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Searched refs:getSeqEnd (Results 1 – 5 of 5) sorted by relevance

/dports/biology/jalview/jalview/src/jalview/ws/sifts/
H A DMappingOutputPojo.java77 public int getSeqEnd() in getSeqEnd() method in MappingOutputPojo
H A DSiftsClient.java1114 int sEnd = mp.getSeqEnd(); in getMappingOutput()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/bwa/
H A DBwaMemAlignmentUtils.java62 bases = Arrays.copyOfRange(bases, alignment.getSeqStart(), alignment.getSeqEnd()); in applyAlignment()
64 … quals = Arrays.copyOfRange(quals, alignment.getSeqStart(), alignment.getSeqEnd()); in applyAlignment()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/alignment/
H A DAlignmentInterval.java299 this.endInAssembledContig = alignment.getSeqEnd(); in AlignmentInterval()
301 this.startInAssembledContig = unclippedContigLength - alignment.getSeqEnd() + 1; in AlignmentInterval()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/evidence/
H A DAlignedAssemblyOrExcuse.java172 output.writeInt(alignment.getSeqEnd()); in writeAlignment()