Updating pileup conversion code to convert sequences that use the X and = (EQ) CIGAR operators #199
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…nd = (EQ) CIGAR operators.
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All automated tests passed. |
massie
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Apr 2, 2014
Updating pileup conversion code to convert sequences that use the X and = (EQ) CIGAR operators
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Thanks, Frank! |
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| case CigarOperator.X => | ||
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whitespace is a bit funky in this block (below this comment)
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This update patches the pileup converter to allow for the conversion of reads that use the X and = CIGAR operators instead of the M operator for alignment matches. The X and = CIGAR operators provide additional information (specifically, = is base match, X is base mismatch) for alignment blocks that are an alignment match.