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Searched refs:qfin2 (Results 1 – 25 of 38) sorted by relevance

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/dports/biology/bbmap/bbmap/current/template/
H A DA_Sample.java86 qfin2=parser.qfin2; in A_Sample()
176 qfin2=Tools.fixExtension(qfin2); in fixExtensions()
275 …ream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in makeCris()
403 private String qfin2=null; field in A_Sample
H A DA_SampleMT.java86 qfin2=parser.qfin2; in A_SampleMT()
179 qfin2=Tools.fixExtension(qfin2); in fixExtensions()
288 …ream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2);
495 private String qfin2=null;
H A DBBTool_ST.java104 qfin2=parser.qfin2; in BBTool_ST()
268 if(!Tools.testForDuplicateFiles(true, in1, in2, qfin1, qfin2, out1, out2, qfout1, qfout2)){ in startup()
276 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in startup()
410 protected String qfin2=null; field in BBTool_ST
/dports/biology/bbmap/bbmap/current/jgi/
H A DBBQC.java102 qfin2=b; in BBQC()
378 … String in1s=stripDirs(in1), in2s=stripDirs(in2), qfin1s=stripDirs(qfin1), qfin2s=stripDirs(qfin2); in process()
381 ktrim(in1, in2, out1s, out2s, qfin1, qfin2, qfout1s, qfout2s, trimPrefix); in process()
496 if(qfin2!=null){argList.add("qfin2="+qfin2);} in ktrim()
556 …private void filter(String in1, String in2, String out1, String out2, String qfin1, String qfin2, … in filter() argument
589 …if(qfin2!=null){argList.add("qfin2="+(prependIndir ? (tmpDir==null ? outDir : tmpDir) : "")+inPref… in filter()
655 …ivate void dehumanize(String in1, String in2, String out1, String out2, String qfin1, String qfin2, in dehumanize() argument
702 …if(qfin2!=null){argList.add("qfin2="+(prependIndir ? (tmpDir==null ? outDir : tmpDir) : "")+inPref… in dehumanize()
737 …ze(String in1, String in2, String out1, String out2, String qfin1, String qfin2, String qfout1, St… in normalize() argument
789 …if(qfin2!=null){argList.add("qfin2="+(prependIndir ? (tmpDir==null ? outDir : tmpDir) : "")+inPref… in normalize()
[all …]
H A DAdjustHomopolymers.java90 qfin2=parser.qfin2; in AdjustHomopolymers()
184 qfin2=Tools.fixExtension(qfin2); in fixExtensions()
283 …ream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in makeCris()
460 private String qfin2=null; field in AdjustHomopolymers
H A DPartitionReads.java113 qfin2=parser.qfin2; in PartitionReads()
133 if(qfin1!=null && qfin2==null && qfin1.indexOf('#')>-1 && !new File(qfin1).exists()){ in PartitionReads()
134 qfin2=qfin1.replace("#", "2"); in PartitionReads()
242 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process()
374 private String qfin2=null; field in PartitionReads
H A DKmerCountMulti.java138 qfin2=parser.qfin2; in KmerCountMulti()
216 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process()
467 private String qfin2=null;
H A DReplaceHeaders.java114 qfin2=parser.qfin2; in ReplaceHeaders()
219 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process()
402 private String qfin2=null; field in ReplaceHeaders
H A DKExpand.java88 qfin2=parser.qfin2; in KExpand()
247 qfin2=Tools.fixExtension(qfin2); in fixExtensions()
373 …ream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in makeCris()
788 private String qfin2=null; field in KExpand
H A DTranslateSixFrames.java124 qfin2=parser.qfin2; in TranslateSixFrames()
197 …oncurrentReadInputStream.getReadInputStream(maxReads, useSharedHeader, ffin1, ffin2, qfin1, qfin2); in process()
369 private String qfin2=null; field in TranslateSixFrames
H A DCorrelateBarcodes.java109 qfin2=parser.qfin2; in CorrelateBarcodes()
180 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process()
383 private String qfin2=null; field in CorrelateBarcodes
H A DCountBarcodes.java129 qfin2=parser.qfin2; in CountBarcodes()
202 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process()
376 private String qfin2=null; field in CountBarcodes
H A DMergeBarcodes.java112 qfin2=parser.qfin2; in MergeBarcodes()
286 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in mergeWithMap()
405 private String qfin2=null; field in MergeBarcodes
H A DFilterBySequence.java134 qfin2=parser.qfin2; in FilterBySequence()
263 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process()
717 private String qfin2=null;
H A DRenameReads.java109 qfin2=b; in RenameReads()
224 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process()
328 private String qfin2=null; field in RenameReads
/dports/biology/bbmap/bbmap/current/prok/
H A DRiboMaker.java92 qfin2=parser.qfin2; in RiboMaker()
187 qfin2=Tools.fixExtension(qfin2); in fixExtensions()
372 …ream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2);
627 private String qfin2=null;
/dports/biology/bbmap/bbmap/current/tax/
H A DFilterByTaxa.java116 qfin2=parser.qfin2; in FilterByTaxa()
214 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process()
369 private String qfin2=null; field in FilterByTaxa
/dports/biology/bbmap/bbmap/current/driver/
H A DLoadReads.java114 qfin2=parser.qfin2; in LoadReads()
177 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process()
389 private String qfin2=null; field in LoadReads
H A DFilterReadsByName.java175 qfin2=parser.qfin2; in FilterReadsByName()
254 …oncurrentReadInputStream.getReadInputStream(maxReads, useSharedHeader, ffin1, ffin2, qfin1, qfin2); in process()
393 private String qfin2=null; field in FilterReadsByName
/dports/biology/bbmap/bbmap/current/hiseq/
H A DPlotFlowCell.java134 qfin2=parser.qfin2; in PlotFlowCell()
234 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in loadKmers()
259 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in fillTiles()
517 private String qfin2=null; field in PlotFlowCell
/dports/biology/bbmap/bbmap/current/sort/
H A DShuffle.java140 qfin2=parser.qfin2; in Shuffle()
213 …oncurrentReadInputStream.getReadInputStream(maxReads, useSharedHeader, ffin1, ffin2, qfin1, qfin2); in process()
385 private String qfin2=null; field in Shuffle
/dports/biology/bbmap/bbmap/current/sketch/
H A DKmerLimit.java151 qfin2=parser.qfin2; in KmerLimit()
255 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process()
580 private String qfin2=null; field in KmerLimit
H A DKmerLimit2.java158 qfin2=parser.qfin2; in KmerLimit2()
352 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2);
412 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2);
893 private String qfin2=null; field in KmerLimit2
/dports/biology/bbmap/bbmap/current/bloom/
H A DBloomFilterCorrectorWrapper.java252 qfin2=parser.qfin2; in BloomFilterCorrectorWrapper()
282 qfin2=Tools.fixExtension(qfin2); in BloomFilterCorrectorWrapper()
416 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process()
882 private String qfin2=null; field in BloomFilterCorrectorWrapper
H A DBloomFilterWrapper.java191 qfin2=parser.qfin2; in BloomFilterWrapper()
310 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process()
598 private String qfin2=null; field in BloomFilterWrapper

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