James Bonfield
James Bonfield
This is as per ksw_global, but permits control over whether gaps at the start and/or end of query and target sequences are penalised. For experimentation I also added another test...
An alternative to @mlin's #1369 for consideration. The two implementations differ by: - Using kstring's kgetline3 (a new variant of kgetline2), vs manual newline scanning. - Efficiency (my version has...
If I have a VCF file with a missing `##FORMAT` record, then a straight `bcftools view` issues a warning: ``` @ seq4-head2[tmp/vcf]; bcftools view passed_ploidy_001.vcf|wc [W::vcf_parse_format] FORMAT 'PL' at 1:61462...
(Put here simply so we don't forget it.) The (now merged) Samtools PR https://github.com/samtools/samtools/pull/516 copies over the `aux_type2size` and `skip_aux` functions as it has a mechanism of iterating through the...
TODO: Fix the 28-bit limit on CIGAR length size in the internal memory structures. While we have no immediate plans to support reads several Gb long, we do support references...
A reminder to my future self, or to inspire others with time on their hands. :-) An htslib built without finding xz-utils / lzma library is possible, with appropriate configure...
We have the BCF synched reader code which can on-the-fly merge (and dedup / intersect) multiple BCF files. I'm thinking there is room for a similar action in the SAM...
See Will Stokes' request at https://sourceforge.net/p/samtools/mailman/message/36454348/ We desire a way to construct a BAM record from the component pieces that isn't just a manual mess of bit/byte shuffling. Most of...
We can now count the depth anywhere along the read rather than only at the left end. It's not buffering reads up so it doesn't know what's about to come,...
If we're reading and writing VCF without intervening change to BCF or use of bcf_unpack with BCF_UN_FMT (so no querying and/or modification of the per-sample FORMAT columns), then we keep...