| /dports/biology/bbmap/bbmap/jni/ |
| H A D | BandedAlignerJNI.c | 38 jbyte * baseToNumber
56 jbyte * baseToNumber,
75 jbyte * baseToNumber
93 jbyte * baseToNumber,
138 jbyte * baseToNumber in alignForward() argument
190 const jint score=(q==r || (inexact && (!(baseToNumber[q]>=0) || !(baseToNumber[r]>=0))) ? 0 : 1); in alignForward()
256 jbyte * baseToNumber, in alignForwardRC() argument
309 const jint score=(q==r || (inexact && (!(baseToNumber[q]>=0) || !(baseToNumber[r]>=0))) ? 0 : 1); in alignForwardRC()
372 jbyte * baseToNumber in alignReverse() argument
424 const jint score=(q==r || (inexact && (!(baseToNumber[q]>=0) || !(baseToNumber[r]>=0))) ? 0 : 1); in alignReverse()
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| H A D | MultiStateAligner11tsJNI.c | 380 jbyte * baseToNumber, in fillLimitedX() argument
418 if(baseToNumber[c]>=0){ in fillLimitedX()
431 if(baseToNumber[c]>=0){ in fillLimitedX()
772 jbyteArray baseToNumber, in Java_align2_MultiStateAligner11tsJNI_fillLimitedXJNI() argument
789 jbyte * jbaseToNumber=(jbyte*)(*env)->GetPrimitiveArrayCritical(env, baseToNumber, NULL); in Java_align2_MultiStateAligner11tsJNI_fillLimitedXJNI()
808 (*env)->ReleasePrimitiveArrayCritical(env, baseToNumber, jbaseToNumber, JNI_ABORT); in Java_align2_MultiStateAligner11tsJNI_fillLimitedXJNI()
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| /dports/biology/bbmap/bbmap/current/align2/ |
| H A D | BandedAlignerJNI.java | 18 …qstart, int rstart, int maxEdits, boolean exact, int maxWidth, byte[] baseToNumber, int[] returnVa… in alignForwardJNI() argument
20 …qstart, int rstart, int maxEdits, boolean exact, int maxWidth, byte[] baseToNumber, byte[] baseToC… in alignForwardRCJNI() argument
22 …qstart, int rstart, int maxEdits, boolean exact, int maxWidth, byte[] baseToNumber, int[] returnVa… in alignReverseJNI() argument
24 …qstart, int rstart, int maxEdits, boolean exact, int maxWidth, byte[] baseToNumber, byte[] baseToC… in alignReverseRCJNI() argument
79 …alignForwardJNI(query,ref,qstart,rstart,maxEdits,exact,maxWidth,AminoAcid.baseToNumber,returnVals); in alignForward()
103 …orwardRCJNI(query,ref,qstart,rstart,maxEdits,exact,maxWidth,AminoAcid.baseToNumber,AminoAcid.baseT… in alignForwardRC()
127 …alignReverseJNI(query,ref,qstart,rstart,maxEdits,exact,maxWidth,AminoAcid.baseToNumber,returnVals); in alignReverse()
151 …everseRCJNI(query,ref,qstart,rstart,maxEdits,exact,maxWidth,AminoAcid.baseToNumber,AminoAcid.baseT… in alignReverseRC()
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| /dports/biology/bbmap/bbmap/current/jgi/ |
| H A D | Info.java | 103 byte num=baseToNumber[array[i]]; in info()
140 byte num=baseToNumber[array[i]]; in prefixForInfo()
178 public static final byte[] baseToNumber=new byte[128]; field in Info
181 Arrays.fill(baseToNumber, (byte)-1); in Arrays.fill() argument
185 baseToNumber[x]=(byte)i;
186 baseToNumber[Tools.toLowerCase(x)]=(byte)i;
189 baseToNumber['U']=3;
190 baseToNumber['u']=3;
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| /dports/biology/bbmap/bbmap/current/fun/ |
| H A D | ProbShared2.java | 40 long x=baseToNumber[b]; in simulateOnePair()
52 long x=baseToNumber[b]; in simulateOnePair()
73 static final byte[] baseToNumber=AminoAcid.baseToNumber; field in ProbShared2
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| /dports/biology/bbmap/bbmap/current/dna/ |
| H A D | AminoAcid.java | 77 kmer=(kmer<<2)|(baseToNumber[c]); in stringToKmer()
388 byte a=baseToNumber[base1]; in baseToColor()
389 byte b=baseToNumber[base2]; in baseToColor()
400 byte a=baseToNumber[base1]; in colorToBase()
461 return baseToNumber[base]>=0; in isFullyDefined()
