| /dports/biology/bbmap/bbmap/current/jgi/ |
| H A D | MakeContaminatedGenomes.java | 220 …limiter+ReadWrite.stripToCore(inA)+delimiter+sizeB+delimiter+String.format(Locale.ROOT, "%.3f", fr… in writeChimera()
230 …limiter+ReadWrite.stripToCore(inB)+delimiter+sizeA+delimiter+String.format(Locale.ROOT, "%.3f", fr… in writeChimera()
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| H A D | SealRefInfo.java | 182 final String name=ReadWrite.stripToCore(refNames.get(i)); in writeRefStats()
229 final String name=ReadWrite.stripToCore(refNames.get(i)); in writeRefStats_BBSplitStyle()
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| H A D | DecontaminateByNormalization.java | 311 final String core=ReadWrite.stripToCore(in); in renameAndMux_ST()
530 sb.append(ReadWrite.stripToCore(s)); in demux()
565 final String core=ReadWrite.stripToCore(path); in map()
611 String core=ReadWrite.stripToCore(path); in filter()
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| H A D | SynthMDA.java | 147 …out1=ReadWrite.stripToCore(ref)+"_"+Long.toHexString(new Random().nextLong()&Long.MAX_VALUE)+".fa"; in SynthMDA()
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| H A D | FindPrimers.java | 218 bb.append(oneColumn ? ReadWrite.stripToCore(outIdHist) : "ID\tCount").nl(); in process()
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| H A D | FilterByCoverage.java | 150 name=ReadWrite.stripToCore(in1); in FilterByCoverage()
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| H A D | KmerCountExact.java | 852 sketch.setName0(ReadWrite.stripToCore(ffSketch.name())); in makeSketch()
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| H A D | MutateGenome.java | 656 …ID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t"+(out1==null ? "sample" : ReadWrite.stripToCore(out1))); in writeVars()
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| H A D | Seal.java | 986 final String name=ReadWrite.stripToCore(refNames.get(i));
1032 final String name=ReadWrite.stripToCore(refNames.get(i));
1191 final String core=ReadWrite.stripToCore(refname);
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| H A D | MutateGenome2.java | 807 …ID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t"+(out1==null ? "sample" : ReadWrite.stripToCore(out1))); in writeVars()
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| H A D | BBDuk2.java | 1167 final String name=ReadWrite.stripToCore(refNames.get(i)); in writeRefStats()
1327 final String name=ReadWrite.stripToCore(refNames.get(r)); in toRefNames()
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| H A D | BBDuk.java | 1548 final String name=ReadWrite.stripToCore(refNames.get(i)); in writeRefStats()
1697 final String name=ReadWrite.stripToCore(refNames.get(r)); in toRefNames()
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| /dports/biology/bbmap/bbmap/current/sketch/ |
| H A D | ResultLineParser.java | 92 String name=ReadWrite.stripToCore(fname); in getTaxNode()
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| H A D | BlacklistMaker2.java | 200 sketchName=ReadWrite.stripToCore(sketchName); in BlacklistMaker2()
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| H A D | BlacklistMaker.java | 252 sketchName=ReadWrite.stripToCore(sketchName); in BlacklistMaker()
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| H A D | Sketch.java | 1024 public String filePrefix(){return ReadWrite.stripToCore(fname);} in filePrefix()
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| /dports/biology/bbmap/bbmap/current/driver/ |
| H A D | CountSharedLines.java | 196 tsw.print(ReadWrite.stripToCore(fname2)+"\t"+shared+"\n"); in processInner()
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| H A D | RenameAndMux.java | 388 final String core=ReadWrite.stripToCore(in1); in renameAndMergeOneFile()
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| /dports/biology/bbmap/bbmap/current/covid/ |
| H A D | SummarizeCoverage.java | 182 String name=ReadWrite.stripToCore(fname); in process()
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| /dports/biology/bbmap/bbmap/current/clump/ |
| H A D | Clumpify.java | 514 core=ReadWrite.stripToCore(out1)+"_"+core;
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| /dports/biology/bbmap/bbmap/current/kmer/ |
| H A D | TableLoaderLockFree.java | 354 final String name=ReadWrite.stripToCore(refNames.get(r)); in toRefNames()
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| /dports/biology/bbmap/bbmap/current/var2/ |
| H A D | CallVariants2.java | 336 String core=ReadWrite.stripToCore(s); in fixSampleNames()
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| H A D | CallVariants.java | 377 sampleName=ReadWrite.stripToCore(ffin.get(0).name()); in CallVariants()
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| /dports/biology/bbmap/bbmap/current/fileIO/ |
| H A D | ReadWrite.java | 1346 public static String stripToCore(String fname){ in stripToCore() method
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| /dports/biology/bbmap/bbmap/current/shared/ |
| H A D | Parser.java | 1251 fname=ReadWrite.stripToCore(fname); in postparseReadgroup()
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