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Searched refs:basesProcessed (Results 1 – 25 of 121) sorted by relevance

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/dports/biology/bbmap/bbmap/current/jgi/
H A DCountUniqueness.java32 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
H A DMergeBarcodes.java209 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()
H A DMakeChimeras.java137 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()
H A DAddAdapters.java360 …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 …]
H A DShred.java190 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;
H A DAdjustHomopolymers.java255 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
H A DFungalRelease.java225 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
/dports/biology/bbmap/bbmap/current/driver/
H A DReduceSilva.java162 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
H A DRenameAndMux.java161 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()
H A DLoadReads.java187 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
/dports/biology/bbmap/bbmap/current/template/
H A DBBTool_ST.java253 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
H A DA_Sample.java247 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
H A DA_Sample_Generator.java223 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
H A DA_Sample_Unpaired.java155 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()
H A DA_SampleSamStreamer.java252 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
H A DA_SampleMT.java261 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;
/dports/biology/bbmap/bbmap/current/stream/
H A DSamStreamerMF.java78 basesProcessed=0; in start()
98 basesProcessed+=srs.basesProcessed; in nextReads()
147 protected long basesProcessed=0; field in SamStreamerMF
H A DSamStreamerWrapper.java132 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()
/dports/biology/bbmap/bbmap/current/icecream/
H A DIceCreamGrader.java128 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()
/dports/biology/bbmap/bbmap/current/tax/
H A DTaxSize.java176 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
H A DExplodeTree.java208 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
H A DFilterByTaxa.java236 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
H A DSplitByTaxa.java220 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
/dports/biology/bbmap/bbmap/current/prok/
H A DFilterSilva.java162 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()
H A DMergeRibo_Fast.java220 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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