465 return base>=0 && baseToNumber[base]>=0; in isFullyDefined()
547 int x=baseToNumber[c]; in toNumber()
573 int a=baseToNumber[c1], b=baseToNumber[c2], c=baseToNumber[c3]; in toByte()
783 Arrays.fill(baseToNumber, (byte)-1); in Arrays.fill() argument
792 baseToNumber0['U']=baseToNumber['U']=3;
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| H A D | ChromosomeArray.java | 262 return AminoAcid.baseToNumber[array[loc]]; in getNumber()
267 int x=AminoAcid.baseToNumber[array[i]]; in isFullyDefined()
275 int x=AminoAcid.baseToNumber[array[i]]; in isFullyUndefined()
288 int x=AminoAcid.baseToNumber[array[i]]; in countDefinedBases()
303 int x=AminoAcid.baseToNumber[bases[i]]; in toNumber()
313 int x=AminoAcid.baseToNumber[bases.charAt(i)]; in toNumber()
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| /dports/biology/bbmap/bbmap/current/ukmer/ |
| H A D | KmerTableSetU.java | 565 final long x=AminoAcid.baseToNumber[b]; in addKmersToTable()
622 final long x=AminoAcid.baseToNumber[b]; in addKmersToTable_onePass()
695 final long x=AminoAcid.baseToNumber[base]; in regenerateCounts()
710 final long x=AminoAcid.baseToNumber[base]; in regenerateCounts()
886 final long x=AminoAcid.baseToNumber[b]; in rightmostKmer()
915 final long x=AminoAcid.baseToNumber[b]; in leftmostKmer()
959 final long x=AminoAcid.baseToNumber[b]; in calcCoverage()
987 final long x=AminoAcid.baseToNumber[b]; in calcCoverage()
1017 final long x=AminoAcid.baseToNumber[b]; in claim()
1058 final long x=AminoAcid.baseToNumber[b]; in release()
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| H A D | Kmer.java | 163 long x=AminoAcid.baseToNumber[b];
168 long x=AminoAcid.baseToNumber[b];
173 long x=AminoAcid.baseToNumber[b];
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| /dports/biology/bbmap/bbmap/current/bloom/ |
| H A D | KmerCount4.java | 244 int x=AminoAcid.baseToNumber[b]; in addRead()
282 int x1=AminoAcid.baseToNumber[bases[i]]; in addReadSplit()
283 int x2=AminoAcid.baseToNumber[bases[j]]; in addReadSplit()
325 int x1=AminoAcid.baseToNumber[bases[i]]; in addReadSplit()
326 int x2=AminoAcid.baseToNumber[bases[j]]; in addReadSplit()
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| H A D | BloomFilter.java | 287 long x=AminoAcid.baseToNumber[b]; in minCount()
322 long x=AminoAcid.baseToNumber[b]; in hasHighCountFraction()
364 long x=AminoAcid.baseToNumber[b]; in getLeftCount()
391 long x=AminoAcid.baseToNumber[b]; in getRightCount()
419 long x=AminoAcid.baseToNumber[b]; in passes()
461 long x=AminoAcid.baseToNumber[b]; in passes()
523 final long x=AminoAcid.baseToNumber[base]; in fillCounts()
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| H A D | KmerCount6.java | 320 int x=AminoAcid.baseToNumber[b]; in addRead()
358 int x1=AminoAcid.baseToNumber[bases[i]]; in addReadSplit()
359 int x2=AminoAcid.baseToNumber[bases[j]]; in addReadSplit()
401 int x1=AminoAcid.baseToNumber[bases[i]]; in addReadSplit()
402 int x2=AminoAcid.baseToNumber[bases[j]]; in addReadSplit()
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| H A D | ErrorCorrect.java | 363 int x=AminoAcid.baseToNumber[b]; in detectErrors()
400 int x=AminoAcid.baseToNumber[b]; in detectErrorsBulk()
440 int x=AminoAcid.baseToNumber[b]; in detectTrusted()
480 int x=AminoAcid.baseToNumber[b]; in detectErrorsTips()
602 int x=AminoAcid.baseToNumber[b]; in correctFromLeft()
635 int x=AminoAcid.baseToNumber[c]; in correctFromLeft()
702 int x=AminoAcid.baseToNumber[b]; in correctFromRight()
747 int x=AminoAcid.baseToNumber[c]; in correctFromRight()
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| H A D | KmerCount5.java | 345 int x=AminoAcid.baseToNumber[b]; in addRead()
