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Searched defs:cris (Results 1 – 25 of 160) sorted by relevance

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/dports/biology/bbmap/bbmap/current/clump/
H A DStreamToOutput.java18 …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
H A DPivotSet.java172 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
H A DKmerSplit.java282 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
H A DKmerReduce.java229 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
/dports/biology/bbmap/bbmap/current/pacbio/
H A DMergeReadsAndGenome.java117 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()
H A DPartitionReads.java111 final ConcurrentReadInputStream cris; in main() local
143 …tic long process(TextStreamWriter[] tsw1, TextStreamWriter[] tsw2, ConcurrentReadInputStream cris){ in process()
/dports/biology/bbmap/bbmap/current/template/
H A DA_Sample.java240 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()
H A DA_Sample_Generator.java215 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()
H A DBBTool_ST.java272 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()
/dports/biology/bbmap/bbmap/current/stream/
H A DCrisContainer.java74 public ConcurrentReadInputStream cris(){return cris;} in cris() method in CrisContainer
76 final ConcurrentReadInputStream cris; field in CrisContainer
/dports/biology/bbmap/bbmap/current/jgi/
H A DAdjustHomopolymers.java248 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()
H A DIdentityMatrix.java96 …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
H A DSplitPairsAndSingles.java249 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()
H A DFungalRelease.java198 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()
/dports/biology/bbmap/bbmap/current/sketch/
H A DSSUMap.java47 ConcurrentReadInputStream cris=makeCris(ff, outstream); in loadSSU() local
87 ConcurrentReadInputStream cris=ConcurrentReadInputStream.getReadInputStream(-1, false, ff, null); in makeCris() local
/dports/biology/bbmap/bbmap/current/hiseq/
H A DPlotFlowCell.java232 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()
H A DAnalyzeFlowCell.java346 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()
/dports/biology/bbmap/bbmap/current/align2/
H A DMakeQualityHistogram.java23 ConcurrentLegacyReadInputStream cris=new ConcurrentLegacyReadInputStream(rtis, maxReads); in main() local
54 public static int[][][] process(ConcurrentLegacyReadInputStream cris){ in process()
/dports/biology/bbmap/bbmap/current/icecream/
H A DIceCreamMaker.java304 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()
H A DZMWStreamer.java73 …ConcurrentReadInputStream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ff, nu… in makeCris() local
237 private final ConcurrentReadInputStream cris; field in ZMWStreamer
/dports/biology/bbmap/bbmap/current/cluster/
H A DReclusterByKmer.java191 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
/dports/biology/bbmap/bbmap/current/var2/
H A DApplyVariants.java249 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()
H A DCallVariants2.java701 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
/dports/biology/bbmap/bbmap/current/bloom/
H A DKmerCount6MT.java221 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
H A DKmerCount6.java118 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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