| /dports/biology/bbmap/bbmap/current/stream/ |
| H A D | CrisWrapper.java | 26 public CrisWrapper(ConcurrentReadInputStream cris_, boolean start){ in CrisWrapper() argument
27 initialize(cris_, start); in CrisWrapper()
30 public void initialize(ConcurrentReadInputStream cris_, boolean start){ in initialize() argument
31 cris=cris_; in initialize()
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| H A D | CrisContainer.java | 20 public CrisContainer(ConcurrentReadInputStream cris_, Comparator<Read> comparator_){ in CrisContainer() argument
22 cris=cris_; in CrisContainer()
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| H A D | ConcurrentReadInputStreamD.java | 23 …public ConcurrentReadInputStreamD(ConcurrentReadInputStream cris_, boolean master_, boolean keepAl… in ConcurrentReadInputStreamD() argument
24 source=cris_; in ConcurrentReadInputStreamD()
29 assert(master==(cris_!=null)); in ConcurrentReadInputStreamD()
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| /dports/biology/bbmap/bbmap/current/clump/ |
| H A D | StreamToOutput.java | 25 …public StreamToOutput(ConcurrentReadInputStream cris_, ConcurrentReadOutputStream[] rosa_, KmerCom… in StreamToOutput() argument
26 cris=cris_; in StreamToOutput()
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| H A D | PivotSet.java | 278 HashThread(ConcurrentReadInputStream cris_, KmerComparator kc_, KCountArray kca_, boolean ecco_){ in HashThread() argument
279 cris=cris_; in HashThread()
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| H A D | KmerReduce.java | 304 HashThread(ConcurrentReadInputStream cris_, ConcurrentReadOutputStream ros_, KmerComparator kc_){ in HashThread() argument
305 cris=cris_; in HashThread()
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| H A D | KmerSort.java | 327 FetchThread1(int id_, ConcurrentReadInputStream cris_, KmerComparator kc_, boolean unpair_){ in FetchThread1() argument
329 cris=cris_; in FetchThread1()
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| H A D | KmerSplit.java | 383 …HashThread(int id_, ConcurrentReadInputStream cris_, ConcurrentReadOutputStream[] ros_, KmerCompar… in HashThread() argument
385 cris=cris_; in HashThread()
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| /dports/biology/bbmap/bbmap/current/icecream/ |
| H A D | ZMWStreamer.java | 42 public ZMWStreamer(ConcurrentReadInputStream cris_, SamStreamer ss_, int queuelen_){ in ZMWStreamer() argument
43 cris=cris_; in ZMWStreamer()
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| /dports/biology/bbmap/bbmap/current/jgi/ |
| H A D | FilterBySequence.java | 434 …ProcessThread(final ConcurrentReadInputStream cris_, final ConcurrentReadOutputStream ros_, final …
435 cris=cris_;
556 LoadThread(final ConcurrentReadInputStream cris_, final int tid_){
557 cris=cris_;
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| H A D | IdentityMatrix.java | 218 ProcessThread(ConcurrentReadInputStream cris_){ in ProcessThread() argument
219 cris=cris_; in ProcessThread()
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| H A D | KmerCountMulti.java | 363 ProcessThread(final ConcurrentReadInputStream cris_, final int tid_){
364 cris=cris_;
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| H A D | FindPrimers.java | 299 …ProcessThread(final ConcurrentReadInputStream cris_, final ConcurrentReadOutputStream ros_, final … in ProcessThread() argument
300 cris=cris_; in ProcessThread()
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| /dports/biology/bbmap/bbmap/current/bloom/ |
| H A D | KmerCount6MT.java | 335 …CountThread(final ConcurrentReadInputStream cris_, final int k_, final boolean rcomp_, final KCoun… in CountThread() argument
336 this(cris_, k_, rcomp_, count_, null, 2, 1, true); in CountThread()
339 CountThread(final ConcurrentReadInputStream cris_, final int k_, final boolean rcomp_, in CountThread() argument
341 cris=cris_; in CountThread()
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| H A D | KmerCount7MT.java | 424 …CountThread(final ConcurrentReadInputStream cris_, final int k_, final boolean rcomp_, final KCoun…
425 this(cris_, k_, rcomp_, count_, null, 2, 1, true);
428 CountThread(final ConcurrentReadInputStream cris_, final int k_, final boolean rcomp_,
430 cris=cris_;
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| H A D | BloomFilterWrapper.java | 442 …ProcessThread(final ConcurrentReadInputStream cris_, final ConcurrentReadOutputStream rosu_, final…
443 cris=cris_;
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| /dports/biology/bbmap/bbmap/current/cardinality/ |
| H A D | LogLogWrapper.java | 288 LogLogThread(CardinalityTracker log_, ConcurrentReadInputStream cris_, int tid_){ in LogLogThread() argument
290 cris=cris_; in LogLogThread()
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| H A D | LogLog_old.java | 478 LogLogThread(LogLog_old log_, ConcurrentReadInputStream cris_){ in LogLogThread() argument
480 cris=cris_; in LogLogThread()
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| /dports/biology/bbmap/bbmap/current/template/ |
| H A D | A_SampleMT.java | 363 …ProcessThread(final ConcurrentReadInputStream cris_, final ConcurrentReadOutputStream ros_, final …
364 cris=cris_;
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| /dports/biology/bbmap/bbmap/current/prok/ |
| H A D | MergeRibo_Fast.java | 334 ProcessThread(final ConcurrentReadInputStream cris_, final int tid_){
335 cris=cris_;
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| H A D | SplitRibo.java | 382 …ProcessThread(final ConcurrentReadInputStream cris_, final ConcurrentReadOutputStream[] rosa_, fin…
383 cris=cris_;
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| H A D | RiboMaker.java | 468 ProcessThread(final ConcurrentReadInputStream cris_, final int tid_){
469 cris=cris_;
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| /dports/biology/bbmap/bbmap/current/var2/ |
| H A D | Realign.java | 343 …ProcessThread(final ConcurrentReadInputStream cris_, final ConcurrentReadOutputStream ros_, final …
344 cris=cris_;
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| /dports/biology/bbmap/bbmap/current/sketch/ |
| H A D | KmerLimit.java | 373 …ProcessThread(final ConcurrentReadInputStream cris_, final ConcurrentReadOutputStream ros_, final …
374 cris=cris_;
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| /dports/biology/bbmap/bbmap/current/cluster/ |
| H A D | ReclusterByKmer.java | 376 public ClusterThread(int id_, int clusterMode_, int ambigMode_, ConcurrentReadInputStream cris_){ in ClusterThread() argument
380 cris=cris_; in ClusterThread()
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