383 int x1=AminoAcid.baseToNumber[bases[i]]; in addReadSplit()
384 int x2=AminoAcid.baseToNumber[bases[j]]; in addReadSplit()
426 int x1=AminoAcid.baseToNumber[bases[i]]; in addReadSplit()
427 int x2=AminoAcid.baseToNumber[bases[j]]; in addReadSplit()
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| H A D | KmerCount3.java | 113 int x=AminoAcid.baseToNumber[b]; in countFastq()
139 int x=AminoAcid.baseToNumber[b]; in countFastq()
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| H A D | TestLargeKmer.java | 88 int x=AminoAcid.baseToNumber[b]; in countK2()
132 int x=AminoAcid.baseToNumber[b]; in countK2()
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| H A D | LargeKmerCount.java | 124 int x=AminoAcid.baseToNumber[b]; in countFastq()
156 int x=AminoAcid.baseToNumber[b]; in countFastq()
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| /dports/biology/bbmap/bbmap/current/kmer/ |
| H A D | KmerTableSet.java | 656 final long x=AminoAcid.baseToNumber[b]; in addKmersToTable()
713 final long x=AminoAcid.baseToNumber[b]; in addKmersToTable_onePass()
788 final long x=AminoAcid.baseToNumber[b]; in regenerateKmers()
967 final long x=AminoAcid.baseToNumber[b]; in fillKmers()
1061 final long x=AminoAcid.baseToNumber[b]; in rightmostKmer()
1095 final long x=AminoAcid.baseToNumber[b]; in leftmostKmer()
1142 final long x=AminoAcid.baseToNumber[b]; in calcCoverage()
1175 final long x=AminoAcid.baseToNumber[b]; in calcCoverage()
1208 final long x=AminoAcid.baseToNumber[b]; in claim()
1255 final long x=AminoAcid.baseToNumber[b]; in release()
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| /dports/biology/bbmap/bbmap/current/prok/ |
| H A D | FrameStats.java | 119 int x=AminoAcid.baseToNumber[b]; in scorePoint()
150 int x=AminoAcid.baseToNumber[b]; in processCDSFrames()
186 int x=AminoAcid.baseToNumber[b]; in processPoint()
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| /dports/biology/bbmap/bbmap/current/cluster/ |
| H A D | ClusterTools.java | 37 int x=Dedupe.baseToNumber[b]; in toKmers()
67 int x=Dedupe.baseToNumber[b]; in toKmerCounts()
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| /dports/biology/bbmap/bbmap/current/clump/ |
| H A D | KmerComparator.java | 167 long x=AminoAcid.baseToNumber[b]; in fillMax()
263 long x=AminoAcid.baseToNumber[b];//2-bit value, 0, 1, 2, 3, or -1 in example1()
305 long x=AminoAcid.baseToNumber[b]; in example2()
352 long x=AminoAcid.baseToNumber[b]; in example3()
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| H A D | Splitter.java | 120 byte x=AminoAcid.baseToNumber[cb]; in findReadVariants()
253 final int readAllele=AminoAcid.baseToNumber[r.bases[rloc]]; in containsVar()
270 final int readAllele=AminoAcid.baseToNumber[r.bases[rloc]]; in hasDifferentAllele()
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| /dports/biology/bbmap/bbmap/current/cardinality/ |
| H A D | CardinalityTracker.java | 221 long x=AminoAcid.baseToNumber[b]; in hashSmall()
249 long x=AminoAcid.baseToNumber[b]; in hashSmall()
278 long x=Dedupe.baseToNumber[b]; in hashBig()
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| /dports/biology/bbmap/bbmap/current/consensus/ |
| H A D | BaseNode.java | 48 int num=AminoAcid.baseToNumber[base]; in add()
126 int x=AminoAcid.baseToNumber[b]; in baseProb()
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| /dports/biology/bbmap/bbmap/current/assemble/ |
| H A D | Contig.java | 119 int x=AminoAcid.baseToNumber[b]; in gc()
136 byte x=AminoAcid.baseToNumber[b]; in leftKmer()
148 byte x=AminoAcid.baseToNumber[b];
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