Fix how stats handles Supp reads on alternate haplotypes #469
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case 1 should almost certainly be case '1'.
…imilar to secondary SUPPLEMENTARY reads on alternate contigs are different from those on the main chromosomes and should be treated like SECONDARY reads.
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Get rid of f2e0a75, as noted previously. |
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Please explain how this has been tested. |
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This is an important fix but it needs work. This fix was giving the improvement I wanted but due to a bug it was doing it by doing the opposite of what I intended (aka excluding the SUPP's on primary contigs not alt). I will work on this further in the near future. |
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Fix how stats handles Supp reads on alternate haplotypes by treating them similar to reads flagged secondary.
Fix typo in getopt_long case statement where it's case 1 rather than case '1'