/dports/biology/bbmap/bbmap/current/jgi/ |
H A D | CountUniqueness.java | 32 double bpnano=basesProcessed/(double)(t.elapsed); in process() 35 …String bpstring=(basesProcessed<100000 ? ""+basesProcessed : basesProcessed<100000000 ? (basesProc… in process() 52 basesProcessed+=r1.length(); in process() 54 basesProcessed+=r2.length(); in process() 106 private long basesProcessed=0; field in CountUniqueness
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H A D | MergeBarcodes.java | 209 long basesProcessed=0; in loadBarcodes() local 236 basesProcessed+=initialLength1; in loadBarcodes() 240 basesProcessed+=initialLength2; in loadBarcodes() 261 double bpnano=basesProcessed/(double)(t.elapsed); in loadBarcodes() 264 String bpstring=Tools.padKM(basesProcessed, 8); in loadBarcodes() 309 long basesProcessed=0; in mergeWithMap() local 337 basesProcessed+=initialLength1; in mergeWithMap() 342 basesProcessed+=initialLength2; in mergeWithMap() 386 outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8)); in mergeWithMap()
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H A D | MakeChimeras.java | 137 long basesProcessed=0; in process() local 164 basesProcessed+=initialLength1; in process() 179 outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8)); in process() 198 long basesProcessed=0; in process() local 210 basesProcessed+=c.length(); in process() 218 outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8)); in process()
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H A D | AddAdapters.java | 360 …esAdded+" bases ("+String.format(Locale.ROOT, "%.2f",adapterBasesAdded*100.0/basesProcessed)+"%)"); in write() 363 validBases+" bases ("+String.format(Locale.ROOT, "%.2f",validBases*100.0/basesProcessed)+"%)"); in write() 366 outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8)); in write() 381 basesProcessed+=initial; in addAdapter() 516 long incorrectBases=basesProcessed-correctBases; in read() 518 … \t"+readsProcessed+" reads \t"+basesProcessed+" bases … in read() 520 …correctBases+" bases ("+String.format(Locale.ROOT, "%.3f",correctBases*100.0/basesProcessed)+"%)"); in read() 522 …rrectBases+" bases ("+String.format(Locale.ROOT, "%.3f",incorrectBases*100.0/basesProcessed)+"%)"); in read() 530 …ing+" bases ("+String.format(Locale.ROOT, "%.3f",adapterBasesRemaining*100.0/basesProcessed)+"%)"); in read() 592 basesProcessed+=actual; in grade() [all …]
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H A D | Shred.java | 190 basesProcessed=0; in process() 202 outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8)); in process() 203 …outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false… in process() 214 basesProcessed=0; in processInner() 237 basesProcessed+=initialLength1; in processInner() 357 protected long basesProcessed=0;
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H A D | AdjustHomopolymers.java | 255 basesProcessed=basesOut=0; in process() 269 outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8)); in process() 270 …outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false… in process() 368 basesProcessed+=initialLength1+initialLength2; in processList() 490 protected long basesProcessed=0; field in AdjustHomopolymers
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H A D | FungalRelease.java | 225 basesProcessed = 0; in process() 243 outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8)); in process() 244 MetadataWriter.write(null, readsProcessed, basesProcessed, readsOut, basesOut, false); in process() 361 basesProcessed += initialLength1; in getReads() 455 protected long basesProcessed = 0; field in FungalRelease
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/dports/biology/bbmap/bbmap/current/driver/ |
H A D | ReduceSilva.java | 162 basesProcessed=0; in process() 179 double bpnano=basesProcessed/(double)(t.elapsed); in process() 182 String bpstring=""+basesProcessed; in process() 197 …ut: "+bostring+" \t"+String.format(Locale.ROOT, "%.2f%%", basesOut*100.0/basesProcessed)); in process() 208 basesProcessed=0; in processInner() 230 basesProcessed+=initialLength1; in processInner() 293 protected long basesProcessed=0; field in ReduceSilva
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H A D | RenameAndMux.java | 161 final long basesProcessed=basesProcessedA.get(); in process() local 165 outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8)); in process() 341 long basesProcessed=0; in renameAndMergeOneFile() local 419 basesProcessed+=initialLength1; in renameAndMergeOneFile() 424 basesProcessed+=initialLength2; in renameAndMergeOneFile() 448 basesProcessedA.addAndGet(basesProcessed); in renameAndMergeOneFile()
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H A D | LoadReads.java | 187 basesProcessed=0; in process() 221 double basesPerRead=basesProcessed*mult; in process() 287 outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8)); in process() 332 basesProcessed+=initialLength1+initialLength2; in processInner() 401 protected long basesProcessed=0; field in LoadReads
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/dports/biology/bbmap/bbmap/current/template/ |
H A D | BBTool_ST.java | 253 basesProcessed=0; in process() 295 basesProcessed=0; in startup() 320 outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8)); in showStats() 322 showStatsSubclass(t, readsProcessed, basesProcessed); in showStats() 338 basesProcessed=0; in processInner() 362 basesProcessed+=initialLength1; in processInner() 366 basesProcessed+=initialLength2; in processInner() 427 protected long basesProcessed=0; field in BBTool_ST
