| /dports/biology/bbmap/bbmap/current/aligner/ |
| H A D | SingleStateAlignerPacBioAdapter.java | 70 return fillLimitedX(read, ref, refStartLoc, refEndLoc, minScore); in fillLimited()
76 …private final int[] fillLimitedX(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillLimitedX() method in SingleStateAlignerPacBioAdapter
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| H A D | MultiStateAligner9PacBioAdapter.java | 83 return fillLimitedX(read, ref, refStartLoc, refEndLoc, minScore); in fillLimited()
89 …private final int[] fillLimitedX(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillLimitedX() method in MultiStateAligner9PacBioAdapter
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| H A D | MultiStateAligner9PacBioAdapter_WithBarriers.java | 115 if(gaps==null){return fillLimitedX(read, ref, refStartLoc, refEndLoc, minScore);} in fillLimited()
119 return fillLimitedX(read, gref, 0, greflimit, minScore); in fillLimited()
126 …private final int[] fillLimitedX(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillLimitedX() method in MultiStateAligner9PacBioAdapter_WithBarriers
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| H A D | MultiStateAligner9PacBioAdapter2.java | 142 return fillLimitedX(read, ref, refStartLoc, refEndLoc, minScore); in fillLimited()
148 …private final int[] fillLimitedX(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillLimitedX() method in MultiStateAligner9PacBioAdapter2
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| H A D | MultiStateAligner9PacBioAdapter3.java | 79 return fillLimitedX(read, ref, refStartLoc, refEndLoc, minScore); in fillLimited()
85 …private final int[] fillLimitedX(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillLimitedX() method in MultiStateAligner9PacBioAdapter3
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| /dports/biology/bbmap/bbmap/jni/ |
| H A D | MultiStateAligner11tsJNI.c | 361 void fillLimitedX( in fillLimitedX() function
796 …fillLimitedX(jread,jref,read_length,ref_length,refStartLoc,refEndLoc,minScore,jresult,iterationsLi… in Java_align2_MultiStateAligner11tsJNI_fillLimitedXJNI()
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| /dports/biology/bbmap/bbmap/current/align2/ |
| H A D | MultiStateAligner11tsJNI.java | 76 if(gaps==null){return fillLimitedX(read, ref, refStartLoc, refEndLoc, minScore);} in fillLimited()
85 return fillLimitedX(read, gref, 0, greflimit, minScore); in fillLimited()
91 …private final int[] fillLimitedX(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillLimitedX() method in MultiStateAligner11tsJNI
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| H A D | MultiStateAligner11ts.java | 96 if(gaps==null){return fillLimitedX(read, ref, refStartLoc, refEndLoc, minScore);} in fillLimited()
105 return fillLimitedX(read, gref, 0, greflimit, minScore); in fillLimited()
112 …private final int[] fillLimitedX(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillLimitedX() method in MultiStateAligner11ts
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| H A D | MultiStateAligner9XFlat.java | 92 if(gaps==null){return fillLimitedX(read, ref, refStartLoc, refEndLoc, minScore);} in fillLimited()
101 return fillLimitedX(read, gref, 0, greflimit, minScore); in fillLimited()
108 …private final int[] fillLimitedX(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillLimitedX() method in MultiStateAligner9XFlat
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| H A D | MultiStateAligner9ts.java | 94 if(gaps==null){return fillLimitedX(read, ref, refStartLoc, refEndLoc, minScore);} in fillLimited()
98 return fillLimitedX(read, gref, 0, greflimit, minScore); in fillLimited()
105 …private final int[] fillLimitedX(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillLimitedX() method in MultiStateAligner9ts
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| H A D | MultiStateAligner9Flat.java | 93 if(gaps==null){return fillLimitedX(read, ref, refStartLoc, refEndLoc, minScore);} in fillLimited()
102 return fillLimitedX(read, gref, 0, greflimit, minScore); in fillLimited()
109 …private final int[] fillLimitedX(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillLimitedX() method in MultiStateAligner9Flat
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| H A D | MultiStateAligner9PacBio.java | 93 if(gaps==null){return fillLimitedX(read, ref, refStartLoc, refEndLoc, minScore);} in fillLimited()
102 return fillLimitedX(read, gref, 0, greflimit, minScore); in fillLimited()
109 …private final int[] fillLimitedX(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillLimitedX() method in MultiStateAligner9PacBio
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| H A D | MultiStateAligner10ts.java | 107 if(gaps==null){return fillLimitedX(read, ref, refStartLoc, refEndLoc, minScore);} in fillLimited()
116 return fillLimitedX(read, gref, 0, greflimit, minScore); in fillLimited()
123 …private final int[] fillLimitedX(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillLimitedX() method in MultiStateAligner10ts
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