Daniel Cameron
Daniel Cameron
If I have two nearby unphased indel variants it is unclear how they are supposed to be normalised. Following https://vrs.ga4gh.org/en/stable/impl-guide/normalization.html, I get to the step 3a: `is equal to the...
Running `kraken2-build --download-library human` fails at it appear to write to assembly_summary.txt multiple times. Even if selecting `y` to overwrite, the move fails: ``` mv: replace 'assembly_summary.txt', overriding mode 0555...
In light of https://github.com/samtools/hts-specs/issues/756 and further discussion with implementations, it appears that the current definition of GQ is problematic. `GQ (Integer): Conditional genotype quality, encoded as a phred quality −10log10...
I encountered an edge case where I needed have a free query end alignment so I refactored the C API to export all 32 possible template values. To avoid writing...
Crash when running on certain input data with free query gap: ``` use std::cmp::max; use block_aligner::{cigar::*, scan_block::*, scores::*}; fn aln( qstr: &[u8], rstr: &[u8], xdrop: i32, ) -> String {...
For 1 and 2 length sequences, FREE_QUERY_END_GAPS=true returns the incorrect alignment. Reproduction steps: ``` use block_aligner::{cigar::*, scan_block::*, scores::*}; fn aln( qstr: &[u8], rstr: &[u8], ) -> String { let min_block_size...
As much as a specs issue as a noodles issues: `:` in the INFO field does not have a special meaning in so does not need to be/should not be...
htslib appears to lack a clean index querying API. The internals of hts_idx_t are not publicly visible, and there does not appear to be a function to find the appropriate...