clintval / vartovcf / 37145707700

98%

Build Type

push

github

Committed by web-flow

Commit Message

feat: add opt-in FILTER labelling, starting with NEAR_READ_END (#121)

FILTER labels now live in a new filter module and are applied only when their option is given; with none given, FILTER stays `.` as before. Once any label is applied, a call that fails none of them is PASS and a record without an ALT allele stays `.`, and each applied label is declared with its threshold in its ##FILTER description.

The first label is NEAR_READ_END, from --filter-near-read-end: the call's mean distance from the variant to the nearer end of the ALT reads' aligned parts (MEAN_DIST_TO_READ_END) is below the threshold, the signature of read-end artifacts. The README now describes the opt-in filters.

Coverage Stats

74 of 74 new or added lines in 4 files covered. (100.0%)

2 existing lines in 1 file now uncovered.

729 of 746 relevant lines covered (97.72%)

30.83 hits per line