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Searched refs:basesOut (Results 1 – 25 of 56) sorted by relevance

123

/dports/biology/bbmap/bbmap/current/shared/
H A DMetadataWriter.java14 …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()
/dports/biology/bbmap/bbmap/current/jgi/
H A DShred.java203 …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;
H A DRQCFilterStats.java14 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()
H A DTranslateSixFrames.java320 long basesOut=basesOut1+basesOut2; in process() local
323 …String aastring=(basesOut<100000 ? ""+basesOut : basesOut<100000000 ? (basesOut/1000)+"k" : (bases… in process()
H A DAdjustHomopolymers.java255 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
H A DFungalRelease.java227 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
H A DDemuxByName.java389 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()
H A DSplitPairsAndSingles.java232 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
H A DKeepBestCopy.java152 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()
H A DRQCFilter2.java1902 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 …]
/dports/biology/bbmap/bbmap/current/driver/
H A DReduceSilva.java165 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
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/transformers/
H A DBaseQualityClipReadTransformerTest.java41 …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()
/dports/biology/bbmap/bbmap/current/prok/
H A DSplitRibo.java101 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;
H A DMergeRibo_Fast.java220 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;
H A DFilterSilva.java162 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()
/dports/biology/bbmap/bbmap/current/pacbio/
H A DRemoveAdapters2.java223 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;
/dports/biology/bbmap/bbmap/current/template/
H A DA_Sample.java247 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
H A DA_Sample_Generator.java223 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
H A DA_SampleSamStreamer.java252 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
H A DA_Sample_Unpaired.java155 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()
H A DA_SampleMT.java261 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;
/dports/biology/bbmap/bbmap/current/stream/
H A DSamStreamerWrapper.java132 long basesProcessed=0, basesOut=0; in process() local
168 basesOut+=len; in process()
182 outstream.println("Bases Out: "+basesOut); in process()
/dports/biology/bbmap/bbmap/current/gff/
H A DCutGff.java283 …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
/dports/biology/bbmap/bbmap/current/sketch/
H A DKmerLimit2.java276 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
/dports/biology/bbmap/bbmap/current/tax/
H A DExplodeTree.java224 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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