/dports/biology/bbmap/bbmap/current/clump/ |
H A D | StreamToOutput.java | 18 …final ConcurrentReadInputStream cris=ConcurrentReadInputStream.getReadInputStream(-1, false, ffin1… in StreamToOutput() local 62 public void processSingle(ConcurrentReadInputStream cris){ in processSingle() 86 public void processMulti(ConcurrentReadInputStream cris){ in processMulti() 128 ConcurrentReadInputStream cris; field in StreamToOutput
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H A D | PivotSet.java | 172 final ConcurrentReadInputStream cris; in process() local 206 …public static KCountArray makeKcaStatic(final ConcurrentReadInputStream cris, int k, int minCount,… in makeKcaStatic() 242 public void processInner(final ConcurrentReadInputStream cris, KCountArray kca){ in processInner() 321 final ConcurrentReadInputStream cris; field in PivotSet.HashThread
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H A D | KmerSplit.java | 282 final ConcurrentReadInputStream cris; in process() local 327 void processInner(final ConcurrentReadInputStream cris, final ConcurrentReadOutputStream[] ros){ in processInner() 339 …public void splitReads(final ConcurrentReadInputStream cris, final ConcurrentReadOutputStream[] ro… in splitReads() 471 final ConcurrentReadInputStream cris; field in KmerSplit.HashThread
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H A D | KmerReduce.java | 229 final ConcurrentReadInputStream cris; in process() local 269 …public void processInner(final ConcurrentReadInputStream cris, final ConcurrentReadOutputStream ro… in processInner() 340 final ConcurrentReadInputStream cris; field in KmerReduce.HashThread
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/dports/biology/bbmap/bbmap/current/pacbio/ |
H A D | MergeReadsAndGenome.java | 117 ConcurrentLegacyReadInputStream cris=new ConcurrentLegacyReadInputStream(ris, reads); in main() local 125 final ConcurrentReadInputStream cris; in main() local 141 public static long appendReads(ConcurrentReadInputStream cris, TextStreamWriter tsw, long id){ in appendReads()
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H A D | PartitionReads.java | 111 final ConcurrentReadInputStream cris; in main() local 143 …tic long process(TextStreamWriter[] tsw1, TextStreamWriter[] tsw2, ConcurrentReadInputStream cris){ in process()
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/dports/biology/bbmap/bbmap/current/template/ |
H A D | A_Sample.java | 240 final ConcurrentReadInputStream cris=makeCris(); in process() local 275 …ConcurrentReadInputStream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1,… in makeCris() local 300 void processInner(final ConcurrentReadInputStream cris, final ConcurrentReadOutputStream ros){ in processInner() 340 …void processList(ListNum<Read> ln, final ConcurrentReadInputStream cris, final ConcurrentReadOutpu… in processList()
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H A D | A_Sample_Generator.java | 215 final ConcurrentReadInputStream cris=makeCris(); in process() local 253 …ConcurrentReadInputStream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1,… in makeCris() local 278 …private void spawnThreads(final ConcurrentReadInputStream cris, final ConcurrentReadOutputStream r… in spawnThreads() 335 private ArrayList<Read> loadData(ConcurrentReadInputStream cris){ in loadData()
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H A D | BBTool_ST.java | 272 final ConcurrentReadInputStream cris; in startup() local 304 …protected final void shutdown(final ConcurrentReadInputStream cris, final ConcurrentReadOutputStre… in shutdown() 335 …protected void processInner(final ConcurrentReadInputStream cris, final ConcurrentReadOutputStream… in processInner()
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/dports/biology/bbmap/bbmap/current/stream/ |
H A D | CrisContainer.java | 74 public ConcurrentReadInputStream cris(){return cris;} in cris() method in CrisContainer 76 final ConcurrentReadInputStream cris; field in CrisContainer
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/dports/biology/bbmap/bbmap/current/jgi/ |
H A D | AdjustHomopolymers.java | 248 final ConcurrentReadInputStream cris=makeCris(); in process() local 283 …ConcurrentReadInputStream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1,… in makeCris() local 308 void processInner(final ConcurrentReadInputStream cris, final ConcurrentReadOutputStream ros){ in processInner() 348 …void processList(ListNum<Read> ln, final ConcurrentReadInputStream cris, final ConcurrentReadOutpu… in processList()
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H A D | IdentityMatrix.java | 96 …ConcurrentCollectionReadInputStream cris=new ConcurrentCollectionReadInputStream(allReads, null, -… in process() local 160 final ConcurrentReadInputStream cris; in load() local 280 private final ConcurrentReadInputStream cris; field in IdentityMatrix.ProcessThread
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H A D | SplitPairsAndSingles.java | 249 final ConcurrentReadInputStream cris; in process2() local 391 …private void process3(final ConcurrentReadInputStream cris, final ConcurrentReadOutputStream ros, … in process3() 428 …private void process3_fixInterleaving(final ConcurrentReadInputStream cris, final ConcurrentReadOu… in process3_fixInterleaving() 499 …private void process3_repair(final DualCris cris, final ConcurrentReadOutputStream ros, final Conc… in process3_repair() 560 …private void process3_repair(final ConcurrentReadInputStream cris, final ConcurrentReadOutputStrea… in process3_repair()
