Petr Danecek

The mode `--regions-overlap variant|2` is supposed to recognize the actual bases affected by the variant. This is trickier than currently implemented in https://github.com/samtools/htslib/blob/develop/synced_bcf_reader.c#L569. The existing code trims variants from the...

Add VCF/BCF support for POS=0 coordinate

5

Resolves #1571 See also https://github.com/samtools/bcftools/pull/1875

bcf_hdr_remove leaves hash keys behind

10

Somehow this issue https://github.com/samtools/htslib/issues/842 has not been fully addressed. The following code shows the problem: ``` $ echo '#include int main() { htsFile *in = hts_open("-", "r"); bcf_hdr_t *hdr =...

Remember last file grouping mode

12

When I open a fresh geeqie window, both CR3 and JPG files with the same base name are shown and the JPG file has `[NO GROUPING]` added. I select all...

Possible 4x speed up of merge --gvcf ref.fa

1

This needs to be tested, but it appears that `merge --gvcf ref.fa` is 4x slower than `merge --gvcf -`. This may be caused by inefficient use of `faidx_fetch_seq`; would pre-loading...

This follows changes in https://github.com/samtools/htslib/pull/1573 See also https://github.com/samtools/htslib/issues/1571

The code in `mpileup2/*` subdirectory is intended to live in htslib in future

### Discussed in https://github.com/samtools/bcftools/discussions/1926 Originally posted by **jrm5100** May 19, 2023 The [cmp_bcf_pos](https://github.com/samtools/bcftools/blob/875c067bdd31b3021e8148fc129dbedebda6208f/vcfsort.c#L97-L119) function looks at: - id - pos - alleles However, if all of these match the records...

Setting --dpi has no effect on the PNG output

2

In version 4.1.1 setting the `-d, --dpi` option has no effect. Steps to reproduce: ``` $ qrencode -V qrencode version 4.1.1 Copyright (C) 2006-2017 Kentaro Fukuchi $ qrencode -d 72...

Please see here for a more detailed description https://github.com/Ensembl/ensembl-vep/issues/1351