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Searched refs:baseToComplementNumber (Results 1 – 25 of 28) sorted by relevance

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/dports/biology/bbmap/bbmap/current/dna/
H A DAminoAcid.java179 return amino ? acidToNumber : baseToComplementNumber; in symbolToComplementNumber()
209 public static final byte[] baseToComplementNumber=new byte[128]; field in AminoAcid
795 Arrays.fill(baseToComplementNumber, (byte)-1); in Arrays.fill() argument
796 baseToComplementNumber['A']=baseToComplementNumber['a']=3;
797 baseToComplementNumber['C']=baseToComplementNumber['c']=2;
798 baseToComplementNumber['G']=baseToComplementNumber['g']=1;
799 baseToComplementNumber['T']=baseToComplementNumber['t']=0;
800 baseToComplementNumber['U']=baseToComplementNumber['u']=0;
/dports/biology/bbmap/bbmap/current/bloom/
H A DBloomFilter.java288 long x2=AminoAcid.baseToComplementNumber[b]; in minCount()
323 long x2=AminoAcid.baseToComplementNumber[b]; in hasHighCountFraction()
365 long x2=AminoAcid.baseToComplementNumber[b]; in getLeftCount()
392 long x2=AminoAcid.baseToComplementNumber[b]; in getRightCount()
420 long x2=AminoAcid.baseToComplementNumber[b]; in passes()
462 long x2=AminoAcid.baseToComplementNumber[b]; in passes()
524 final long x2=AminoAcid.baseToComplementNumber[base]; in fillCounts()
H A DBloomFilterCorrector.java468 final long x2=AminoAcid.baseToComplementNumber[base]; in regenerateCounts()
568 final long x2=AminoAcid.baseToComplementNumber[aBase]; in reassemble_inner()
944 final long x2=AminoAcid.baseToComplementNumber[b]; in extendToRight2()
1109 final long x2=AminoAcid.baseToComplementNumber[b]; in regenerateKmers()
1361 final long x2=AminoAcid.baseToComplementNumber[base]; in regenerateCounts()
H A DKmerCount7MTA.java1101 long x2=AminoAcid.baseToComplementNumber[b];
1349 long x2=AminoAcid.baseToComplementNumber[b];
/dports/biology/bbmap/bbmap/current/kmer/
H A DKmerTableSet.java657 final long x2=AminoAcid.baseToComplementNumber[b]; in addKmersToTable()
714 final long x2=AminoAcid.baseToComplementNumber[b]; in addKmersToTable_onePass()
789 final long x2=AminoAcid.baseToComplementNumber[b]; in regenerateKmers()
831 final long x2=AminoAcid.baseToComplementNumber[base]; in regenerateCounts()
1062 final long x2=AminoAcid.baseToComplementNumber[b]; in rightmostKmer()
1096 final long x2=AminoAcid.baseToComplementNumber[b]; in leftmostKmer()
1143 final long x2=AminoAcid.baseToComplementNumber[b]; in calcCoverage()
1176 final long x2=AminoAcid.baseToComplementNumber[b]; in calcCoverage()
1209 final long x2=AminoAcid.baseToComplementNumber[b]; in claim()
1256 final long x2=AminoAcid.baseToComplementNumber[b]; in release()
[all …]
H A DTableReader.java323 long x2=Dedupe.baseToComplementNumber[b]; in markBits()
357 long x2=Dedupe.baseToComplementNumber[b]; in markBits()
H A DTableLoaderLockFree.java447 long x2=AminoAcid.baseToComplementNumber[b]; in addToMap()
468 long x2=AminoAcid.baseToComplementNumber[b]; in addToMap()
/dports/biology/bbmap/bbmap/current/cluster/
H A DClusterTools.java38 int x2=Dedupe.baseToComplementNumber[b]; in toKmers()
68 int x2=Dedupe.baseToComplementNumber[b]; in toKmerCounts()
/dports/biology/bbmap/bbmap/current/clump/
H A DKmerComparator.java168 long x2=AminoAcid.baseToComplementNumber[b]; in fillMax()
306 long x2=AminoAcid.baseToComplementNumber[b]; in example2()
353 long x2=AminoAcid.baseToComplementNumber[b]; in example3()
H A DClumpList.java304 long x2=AminoAcid.baseToComplementNumber[b]; in fillMap()
/dports/biology/bbmap/bbmap/current/cardinality/
H A DCardinalityTracker.java222 long x2=AminoAcid.baseToComplementNumber[b]; in hashSmall()
250 long x2=AminoAcid.baseToComplementNumber[b]; in hashSmall()