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H A D | A_Sample.java | 247 basesProcessed=basesOut=0; in process() 261 outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8)); in process() 262 …outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false… in process() 360 basesProcessed+=initialLength1+initialLength2; in processList() 426 protected long basesProcessed=0; field in A_Sample
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H A D | A_Sample_Generator.java | 223 basesProcessed=basesOut=0; in process() 242 outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8)); in process() 243 …outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false… in process() 355 basesProcessed+=r.pairLength(); in loadData() 490 protected long basesProcessed=0; field in A_Sample_Generator
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H A D | A_Sample_Unpaired.java | 155 long basesProcessed=0, basesOut=0; in process() local 184 basesProcessed+=initialLength1; in process() 203 outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8)); in process() 204 …outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false… in process()
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H A D | A_SampleSamStreamer.java | 252 basesProcessed=basesOut=0; in process() 269 outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8)); in process() 270 …outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false… in process() 356 basesProcessed+=pt.basesProcessedT; 511 protected long basesProcessed=0; local
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H A D | A_SampleMT.java | 261 basesProcessed=basesOut=0; in process() 278 outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8)); in process() 279 …outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false… in process() 341 basesProcessed+=pt.basesProcessedT; 518 protected long basesProcessed=0;
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/dports/biology/bbmap/bbmap/current/stream/ |
H A D | SamStreamerMF.java | 78 basesProcessed=0; in start() 98 basesProcessed+=srs.basesProcessed; in nextReads() 147 protected long basesProcessed=0; field in SamStreamerMF
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H A D | SamStreamerWrapper.java | 132 long basesProcessed=0, basesOut=0; in process() local 140 basesProcessed+=len; in process() 180 …tream.println("Bases Processed: "+basesProcessed+" \t"+String.format(Locale.ROOT, "%.2f Mbp/sec… in process()
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/dports/biology/bbmap/bbmap/current/icecream/ |
H A D | IceCreamGrader.java | 128 long basesProcessed=0, basesOut=0; in process() local 157 basesProcessed+=initialLength1; in process() 174 outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8)); in process() 178 …outstream.println(Tools.numberPercent("Good Bases:", goodBases, goodBases*100.0/basesProcessed, 3,… in process() 180 …outstream.println(Tools.numberPercent("Bad Bases:", badBases, badBases*100.0/basesProcessed, 3, 8)… in process()
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/dports/biology/bbmap/bbmap/current/tax/ |
H A D | TaxSize.java | 176 double bpnano=basesProcessed/(double)(t.elapsed); in process() 181 String bpstring=Tools.padKM(basesProcessed, 8); in process() 191 outstream.println(ri+"\t"+basesProcessed+" bases"); in process() 254 basesProcessed+=line.length; in processInner() 298 protected long basesProcessed=0; field in TaxSize
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H A D | ExplodeTree.java | 208 double bpnano=basesProcessed/(double)(t.elapsed); in process() 213 String bpstring=Tools.padKM(basesProcessed, 8); in process() 223 outstream.println(ri+"\t"+basesProcessed+" bases"); in process() 278 basesProcessed+=line.length; in processInner() 326 protected long basesProcessed=0; field in ExplodeTree
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H A D | FilterByTaxa.java | 236 basesProcessed=0; in process() 256 outstream.println(ri+"\t"+basesProcessed+" bases"); in process() 259 outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8)); in process() 300 basesProcessed+=initialLength1+initialLength2; in processInner() 400 protected long basesProcessed=0; field in FilterByTaxa
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H A D | SplitByTaxa.java | 220 basesProcessed=0; in process() 240 …outstream.println("Reads In: \t"+readsProcessed+" reads \t"+basesProcessed+" b… in process() 242 outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8)); in process() 279 basesProcessed+=initialLength1+initialLength2; in processInner() 353 protected long basesProcessed=0; field in SplitByTaxa
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/dports/biology/bbmap/bbmap/current/prok/ |
H A D | FilterSilva.java | 162 long basesProcessed=0, basesOut=0; in process() local 191 basesProcessed+=initialLength1; in process() 210 outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8)); in process() 211 …outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false… in process()
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H A D | MergeRibo_Fast.java | 220 basesProcessed=basesOut=0; in process() 259 outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8)); in process() 260 …outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false… in process() 314 basesProcessed+=pt.basesProcessedT; 516 protected long basesProcessed=0;
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