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* @param read the mapped read to test * @return */ public ReferenceContext getReferenceContext( final SAMRecord read ) { GenomeLoc loc = genomeLocParser.createGenomeLoc(read); return new ReferenceContext( genomeLocParser, loc, loc, getReferenceBasesProvider(loc) ); }
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referenceSequence = reference.getSequence(genomeLoc.getContig()); refStart = (int)window.getStart()-1; } int len = (int)window.size(); return new ReferenceContext( genomeLocParser, genomeLoc, window, new Provider(refStart, len)); }