Daniel Cameron
Daniel Cameron
I'm writing up a VCFv4.4 parser and I've run into trouble with `END`. Existing design: `END` is a per-record field due to gVCF-style `` and compatibility with existing VCF indexing...
It is very easy to have an off-by-one error in symoblic SVs. The specifications should clarify exactly which bases are impacted. Take the example in the specs themselves: ``` 2...
Various drafts of improved Structural Variant support have been floating around for 2.5 years (see #231, #266) but never merged. I'm attempting to collate everything together in this PR but...
PR for discussing proposed SAM Strict rule changes. Work in progress continuing from #281 discussion.
IMPRECISE + CIPOS indicates the caller does not have base-pair accurate calling. CIPOS alone indicates a precise variant with microhomology (See section 5.4.8 and Figure 9 for the example) The...
The specs don't explicitly state that breakend positions must match. https://github.com/PapenfussLab/gridss/issues/383 is an example where the two sides of a breakpoint give equivalent but different calls due to the presence...
When a user parses a bam file they sometimes either forget or don't realise that they have to call `read_header()`, `read_reference_sequences()` then `.records()`. If this not done, it results in...
I'm attempting to write a small utility that process bam records and I can't figure out the aysnc API. I'm attempting to adapt the noodles-bam/examples/bam_reheader_async.rs example and I've been running...
Please review and provide feedback. - Rebased #434 onto VCFv4.5 - Made LAA 0-based inclusive of REF - Added FORMAT END instead of #435 Logic behind going with FORMAT END:...
We need to add test/validation files - particularly those that change vs 4.3 (e.g. GT / END redefinitions).