/dports/biology/bbmap/bbmap/current/dna/ |
H A D | AminoAcid.java | 179 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;
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/dports/biology/bbmap/bbmap/current/bloom/ |
H A D | BloomFilter.java | 288 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()
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H A D | BloomFilterCorrector.java | 468 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()
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H A D | KmerCount7MTA.java | 1101 long x2=AminoAcid.baseToComplementNumber[b]; 1349 long x2=AminoAcid.baseToComplementNumber[b];
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/dports/biology/bbmap/bbmap/current/kmer/ |
H A D | KmerTableSet.java | 657 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 …]
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H A D | TableReader.java | 323 long x2=Dedupe.baseToComplementNumber[b]; in markBits() 357 long x2=Dedupe.baseToComplementNumber[b]; in markBits()
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H A D | TableLoaderLockFree.java | 447 long x2=AminoAcid.baseToComplementNumber[b]; in addToMap() 468 long x2=AminoAcid.baseToComplementNumber[b]; in addToMap()
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/dports/biology/bbmap/bbmap/current/cluster/ |
H A D | ClusterTools.java | 38 int x2=Dedupe.baseToComplementNumber[b]; in toKmers() 68 int x2=Dedupe.baseToComplementNumber[b]; in toKmerCounts()
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/dports/biology/bbmap/bbmap/current/clump/ |
H A D | KmerComparator.java | 168 long x2=AminoAcid.baseToComplementNumber[b]; in fillMax() 306 long x2=AminoAcid.baseToComplementNumber[b]; in example2() 353 long x2=AminoAcid.baseToComplementNumber[b]; in example3()
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H A D | ClumpList.java | 304 long x2=AminoAcid.baseToComplementNumber[b]; in fillMap()
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/dports/biology/bbmap/bbmap/current/cardinality/ |
H A D | CardinalityTracker.java | 222 long x2=AminoAcid.baseToComplementNumber[b]; in hashSmall() 250 long x2=AminoAcid.baseToComplementNumber[b]; in hashSmall()
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H A D | LogLog_old.java | 176 long x2=AminoAcid.baseToComplementNumber[b]; 204 long x2=AminoAcid.baseToComplementNumber[b];
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/dports/biology/bbmap/bbmap/current/prok/ |
H A D | RiboMaker.java | 322 long x2=AminoAcid.baseToComplementNumber[b]; 353 long x2=AminoAcid.baseToComplementNumber[b];
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/dports/biology/bbmap/bbmap/current/sketch/ |
H A D | KmerLimit.java | 486 long x2=AminoAcid.baseToComplementNumber[b]; 503 final long x2=AminoAcid.baseToComplementNumber[b];
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H A D | SketchMakerMini.java | 313 long x2=AminoAcid.baseToComplementNumber[b]; in processReadNucleotide() 365 final long x2=AminoAcid.baseToComplementNumber[b]; in processReadNucleotide()
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H A D | KmerLimit2.java | 805 long x2=AminoAcid.baseToComplementNumber[b]; in processReadNucleotide() 822 final long x2=AminoAcid.baseToComplementNumber[b]; in processReadNucleotide()
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H A D | InvertKey.java | 254 long x2=AminoAcid.baseToComplementNumber[b]; in invert()
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H A D | BlacklistMaker.java | 729 long x2=AminoAcid.baseToComplementNumber[b];
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/dports/biology/bbmap/bbmap/current/align2/ |
H A D | QualityTools.java | 228 final int x2=AminoAcid.baseToComplementNumber[b]; in makeKeyProbs() 262 final int x2=AminoAcid.baseToComplementNumber[b];
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/dports/biology/bbmap/bbmap/current/assemble/ |
H A D | Tadpole1.java | 913 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()
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H A D | KmerCompressor.java | 627 final long x2=AminoAcid.baseToComplementNumber[b]; in extendToRight() 743 final long x2=AminoAcid.baseToComplementNumber[b]; in extendToRight_RcompOnly()
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/dports/biology/bbmap/bbmap/current/jgi/ |
H A D | BBDuk2.java | 1751 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 …]
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H A D | Dedupe.java | 3254 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;
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H A D | Dedupe2.java | 3173 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;
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H A D | BBMergeOverlapper.java | 800 final long x2=AminoAcid.baseToComplementNumber[b]; in minCoverage()
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