clintval / vartovcf / 37144735713

98%

push

github

feat: write VarDict's SV read support as FORMAT SV_SOFTCLIP_READS and SV_DISCORDANT_READS (#119)

VarDict's SV column holds splits-pairs-clusters for a position. The splits are soft-clipped primary reads whose clipped sequence VarDict matched across the breakpoint, not split alignments, and the pairs are discordant read records, where each mate counts. Both are now FORMAT, Number=A, written only on records with a symbolic ALT allele, because VarDict attaches the column to every row at the position. The cluster count is not written. VarDict's duplication-rate column is not written either: VarDictJava never fills it, so it is always 0.

15 of 15 new or added lines in 2 files covered. (100.0%)

658 of 675 relevant lines covered (97.48%)

31.86 hits per line