/dports/biology/bbmap/bbmap/current/shared/ |
H A D | MetadataWriter.java | 14 …public static void write(String fname, long readsIn, long basesIn, long readsOut, long basesOut, b… in write() argument 20 s=toJson(readsIn, basesIn, readsOut, basesOut); in write() 22 s=toTsv(readsIn, basesIn, readsOut, basesOut); in write() 27 public static String toTsv(long readsIn, long basesIn, long readsOut, long basesOut){ in toTsv() argument 46 sb.append("BasesOut\t").append(basesOut).append('\n'); in toTsv() 50 public static String toJson(long readsIn, long basesIn, long readsOut, long basesOut){ in toJson() argument 71 jo.add("BasesOut", basesOut); in toJson()
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/dports/biology/bbmap/bbmap/current/jgi/ |
H A D | Shred.java | 203 …outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false… in process() 217 basesOut=0; in processInner() 270 basesOut+=r1.length(); in processRead() 299 basesOut+=shred.length(); in processEvenly() 316 basesOut+=shred.length(); in processUnevenly() 336 basesOut+=shred.length(); 359 protected long basesOut=0;
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H A D | RQCFilterStats.java | 14 long basesOut; field in RQCFilterStats 97 assert(skipAssertion || basesIn>=basesOut) : toString(true); in toString() 99 …rtion || basesIn-totalBasesRemoved()==basesOut) : toString(true)+"\n"+basesIn+"-"+totalBasesRemove… in toString() 103 sb.append(format("Output", readsOut, basesOut, readsIn, basesIn)); in toString()
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H A D | TranslateSixFrames.java | 320 long basesOut=basesOut1+basesOut2; in process() local 323 …String aastring=(basesOut<100000 ? ""+basesOut : basesOut<100000000 ? (basesOut/1000)+"k" : (bases… in process()
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H A D | AdjustHomopolymers.java | 255 basesProcessed=basesOut=0; in process() 270 …outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false… in process() 377 basesOut+=r1.pairLength(); in processList() 495 protected long basesOut=0; field in AdjustHomopolymers
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H A D | FungalRelease.java | 227 basesOut = 0; in process() 244 MetadataWriter.write(null, readsProcessed, basesProcessed, readsOut, basesOut, false); in process() 367 basesOut += initialLength1; in getReads() 460 protected long basesOut = 0; field in FungalRelease
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H A D | DemuxByName.java | 389 long basesOut=0; in process() local 441 basesOut+=initialLength1; in process() 444 basesOut+=initialLength2; in process() 451 basesOut+=initialLength1; in process() 455 basesOut+=initialLength2; in process() 539 outstream.println("Bases Out: "+basesOut); in process()
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H A D | SplitPairsAndSingles.java | 232 basesOut+" bases ("+String.format(Locale.ROOT, "%.2f",basesOut*100.0/basesIn)+"%)"); in process() 425 basesOut+=singleBasesOut+pairBasesOut; in process3() 496 basesOut+=singleBasesOut+pairBasesOut; in process3_fixInterleaving() 557 basesOut+=singleBasesOut+pairBasesOut; in process3_repair() 609 basesOut+=singleBasesOut+pairBasesOut; in process3_repair() 773 long basesOut=0; field in SplitPairsAndSingles
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H A D | KeepBestCopy.java | 152 long basesProcessed=0, basesOut=0; in process() local 207 basesOut+=r.length(); in process() 222 …outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false… in process()
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H A D | RQCFilter2.java | 1902 filterstats.basesOut=duk.basesOut; in ktrim() 2164 long bRemoved=duk.basesIn-duk.basesOut; in filter1() 2179 filterstats.basesOut=duk.basesOut; in filter1() 2283 filterstats.basesOut=duk.basesOut; in filter2() 2369 filterstats.basesOut=duk.basesOut; in filterRibo() 2632 assert(lastBasesIn==filterstats.basesOut) : lastBasesIn+", "+filterstats.basesOut; in dehumanize() 2654 filterstats.basesOut=lastBasesOut; in dehumanize() 2759 return fbt.basesOut>0 ? temp : null; in taxFilter() 2994 assert(lastBasesIn==filterstats.basesOut) : lastBasesIn+", "+filterstats.basesOut; in removeCommonMicrobes() 3004 filterstats.basesOut=lastBasesOut; in removeCommonMicrobes() [all …]
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/dports/biology/bbmap/bbmap/current/driver/ |
H A D | ReduceSilva.java | 165 basesOut=0; in process() 184 String bostring=""+basesOut; in process() 197 …ses Out: "+bostring+" \t"+String.format(Locale.ROOT, "%.2f%%", basesOut*100.0/basesProces… in process() 236 basesOut+=initialLength1; in processInner() 296 protected long basesOut=0; field in ReduceSilva
