| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/utils/ |
| H A D | SVKmerShortUnitTest.java | 53 final SVKmer kkk = SVKmerizer.toKmer(str, new SVKmerShort(str.length())); in testSuccessor()
139 final SVKmer kkk = SVKmerizer.toKmer(str, new SVKmerShort(str.length())); in testPredecessor()
151 …Assert.assertEquals(SVKmerizer.toKmer("ACGTACGA", new SVKmerShort(8)).reverseComplement(8), SVKmer… in testReverseComplementation()
152 …Assert.assertEquals(SVKmerizer.toKmer("ACGTACGTC", new SVKmerShort(9)).reverseComplement(9), SVKme… in testReverseComplementation()
153 …Assert.assertEquals(SVKmerizer.toKmer("ACGTCCGTC", new SVKmerShort(9)).reverseComplement(9), SVKme… in testReverseComplementation()
154 …Assert.assertEquals(SVKmerizer.toKmer("ACGTGCGTC", new SVKmerShort(9)).reverseComplement(9), SVKme… in testReverseComplementation()
155 …Assert.assertEquals(SVKmerizer.toKmer("ACGTTCGTC", new SVKmerShort(9)).reverseComplement(9), SVKme… in testReverseComplementation()
160 …Assert.assertEquals(SVKmerizer.toKmer("ACGTACGTC", new SVKmerShort(9)).canonical(9), SVKmerizer.to… in testCanonicalization()
161 …Assert.assertEquals(SVKmerizer.toKmer("GACGTACGT", new SVKmerShort(9)).canonical(9), SVKmerizer.to… in testCanonicalization()
176 …Assert.assertNotEquals(SVKmerizer.toKmer("TAGCGTA", new SVKmerShort(7)).hashCode(), SVKmerizer.toK… in testHashCode()
[all …]
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| H A D | SVKmerLongUnitTest.java | 54 final SVKmer kkk = SVKmerizer.toKmer(str,new SVKmerLong(str.length())); in testSuccessor()
70 final SVKmer kkk = SVKmerizer.toKmer(str,new SVKmerLong(str.length())); in testPredecessor()
82 …Assert.assertEquals(SVKmerizer.toKmer("ACGTACGA",new SVKmerLong(8)).reverseComplement(8), SVKmeriz… in testReverseComplementation()
83 …Assert.assertEquals(SVKmerizer.toKmer("ACGTACGTC",new SVKmerLong(9)).reverseComplement(9), SVKmeri… in testReverseComplementation()
84 …Assert.assertEquals(SVKmerizer.toKmer("ACGTCCGTC",new SVKmerLong(9)).reverseComplement(9), SVKmeri… in testReverseComplementation()
85 …Assert.assertEquals(SVKmerizer.toKmer("ACGTGCGTC",new SVKmerLong(9)).reverseComplement(9), SVKmeri… in testReverseComplementation()
86 …Assert.assertEquals(SVKmerizer.toKmer("ACGTTCGTC",new SVKmerLong(9)).reverseComplement(9), SVKmeri… in testReverseComplementation()
91 …Assert.assertEquals(SVKmerizer.toKmer("ACGTACGTC",new SVKmerLong(9)).canonical(9), SVKmerizer.toKm… in testCanonicalization()
92 …Assert.assertEquals(SVKmerizer.toKmer("GACGTACGT",new SVKmerLong(9)).canonical(9), SVKmerizer.toKm… in testCanonicalization()
107 …Assert.assertNotEquals(SVKmerizer.toKmer("TAGCGTA",new SVKmerLong(7)).hashCode(), SVKmerizer.toKme… in testHashCode()
[all …]
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/utils/ |
| H A D | SVKmerizer.java | 65 public static SVKmer toKmer(final CharSequence seq, SVKmer kmer) { in toKmer() method in SVKmerizer
71 public static SVKmer toKmer( final byte[] seq, final SVKmer kmer ) { in toKmer() method in SVKmerizer
72 return toKmer(new ASCIICharSequence(seq),kmer); in toKmer()
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| /dports/biology/bbmap/bbmap/current/jgi/ |
| H A D | CalcUniqueness.java | 372 final long kmer=toKmer(bases1, quals1, singleOffset, k); in process()
377 final long kmer=toKmer(bases1, quals1, randy.nextInt(length1-k2), k); in process()
394 final long kmer=toKmer(bases2, quals2, singleOffset, k); in process()
399 final long kmer=toKmer(bases2, quals2, randy.nextInt(length2-k2), k); in process()
410 final long kmer1=toKmer(bases1, quals1, PAIR_OFFSET, k); in process()
411 final long kmer2=toKmer(bases2, quals2, PAIR_OFFSET, k); in process()
553 private final long toKmer(final byte[] bases, byte[] quals, final int start, final int klen){ in toKmer() method in CalcUniqueness
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| /dports/biology/bbmap/bbmap/current/hiseq/ |
| H A D | PlotFlowCell.java | 317 final long kmer=toKmer(r1.bases, randy.nextInt(initialLength1-k2), k); in loadKmersInner()
325 final long kmer=toKmer(r2.bases, randy.nextInt(initialLength2-k2), k); in loadKmersInner()
392 final long kmer=toKmer(r1.bases, randy.nextInt(initialLength1-k2), k); in fillTilesInner()
401 final long kmer=toKmer(r1.bases, randy.nextInt(initialLength1-k2), k); in fillTilesInner()
494 private static final long toKmer(final byte[] bases, final int start, final int klen){ in toKmer() method in PlotFlowCell
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| H A D | AnalyzeFlowCell.java | 571 final long kmer=toKmer(r1.bases, r1.quality, randy.nextInt(initialLength1-k2), k); in loadKmersInner()
579 final long kmer=toKmer(r2.bases, r2.quality, randy.nextInt(initialLength2-k2), k); in loadKmersInner()
646 final long kmer=toKmer(r1.bases, r1.quality, randy.nextInt(initialLength1-k2), k); in fillTilesInner()
655 final long kmer=toKmer(r1.bases, r1.quality, randy.nextInt(initialLength1-k2), k); in fillTilesInner()
834 …private static final long toKmer(final byte[] bases, byte[] quals, final int start, final int klen… in toKmer() method in AnalyzeFlowCell
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/evidence/ |
| H A D | FindBreakpointEvidenceSparkUnitTest.java | 93 killSet.add(SVKmerizer.toKmer(seq1,kmer)); in getKmerIntervalsTest()
95 killSet.add(SVKmerizer.toKmer(seq2,kmer)); in getKmerIntervalsTest()
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| H A D | FindBadGenomicKmersSparkUnitTest.java | 55 Assert.assertEquals(badKmers.get(0), SVKmerizer.toKmer(polyA,new SVKmerLong())); in badKmersTest()
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