| /dports/biology/bbmap/bbmap/current/icecream/ |
| H A D | IceCreamAlignerJNI.java | 57 final int maxRpos=retVec[2]+rstart; in alignForward() local
67 …return new AlignmentResult(maxScore, maxQpos, maxRpos, query.length, ref.length, rstart, rstop, ra… in alignForward()
106 final int maxRpos=retVec[2]+rstart; in alignForwardShort() local
116 …return new AlignmentResult(maxScore, maxQpos, maxRpos, query.length, ref.length, rstart, rstop, ra… in alignForwardShort()
137 int maxRpos=-1; in alignForwardPseudo() local
211 maxRpos=apos-1; in alignForwardPseudo()
216 retArray[2]=maxRpos; in alignForwardPseudo()
233 int maxRpos=-1; in alignForwardShortPseudo() local
288 maxRpos=rpos; in alignForwardShortPseudo()
297 retArray[2]=maxRpos; in alignForwardShortPseudo()
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| H A D | IceCreamAlignerJava.java | 32 int maxRpos=-1; in alignForward() local
96 maxRpos=rpos; in alignForward()
104 …return new AlignmentResult(maxScore, maxQpos, maxRpos, query.length, ref.length, rstart, rstop, ra… in alignForward()
132 int maxRpos=-1; in alignForwardShort() local
187 maxRpos=rpos; in alignForwardShort()
200 …return new AlignmentResult(maxScore, maxQpos, maxRpos, query.length, ref.length, rstart, rstop, ra… in alignForwardShort()
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| H A D | IceCreamFinder.java | 1207 ar.junctionLoc=ar.maxRpos/2;
1209 int innerLeft=ar.maxRpos;
1240 ar.junctionLoc=ar.maxRpos/2;
1243 int innerLeft=ar.maxRpos;
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| /dports/biology/bbmap/bbmap/jni/ |
| H A D | IceCreamAlignerJNI.c | 24 int maxRpos=-1; in alignForwardJNI() local
85 maxRpos=apos-1; in alignForwardJNI()
90 retArray[2]=maxRpos; in alignForwardJNI()
109 jshort maxRpos=-1; in alignForward16JNI() local
184 maxRpos=apos-1; in alignForward16JNI()
210 jint maxRpos=-1; in alignForwardShortJNI() local
265 maxRpos=rpos; in alignForwardShortJNI()
298 jshort maxRpos=-1; in alignForwardShort16JNI() local
353 maxRpos=rpos; in alignForwardShort16JNI()
386 jshort maxRpos=-1; in alignForwardShort16JNI_352() local
[all …]
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| /dports/biology/bbmap/bbmap/current/aligner/ |
| H A D | FlatAligner.java | 37 int maxRpos=-1; in alignForward() local
110 maxRpos=rpos; in alignForward()
122 …return new AlignmentResult(maxScore, maxQpos, maxRpos, query.length, ref.length, rstart, rstop, ra… in alignForward()
153 int maxRpos=-1; in alignForwardShort() local
182 maxRpos=rpos; in alignForwardShort()
222 …return new AlignmentResult(maxScore, maxQpos, maxRpos, query.length, ref.length, rstart, rstop, ra… in alignForwardShort()
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| H A D | FlatAligner2.java | 37 int maxRpos=-1; in alignForward() local
110 maxRpos=rpos; in alignForward()
122 …return new AlignmentResult(maxScore, maxQpos, maxRpos, query.length, ref.length, rstart, rstop, ra… in alignForward()
153 int maxRpos=-1; in alignForwardShort() local
182 maxRpos=rpos; in alignForwardShort()
222 …return new AlignmentResult(maxScore, maxQpos, maxRpos, query.length, ref.length, rstart, rstop, ra… in alignForwardShort()
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| H A D | AlignmentResult.java | 9 maxRpos=maxRpos_; in AlignmentResult()
18 public int maxRpos; field in AlignmentResult
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