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/transformers/ |
H A D | BaseQualityClipReadTransformerTest.java | 41 …public void testApply(final String quals_in, final String basesOut, final String qualsOut, final S… in testApply() argument 48 Assert.assertEquals(readOut.getBases(),basesOut.getBytes()); in testApply()
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/dports/biology/bbmap/bbmap/current/prok/ |
H A D | SplitRibo.java | 101 basesOut=new long[numTypes]; in SplitRibo() 262 Arrays.fill(basesOut, 0); in process() 280 long basesOut2=Tools.sum(basesOut)-basesOut[0]; in process() 361 Tools.add(basesOut, pt.basesOutT); 596 final long[] basesOut;
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H A D | MergeRibo_Fast.java | 220 basesProcessed=basesOut=0; in process() 239 basesOut+=r.length(); in process() 260 …outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false… in process() 521 protected long basesOut=0;
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H A D | FilterSilva.java | 162 long basesProcessed=0, basesOut=0; in process() local 187 basesOut+=r1.length(); in process() 211 …outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false… in process()
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/dports/biology/bbmap/bbmap/current/pacbio/ |
H A D | RemoveAdapters2.java | 223 long basesOut=0; in printStatistics() local 232 basesOut+=pt.basesOut; in printStatistics() 254 ….println("Reads Out: \t"+readsOut+" \t("+basesOut+" bases, avg length "+(basesOut/r… in printStatistics() 336 basesOut+=r.length(); 339 basesOut+=r2.length(); 598 long basesOut=0;
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/dports/biology/bbmap/bbmap/current/template/ |
H A D | A_Sample.java | 247 basesProcessed=basesOut=0; in process() 262 …outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false… in process() 369 basesOut+=r1.pairLength(); in processList() 431 protected long basesOut=0; field in A_Sample
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H A D | A_Sample_Generator.java | 223 basesProcessed=basesOut=0; in process() 243 …outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false… in process() 323 basesOut+=pt.basesOutT; in waitForThreads() 495 protected long basesOut=0; field in A_Sample_Generator
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H A D | A_SampleSamStreamer.java | 252 basesProcessed=basesOut=0; in process() 270 …outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false… in process() 358 basesOut+=pt.basesOutT; 516 protected long basesOut=0; local
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H A D | A_Sample_Unpaired.java | 155 long basesProcessed=0, basesOut=0; in process() local 180 basesOut+=r1.length(); in process() 204 …outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false… in process()
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H A D | A_SampleMT.java | 261 basesProcessed=basesOut=0; in process() 279 …outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false… in process() 343 basesOut+=pt.basesOutT; 523 protected long basesOut=0;
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/dports/biology/bbmap/bbmap/current/stream/ |
H A D | SamStreamerWrapper.java | 132 long basesProcessed=0, basesOut=0; in process() local 168 basesOut+=len; in process() 182 outstream.println("Bases Out: "+basesOut); in process()
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/dports/biology/bbmap/bbmap/current/gff/ |
H A D | CutGff.java | 283 …outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false… in processST() 297 basesProcessed=basesOut=0; in processMT() 313 …outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false… in processMT() 374 basesOut+=r.length(); in processFile() 381 basesOut+=r.length(); in processFile() 634 basesOut+=pt.basesOutT; in accumulate() 782 protected long basesOut=0; field in CutGff
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/dports/biology/bbmap/bbmap/current/sketch/ |
H A D | KmerLimit2.java | 276 basesProcessed=basesOut=0; in process() 336 …outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false… in process() 392 basesOut+=pt.basesOutT; 442 basesOut=0; 474 basesOut+=pt.basesOutT; 918 protected long basesOut=0; field in KmerLimit2
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/dports/biology/bbmap/bbmap/current/tax/ |
H A D | ExplodeTree.java | 224 outstream.println(ro+"\t"+basesOut+" bases"); in process() 283 if(!header){basesOut+=line.length;} in processInner() 333 public long basesOut=0; field in ExplodeTree
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