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H A D | FungalRelease.java | 198 final ConcurrentReadInputStream cris; in process() local 254 void processInner(final ConcurrentReadInputStream cris, final ConcurrentReadOutputStream ros, in processInner() 322 private ArrayList<Read> getReads(final ConcurrentReadInputStream cris) { in getReads()
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/dports/biology/bbmap/bbmap/current/sketch/ |
H A D | SSUMap.java | 47 ConcurrentReadInputStream cris=makeCris(ff, outstream); in loadSSU() local 87 ConcurrentReadInputStream cris=ConcurrentReadInputStream.getReadInputStream(-1, false, ff, null); in makeCris() local
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/dports/biology/bbmap/bbmap/current/hiseq/ |
H A D | PlotFlowCell.java | 232 final ConcurrentReadInputStream cris; in loadKmers() local 257 final ConcurrentReadInputStream cris; in fillTiles() local 276 public void loadKmersInner(final ConcurrentReadInputStream cris){ in loadKmersInner() 352 public void fillTilesInner(final ConcurrentReadInputStream cris){ in fillTilesInner()
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H A D | AnalyzeFlowCell.java | 346 final ConcurrentReadInputStream cris; in loadKmers() local 371 final ConcurrentReadInputStream cris; in fillTiles() local 397 final ConcurrentReadInputStream cris; in processReads() local 458 …void processInner(final ConcurrentReadInputStream cris, final ConcurrentReadOutputStream ros, fina… in processInner() 530 public void loadKmersInner(final ConcurrentReadInputStream cris){ in loadKmersInner() 606 public void fillTilesInner(final ConcurrentReadInputStream cris){ in fillTilesInner()
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/dports/biology/bbmap/bbmap/current/align2/ |
H A D | MakeQualityHistogram.java | 23 ConcurrentLegacyReadInputStream cris=new ConcurrentLegacyReadInputStream(rtis, maxReads); in main() local 54 public static int[][][] process(ConcurrentLegacyReadInputStream cris){ in process()
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/dports/biology/bbmap/bbmap/current/icecream/ |
H A D | IceCreamMaker.java | 304 final ConcurrentReadInputStream cris=makeCris(); in process() local 364 …ConcurrentReadInputStream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1,… in makeCris() local 384 …private void spawnThreads(final ConcurrentReadInputStream cris, final ConcurrentReadOutputStream r… in spawnThreads() 484 private byte[] loadData(ConcurrentReadInputStream cris, Random randy){ in loadData()
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H A D | ZMWStreamer.java | 73 …ConcurrentReadInputStream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ff, nu… in makeCris() local 237 private final ConcurrentReadInputStream cris; field in ZMWStreamer
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/dports/biology/bbmap/bbmap/current/cluster/ |
H A D | ReclusterByKmer.java | 191 final ConcurrentReadInputStream cris; in process() local 300 final ConcurrentReadInputStream cris; in findKmerSpectra() local 340 final ConcurrentReadInputStream cris; in recluster() local 518 final ConcurrentReadInputStream cris; field in ReclusterByKmer.ClusterThread
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/dports/biology/bbmap/bbmap/current/var2/ |
H A D | ApplyVariants.java | 249 final ConcurrentReadInputStream cris=makeCris(); in process() local 284 …ConcurrentReadInputStream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1,… in makeCris() local 304 void processInner(final ConcurrentReadInputStream cris, final ConcurrentReadOutputStream ros){ in processInner() 344 …void processList(ListNum<Read> ln, final ConcurrentReadInputStream cris, final ConcurrentReadOutpu… in processList()
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H A D | CallVariants2.java | 701 final ConcurrentReadInputStream cris; in prefilter() local 771 final ConcurrentReadInputStream cris; in processInput() local 802 private void spawnThreads(final ConcurrentReadInputStream cris, final SamReadStreamer ss, in spawnThreads() 1180 private final ConcurrentReadInputStream cris; field in ProcessThread
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/dports/biology/bbmap/bbmap/current/bloom/ |
H A D | KmerCount6MT.java | 221 final ConcurrentReadInputStream cris; in count() local 286 final ConcurrentReadInputStream cris; in count() local 380 private void count(ConcurrentReadInputStream cris, int k, boolean rcomp, KCountArray count){ in count() 444 private void count(final ConcurrentReadInputStream cris, final int k, final boolean rcomp, in count() 503 …private void countFastqSplit(final ConcurrentReadInputStream cris, final int k, final boolean rcom… in countFastqSplit() 689 private final ConcurrentReadInputStream cris; field in KmerCount6MT.CountThread
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H A D | KmerCount6.java | 118 final ConcurrentReadInputStream cris; in count() local 142 public static void count(ConcurrentReadInputStream cris, int k, boolean rcomp, KCountArray count){ in count() 225 final ConcurrentReadInputStream cris; in count() local 253 public static void count(final ConcurrentReadInputStream cris, final int k, final boolean rcomp, in count()
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