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

/dports/biology/bbmap/bbmap/current/aligner/
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 DSingleStateAlignerFlat2Amino.java79 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 …]
H A DSingleStateAlignerFlat.java95 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 …]
H A DSingleStateAlignerFlat2.java80 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 …]
H A DSingleStateAlignerFlat3.java80 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 …]
H A DSingleStateAlignerPacBioAdapter.java69 …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 …]
H A DSingleStateAlignerFlatFloat.java80 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 …]
H A DSingleStateAlignerFlat2_1D.java68 …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 …]
H A DMultiStateAligner9PacBioAdapter_WithBarriers.java130 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 …]
H A DMultiStateAligner9PacBioAdapter2.java149 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 …]
H A DMultiStateAligner9PacBioAdapter.java83 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 …]
H A DMultiStateAligner9PacBioAdapter3.java79 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 …]
/dports/biology/bbmap/bbmap/current/align2/
H A DMultiStateAligner11tsJNI.java78 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);
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H A DMultiStateAligner11ts.java117 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 …]
H A DMultiStateAligner9XFlat.java113 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 …]
H A DMultiStateAligner9ts.java109 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 …]
H A DMultiStateAligner9Flat.java114 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 …]
H A DMultiStateAligner9PacBio.java114 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 …]
H A DMultiStateAligner10ts.java129 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 …]
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()
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 …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 …]
/dports/biology/bbmap/bbmap/jni/
H A DMultiStateAligner11tsJNI.c106 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()