clintval / vartovcf / 39692857496

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docs: correct statements the code does not match (#157)

* docs: correct the README and comments where they do not match the code

A folded MNV's DP adds partials starting after the MNV's first base as
VarDict wrote it, not after POS, which normalization can move onto the
partial; trimming leaves a substitution no shared base; the dedup's
depth is the tumor's; the substitutions written are remembered for the
whole run, so memory grows with them under --fix-leaky-mnv; the indel
FILTERs test the length change alone, so a Complex call one unit longer
or shorter is labelled too; the filter thresholds are var2vcf_valid.pl's
values, not a reproduction of its rules; the empty field the parser
skips on is the REF allele; and only an MNV row becomes a root.

* docs: describe the indel FILTERs and a folded DP as the code applies them

HOMOPOLYMER_INDEL and TANDEM_REPEAT_INDEL test only the change in allele
length, so their descriptions now name the Complex call they also label;
MNV_PARTIALS adds to DP the partials starting after the MNV's first base
as VarDict wrote it, not after POS. The goldens that carry these header
lines are regenerated.

4 of 4 new or added lines in 2 files covered. (100.0%)

3333 of 3392 relevant lines covered (98.26%)

208327.74 hits per line