Add command-line options for ignoring local deletions #868
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…ations) in BAM entries
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This adds a command-line option "-ignoreD" which will treat any Ds in the CIGAR string as being equivalent to M/X/=. In other words, coverage is calculated ignoring any local deletions.
The functionality to do this was already present in the code in BlockedIntervals.cpp; this patch simply exposes that functionality to the command line.
For reference (including example SAM files), see issue #867.