| /dports/biology/bbmap/bbmap/current/var2/ |
| H A D | VcfWriter.java | 41 readLengthAvg=varMap.readLengthAvg; in VcfWriter()
251 …v.toVCF(bb, properPairRate, totalQualityAvg, totalMapqAvg, readLengthAvg, ploidy, scafMap, filter,… in makeBytes()
253 …v.toText(bb, properPairRate, totalQualityAvg, totalMapqAvg, readLengthAvg, filter.rarity, ploidy, … in makeBytes()
255 …GffLine.toText(bb, v, properPairRate, totalQualityAvg, totalMapqAvg, readLengthAvg, filter.rarity,… in makeBytes()
306 final double readLengthAvg; field in VcfWriter
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| H A D | VarMap.java | 32 readLengthAvg=readLengthAvg_; in VarMap()
145 totalMapqAvg, readLengthAvg, ploidy, scafMap, false);
436 assert(readLengthAvg>0); in processVariants()
439 v.reviseAlleleFraction(readLengthAvg, scafMap.getScaffold(v.scafnum), this); in processVariants()
446 …filter.passesFilter(v, properPairRate, totalQualityAvg, totalMapqAvg, readLengthAvg, ploidy, scafM… in processVariants()
451 …int score=(int)v.phredScore(properPairRate, totalQualityAvg, totalMapqAvg, readLengthAvg, filter.r… in processVariants()
623 readLengthAvg=-1;
700 public double readLengthAvg=-1;
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| H A D | MergeSamples.java | 288 readLengthAvg=0; in processHeader()
290 readLengthAvg+=Float.parseFloat(split[1]); in processHeader()
292 readLengthAvg/=lines.length; in processHeader()
293 bb.append("##readLengthAvg="+String.format(Locale.ROOT, "%.2f\n", readLengthAvg)); in processHeader()
328 …um.toVCF(new ByteBuilder(), properPairRate, totalQualityAvg, mapqAvg, readLengthAvg, ploidy, map, … in merge()
460 double readLengthAvg; field in MergeSamples
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| H A D | Var.java | 1077 final double readLengthAvg=bases/Tools.max(1.0, reads); in toVarHeader() local
1086 sb.append(String.format(Locale.ROOT, "#readLengthAvg\t%.2f\n", readLengthAvg)); in toVarHeader()
1162 bb.append(revisedAlleleFraction(af, readLengthAvg), 4).tab(); in toText()
1174 bb.append(coverageScore(ploidy, rarity, readLengthAvg), 4).tab(); in toText()
1329 final double raf=revisedAlleleFraction(af, readLengthAvg); in toVCF()
1500 double cs=coverageScore(ploidy, rarity, readLengthAvg); in score()
1608 public double coverageScore(int ploidy, double rarity, double readLengthAvg){ in coverageScore() argument
1625 ratio=adjustForInsertionLength(ratio, readLengthAvg); in coverageScore()
1646 final double rafIns=revisedAlleleFraction(afIns, readLengthAvg); in reviseAlleleFraction()
1700 public double revisedAlleleFraction(double af, double readLengthAvg){ in revisedAlleleFraction() argument
[all …]
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| H A D | FilterVCF.java | 283 readLengthAvg=(float) Double.parseDouble(b); in processVcfHeader()
345 readLengthAvg, ploidy, scafMap, countNearby); in processVcfVarsST()
600 readLengthAvg, ploidy, scafMap, countNearby); in processLine()
675 public float readLengthAvg=150; field in FilterVCF
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| H A D | CallVariants2.java | 558 …final double readLengthAvg=trimmedBasesProcessed/(double)Tools.max(1, readsProcessed-readsDiscarde…
565 varMap.readLengthAvg=readLengthAvg;
630 …final double readLengthAvg=trimmedBasesProcessed/(double)Tools.max(1, readsProcessed-readsDiscarde… in process2() local
637 varMap.readLengthAvg=readLengthAvg; in process2()
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| H A D | VcfLoader.java | 114 synchronized(varMap){varMap.readLengthAvg=Double.parseDouble(b);} in loadVarLine()
143 synchronized(varMap){varMap.readLengthAvg=Double.parseDouble(b);} in loadVcfLine()
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| H A D | VarFilter.java | 167 double totalMapqAvg, double readLengthAvg, int ploidy, ScafMap map, boolean considerNearby){ in passesFilter() argument
226 …double phredScore=v.phredScore(pairingRate, totalQualityAvg, totalMapqAvg, readLengthAvg, rarity, … in passesFilter()
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| H A D | CallVariants.java | 586 varMap.readLengthAvg=trimmedBasesProcessed/(double)Tools.max(1, readsProcessed-readsDiscarded); in process()
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| /dports/biology/bbmap/bbmap/current/gff/ |
| H A D | GffLine.java | 138 …e properPairRate, double totalQualityAvg, double totalMapqAvg, double readLengthAvg, double rarity… in GffLine() argument
144 …score=(float)v.score(properPairRate, totalQualityAvg, totalMapqAvg, readLengthAvg, rarity, ploidy,… in GffLine()
233 double totalMapqAvg, double readLengthAvg, double rarity, int ploidy, ScafMap map){ in toText() argument
240 …bb.append(v.score(properPairRate, totalQualityAvg, totalMapqAvg, readLengthAvg, rarity, ploidy, ma… in toText()
257 final double readLengthAvg=bases/Tools.max(1.0, reads); in toHeader() local
266 sb.append(String.format(Locale.ROOT, "#readLengthAvg\t%.2f\n", readLengthAvg)); in toHeader()
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| /dports/biology/bbmap/bbmap/current/jgi/ |
| H A D | TestFormat.java | 258 if(readLengthAvg>0){println("ReadLengthAvg\t"+String.format(Locale.ROOT, "%.2f", readLengthAvg));} in printVariantResults()
654 readLengthAvg=Double.parseDouble(b); in loadVars()
688 readLengthAvg= Double.parseDouble(b); in loadVcf()
1235 double readLengthAvg=-1; field in TestFormat
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