| /dports/biology/bbmap/bbmap/current/clump/ |
| H A D | PivotSet.java | 50 KCountArray kca=x.process(t, false); in makeSet() local
170 …KCountArray kca=KmerCount7MTA.makeKca(null, null, null, k, cbits, 0, cells, filterHashes, 0, true,… in process() local
214 …KCountArray kca=KmerCount7MTA.makeKca(null, null, null, k, cbits, 0, cells, filterHashes, 0, true,… in makeKcaStatic() local
242 public void processInner(final ConcurrentReadInputStream cris, KCountArray kca){ in processInner()
323 final KCountArray kca; field in PivotSet.HashThread
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| /dports/biology/bbmap/bbmap/current/bloom/ |
| H A D | ErrorCorrect.java | 118 …KCountArray kca=makeTable(reads1, reads2, k, cbits, gap, hashes, buildpasses, matrixbits, tablerea… in main() local
134 KCountArray kca=KCountArray.makeNew(1L<<kbits, 1L<<matrixbits, cbits, gap, hashes); in makeTable() local
173 …public static void detect(String reads1, String reads2, KCountArray kca, int k, int thresh, long m… in detect()
222 …public static void detect(ConcurrentReadInputStream cris, KCountArray kca, int k, int thresh, long… in detect()
347 …public static BitSet detectErrors(final Read r, final KCountArray kca, final int k, final int thre… in detectErrors()
384 …public static BitSet detectErrorsBulk(final Read r, final KCountArray kca, final int k, final int … in detectErrorsBulk()
423 …public static BitSet detectTrusted(final Read r, final KCountArray kca, final int k, final int thr… in detectTrusted()
463 …public static BitSet detectErrorsTips(final Read r, final KCountArray kca, final int k, final int … in detectErrorsTips()
502 …public static BitSet correctErrors(final Read r, final KCountArray kca, final int k, final int thr… in correctErrors()
587 …private static boolean correctFromLeft(Read r, KCountArray kca, int k, int thresh, BitSet bs, int … in correctFromLeft()
[all …]
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| H A D | KCountArray2.java | 12 KCountArray2 kca=new KCountArray2(1024, 16); in main() local
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| H A D | BloomFilter.java | 250 …KCountArray7MTA kca=(KCountArray7MTA)KmerCount7MTA.makeKca(in1, in2, extra==null || extra.isEmpty(… in load() local
262 …KCountArray7MTA kca=(KCountArray7MTA)KmerCount7MTA.makeKcaFromIndex(k, cbits, cells, hashes, rcomp… in loadFromIndex() local
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| H A D | KCountArray5MT.java | 34 KCountArray5MT kca=new KCountArray5MT(cells, bits, gap, hashes); in main() local
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| H A D | KCountArray4.java | 32 KCountArray4 kca=new KCountArray4(cells, bits, gap, hashes); in main() local
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| H A D | KCountArray4MT.java | 34 KCountArray4MT kca=new KCountArray4MT(cells, bits, gap, hashes); in main() local
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| H A D | KCountArray6MT.java | 35 KCountArray6MT kca=new KCountArray6MT(cells, bits, gap, hashes); in main() local
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| H A D | KCountArray7MT.java | 37 KCountArray7MT kca=new KCountArray7MT(cells, bits, gap, hashes); in main() local
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| H A D | KCountArray8MT.java | 38 KCountArray8MT kca=new KCountArray8MT(cells, bits, gap, hashes, null); in main() local
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| H A D | KmerCount6MT.java | 145 KCountArray kca=KCountArray.makeNew(1L<<kbits, 1L<<matrixbits, cbits, gap, hashes); in makeKca() local
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| /dports/biology/bbmap/bbmap/current/var2/ |
| H A D | CallVariants2.java | 693 KCountArray7MTA kca=new KCountArray7MTA(precells, cbits, 0, 2, null, minReads); in prefilter() local
762 void processInput(FileFormat ff, KCountArray7MTA kca, VarMap forcedVarsIn, boolean calcCoverage){ in processInput()
803 final KCountArray7MTA kca, final VarMap forced, final boolean calcCoverage){ in spawnThreads()
1147 private final KCountArray7MTA kca; field in ProcessThread
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| H A D | CallVariants.java | 409 KCountArray7MTA kca=new KCountArray7MTA(precells, cbits, 0, 2, null, minReads); in prefilter() local
427 private void prefilter_SF(final KCountArray7MTA kca){ in prefilter_SF()
483 private void prefilter_MF(final KCountArray7MTA kca){ in prefilter_MF()
747 void processInput_SF(FileFormat ff, KCountArray7MTA kca){ in processInput_SF()
775 void processInput_MF(FileFormat[] ff, KCountArray7MTA kca){ in processInput_MF()
796 …adInputStream cris, final SamReadStreamer ss, final SamStreamerMF ssmf, final KCountArray7MTA kca){ in spawnThreads()
1216 private final KCountArray7MTA kca; field in CallVariants.ProcessThread
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| /dports/biology/bbmap/bbmap/current/jgi/ |
| H A D | ReadKmerDepthDistribution.java | 347 KCountArray kca; in main() local
454 public static long count(String in1, String in2, KCountArray kca, int k, long maxReads, in count()