H A DLogLog_old.java176 long x2=AminoAcid.baseToComplementNumber[b];
204 long x2=AminoAcid.baseToComplementNumber[b];
/dports/biology/bbmap/bbmap/current/prok/
H A DRiboMaker.java322 long x2=AminoAcid.baseToComplementNumber[b];
353 long x2=AminoAcid.baseToComplementNumber[b];
/dports/biology/bbmap/bbmap/current/sketch/
H A DKmerLimit.java486 long x2=AminoAcid.baseToComplementNumber[b];
503 final long x2=AminoAcid.baseToComplementNumber[b];
H A DSketchMakerMini.java313 long x2=AminoAcid.baseToComplementNumber[b]; in processReadNucleotide()
365 final long x2=AminoAcid.baseToComplementNumber[b]; in processReadNucleotide()
H A DKmerLimit2.java805 long x2=AminoAcid.baseToComplementNumber[b]; in processReadNucleotide()
822 final long x2=AminoAcid.baseToComplementNumber[b]; in processReadNucleotide()
H A DInvertKey.java254 long x2=AminoAcid.baseToComplementNumber[b]; in invert()
H A DBlacklistMaker.java729 long x2=AminoAcid.baseToComplementNumber[b];
/dports/biology/bbmap/bbmap/current/align2/
H A DQualityTools.java228 final int x2=AminoAcid.baseToComplementNumber[b]; in makeKeyProbs()
262 final int x2=AminoAcid.baseToComplementNumber[b];
/dports/biology/bbmap/bbmap/current/assemble/
H A DTadpole1.java913 final long x2=AminoAcid.baseToComplementNumber[b]; in extendToRight()
1105 final long x2=AminoAcid.baseToComplementNumber[b]; in extendToRight2()
1283 final long x2=AminoAcid.baseToComplementNumber[b]; in isJunk()
1308 final long x2=AminoAcid.baseToComplementNumber[b]; in isJunk()
1366 final long x2=AminoAcid.baseToComplementNumber[b]; in hasKmersAtOrBelow()
1780 final long x2=AminoAcid.baseToComplementNumber[aBase]; in reassemble_inner()
H A DKmerCompressor.java627 final long x2=AminoAcid.baseToComplementNumber[b]; in extendToRight()
743 final long x2=AminoAcid.baseToComplementNumber[b]; in extendToRight_RcompOnly()
/dports/biology/bbmap/bbmap/current/jgi/
H A DBBDuk2.java1751 long x2=AminoAcid.baseToComplementNumber[b]; in addToMap()
1772 long x2=AminoAcid.baseToComplementNumber[b]; in addToMap()
2545 long x2=Dedupe.baseToComplementNumber[b]; in countSetKmers()
2605 long x2=Dedupe.baseToComplementNumber[b]; in findBestMatch()
2686 long x2=Dedupe.baseToComplementNumber[b]; in countSetKmersBig()
2781 long x2=Dedupe.baseToComplementNumber[b]; in ktrim()
2815 long x2=Dedupe.baseToComplementNumber[b]; in ktrim()
2849 long x2=Dedupe.baseToComplementNumber[b]; in ktrim()
2954 long x2=Dedupe.baseToComplementNumber[b]; in kmask()
2988 long x2=Dedupe.baseToComplementNumber[b]; in kmask()
[all …]
H A DDedupe.java3254 long x2=baseToComplementNumber[b];
3333 long x2=baseToComplementNumber[b];
3838 long x2=baseToComplementNumber[b];
5750 public static final byte[] baseToComplementNumber=new byte[128];
5794 baseToComplementNumber['A']=baseToComplementNumber['a']=3;
5795 baseToComplementNumber['C']=baseToComplementNumber['c']=2;
5796 baseToComplementNumber['G']=baseToComplementNumber['g']=1;
5797 baseToComplementNumber['T']=baseToComplementNumber['t']=0;
5798 baseToComplementNumber['U']=baseToComplementNumber['u']=0;
H A DDedupe2.java3173 long x2=baseToComplementNumber[b];
3251 long x2=baseToComplementNumber[b];
3736 long x2=baseToComplementNumber[b];
5571 public static final byte[] baseToComplementNumber=new byte[128];
5615 baseToComplementNumber['A']=baseToComplementNumber['a']=3;
5616 baseToComplementNumber['C']=baseToComplementNumber['c']=2;
5617 baseToComplementNumber['G']=baseToComplementNumber['g']=1;
5618 baseToComplementNumber['T']=baseToComplementNumber['t']=0;
5619 baseToComplementNumber['U']=baseToComplementNumber['u']=0;
H A DBBMergeOverlapper.java800 final long x2=AminoAcid.baseToComplementNumber[b]; in minCoverage()

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