/dports/biology/bbmap/bbmap/current/template/ |
H A D | A_Sample.java | 86 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
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H A D | A_SampleMT.java | 86 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;
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H A D | BBTool_ST.java | 104 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
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/dports/biology/bbmap/bbmap/current/jgi/ |
H A D | BBQC.java | 102 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 …]
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H A D | AdjustHomopolymers.java | 90 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
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H A D | PartitionReads.java | 113 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
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H A D | KmerCountMulti.java | 138 qfin2=parser.qfin2; in KmerCountMulti() 216 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process() 467 private String qfin2=null;
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H A D | ReplaceHeaders.java | 114 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
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H A D | KExpand.java | 88 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
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H A D | TranslateSixFrames.java | 124 qfin2=parser.qfin2; in TranslateSixFrames() 197 …oncurrentReadInputStream.getReadInputStream(maxReads, useSharedHeader, ffin1, ffin2, qfin1, qfin2); in process() 369 private String qfin2=null; field in TranslateSixFrames
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H A D | CorrelateBarcodes.java | 109 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
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H A D | CountBarcodes.java | 129 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
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H A D | MergeBarcodes.java | 112 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
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H A D | FilterBySequence.java | 134 qfin2=parser.qfin2; in FilterBySequence() 263 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process() 717 private String qfin2=null;
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H A D | RenameReads.java | 109 qfin2=b; in RenameReads() 224 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process() 328 private String qfin2=null; field in RenameReads
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/dports/biology/bbmap/bbmap/current/prok/ |
H A D | RiboMaker.java | 92 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;
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/dports/biology/bbmap/bbmap/current/tax/ |
H A D | FilterByTaxa.java | 116 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
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/dports/biology/bbmap/bbmap/current/driver/ |
H A D | LoadReads.java | 114 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
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H A D | FilterReadsByName.java | 175 qfin2=parser.qfin2; in FilterReadsByName() 254 …oncurrentReadInputStream.getReadInputStream(maxReads, useSharedHeader, ffin1, ffin2, qfin1, qfin2); in process() 393 private String qfin2=null; field in FilterReadsByName
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/dports/biology/bbmap/bbmap/current/hiseq/ |
H A D | PlotFlowCell.java | 134 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
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/dports/biology/bbmap/bbmap/current/sort/ |
H A D | Shuffle.java | 140 qfin2=parser.qfin2; in Shuffle() 213 …oncurrentReadInputStream.getReadInputStream(maxReads, useSharedHeader, ffin1, ffin2, qfin1, qfin2); in process() 385 private String qfin2=null; field in Shuffle
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/dports/biology/bbmap/bbmap/current/sketch/ |
H A D | KmerLimit.java | 151 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
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H A D | KmerLimit2.java | 158 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
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/dports/biology/bbmap/bbmap/current/bloom/ |
H A D | BloomFilterCorrectorWrapper.java | 252 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
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H A D | BloomFilterWrapper.java | 191 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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