507 …public static long downsample(ConcurrentReadInputStream cris, KCountArray kca, int k, long maxRead… in downsample()
697 private static void fixSpikes(int[] array, long[] kmers, KCountArray kca, int k){ in fixSpikes()
771 public static int[] generateCoverage(Read r, KCountArray kca, int k, int[] out, long[] kmers) { in generateCoverage()
819 public static int[] generateCoverageLong(Read r, KCountArray kca, int k, int[] out) { in generateCoverageLong()
1012 private final KCountArray kca; field in ReadKmerDepthDistribution.ProcessThread
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| H A D | KmerCoverage.java | 802 public static int[] generateCoverage(Read r, KCountArray kca, int k) { in generateCoverage()
869 public static int[] generateCoverageLong(Read r, KCountArray kca, int k) { in generateCoverageLong()
1157 private final KCountArray kca; field in KmerCoverage.ProcessThread
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| H A D | KmerNormalize.java | 977 KCountArray kca; in runPass() local
1138 public static long count(String in1, String in2, KCountArray kca, int k, long maxReads, in count()
1323 public static long count(String[] list1, String[] list2, KCountArray kca, int k, long maxReads, in count()
1611 …public static long downsample(ConcurrentReadInputStream cris, KCountArray kca, int k, long maxRead… in downsample()
2073 private static void fixSpikes(int[] cov, long[] kmers, KCountArray kca, final int k){ in fixSpikes()
2121 private static int correctErrors(Read r, int[] cov, long[] kmers, KCountArray kca, final int k, in correctErrors()
2172 private static int markErrors(Read r, int[] cov, long[] kmers, KCountArray kca, final int k, in markErrors()
2620 …private static int testRightSuffix(final KCountArray kca, final int k, final long kmer0, final byt… in testRightSuffix()
2725 …public static int[] generateCoverage(Read r, KCountArray kca, final int k, int[] out, long[] kmers… in generateCoverage()
2746 …public static int[] generateCoverage(KCountArray kca, int k, int[] out, long[] kmers, boolean make… in generateCoverage()
[all …]
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| /dports/biology/wise/wise2.4.1/src/dnaindex/ |
| H A D | findbad_kmer.c | 41 KmerCountAllocator * kca; in main() local
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| H A D | kmer_count.c | 7 KmerCount * new_KmerCount_KmerCountAllocator(KmerCountAllocator * kca) in new_KmerCount_KmerCountAllocator()
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| /dports/shells/ohmyzsh/ohmyzsh-6babcbd8841335a3c25ec960ff57ab9a139c9073/plugins/kubectl/ |
| H A D | kubectl.plugin.zsh | 17 alias kca='_kca(){ kubectl "$@" --all-namespaces; unset -f _kca; }; _kca' alias
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| /dports/java/openjdk11/jdk11u-jdk-11.0.13-8-1/src/java.desktop/share/classes/javax/swing/ |
| H A D | JComponent.java | 3510 IntVector kca = getKeyCodeArray(); in registerKeyPressed() local
3523 IntVector kca = getKeyCodeArray(); in registerKeyReleased() local
3535 IntVector kca = getKeyCodeArray(); in keyIsPressed() local
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| /dports/java/openjdk13/jdk13u-jdk-13.0.10-1-1/src/java.desktop/share/classes/javax/swing/ |
| H A D | JComponent.java | 3510 IntVector kca = getKeyCodeArray(); in registerKeyPressed() local
3523 IntVector kca = getKeyCodeArray(); in registerKeyReleased() local
3535 IntVector kca = getKeyCodeArray(); in keyIsPressed() local
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| /dports/java/openjdk11-jre/jdk11u-jdk-11.0.13-8-1/src/java.desktop/share/classes/javax/swing/ |
| H A D | JComponent.java | 3510 IntVector kca = getKeyCodeArray(); in registerKeyPressed() local
3523 IntVector kca = getKeyCodeArray(); in registerKeyReleased() local
3535 IntVector kca = getKeyCodeArray(); in keyIsPressed() local
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| /dports/java/openjdk12/openjdk-jdk12u-jdk-12.0.2-10-4/src/java.desktop/share/classes/javax/swing/ |
| H A D | JComponent.java | 3510 IntVector kca = getKeyCodeArray(); in registerKeyPressed() local
3523 IntVector kca = getKeyCodeArray(); in registerKeyReleased() local
3535 IntVector kca = getKeyCodeArray(); in keyIsPressed() local
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| /dports/java/openjdk16/jdk16u-jdk-16.0.2-7-1/src/java.desktop/share/classes/javax/swing/ |
| H A D | JComponent.java | 3510 IntVector kca = getKeyCodeArray(); in registerKeyPressed() local
3523 IntVector kca = getKeyCodeArray(); in registerKeyReleased() local
3535 IntVector kca = getKeyCodeArray(); in keyIsPressed() local
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| /dports/java/openjdk17/jdk17u-jdk-17.0.1-12-1/src/java.desktop/share/classes/javax/swing/ |
| H A D | JComponent.java | 3557 IntVector kca = getKeyCodeArray(); in registerKeyPressed() local
3570 IntVector kca = getKeyCodeArray(); in registerKeyReleased() local
3582 IntVector kca = getKeyCodeArray(); in keyIsPressed() local
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