Petr Danecek
Petr Danecek
This request is motivated by https://github.com/samtools/bcftools/issues/1704 and the idea is to extend htslib VCF interface as follows ``` #define VCF_REF 0 #define VCF_SNP 1 #define VCF_MNP 2 // #define VCF_OTHER...
The current mpileup API (`bam_mplp_auto()`) gives access to an array of per-read structures but does not give the possibility to store per-position data. One possible use case would be to...
This is a reminder for me to discuss whether we should enforce checks of return codes. Just encountered a nasty case of big truncated data, probably preventable if the chief...
Because the unseen star allele is not supported by `bcf_get_variant_types`, the command `bcftools view --types ref` is unable to distinguish between the star allele and other symbolic alleles, such as...
by switching off an existing heuristics which reduces indelQ and, in the extreme case, has the power to discard an indel entirely when the reference alignment has low score. This...
as triggered by https://github.com/samtools/bcftools/issues/1622 and https://github.com/samtools/hts-specs/issues/593 State explicitly that missing vectors (`.`) in fields of variable length are in BCF represented as `MISSING,END_OF_VECTOR`, i.e. the leading `MISSING` value must be...
**Is your feature request related to a problem? Please describe.** My camera (Canon EOS R5) does a great job with colors for the embedded JPG, but I am unable to...
The removal of large tags introduced by https://github.com/samtools/htslib/commit/b49eea478114759efe19e718c38e7deb00614b21 and https://github.com/samtools/htslib/commit/9db565de3d89235f625de07363f1cd726c43f8f2 could not work correctly, the memmove pointers were wrong! Resolves https://github.com/samtools/htslib/issues/1733 This is a fix of the botched pull request...