Searched refs:cigarEndIndex (Results 1 – 2 of 2) sorted by relevance
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/ |
| H A D | CigarUtils.java | 53 …fBasesAndClips(final List<CigarElement> elems, final int cigarStartIndex, final int cigarEndIndex){ in countRefBasesAndClips() argument
54 return countRefBasesAndMaybeAlsoClips(elems, cigarStartIndex, cigarEndIndex, true, true); in countRefBasesAndClips()
57 …esAndSoftClips(final List<CigarElement> elems, final int cigarStartIndex, final int cigarEndIndex){ in countRefBasesAndSoftClips() argument
58 return countRefBasesAndMaybeAlsoClips(elems, cigarStartIndex, cigarEndIndex, true, false); in countRefBasesAndSoftClips()
61 …(final List<CigarElement> elems, final int cigarStartIndex, final int cigarEndIndex, final boolean… in countRefBasesAndMaybeAlsoClips() argument
63 …Utils.validateArg(cigarStartIndex >= 0 && cigarEndIndex <= elems.size() && cigarStartIndex <= ciga… in countRefBasesAndMaybeAlsoClips()
66 for (final CigarElement elem : elems.subList(cigarStartIndex, cigarEndIndex)) { in countRefBasesAndMaybeAlsoClips()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/ |
| H A D | SplitNCigarReads.java | 283 …asedOnCigar(final GATKRead read, final int cigarStartIndex, final int cigarEndIndex, final Overhan… in splitReadBasedOnCigar() argument
285 int cigarSecondIndex = cigarEndIndex; in splitReadBasedOnCigar()
307 …tRefIndex + CigarUtils.countRefBasesAndClips(elements,cigarFirstIndex,cigarEndIndex); //we use ci… in splitReadBasedOnCigar()
308 final int splitEnd = splitStart + read.getCigarElement(cigarEndIndex).getLength() - 1; in splitReadBasedOnCigar()
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