clintval / vartovcf / 37139207693

98%

push

github

fix: take SVLEN from VarDict's own event length and list only its SV types (#107)

SVLEN was End - Start + 1, negated for deletions. That is one too long for a DEL, whose POS is the padding base, and two too long for a long insertion VarDict writes as a DUP. It now comes from the event length VarDict writes in its genotype column (-N for DEL, +N for DUP, <INVN> for INV), signed as VCF 4.2 asks: negative for DEL, positive for DUP and INV. An SV row whose length cannot be read is refused with an error naming it.

VarDict only writes DEL, DUP and INV, so SVTYPE's Description and the ALT header lines list just those three. The DUP test fixture now carries VarDict's real +N genotype form.

18 of 18 new or added lines in 2 files covered. (100.0%)

524 of 541 relevant lines covered (96.86%)

21.13 hits per line