat.java114 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){
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H A DMultiStateAligner9PacBio.java114 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);
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H A DNeedlemanWunsch.java49 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
H A DMSA.java53 …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
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/dports/biology/bbmap/bbmap/jni/
H A DMultiStateAligner11tsJNI.c105 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
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