Daniel Cooke
Daniel Cooke
It appears it's only possible to create a single working _stdout_ `htsFile` instance in a single execution, even if only one is actually open. Writing to a second instance results...
Would it be possible to make htslib's error reporting optional, perhaps in the form of a preprocessor directive? I'm writing an application which makes heavy use of htslib, and would...
Hi, thanks for the great tool! Would it be possible to recognise reserved annotation names (e.g. `DB` & `SOMATIC`) and use the description given in the VCF spec for such...
In version 4.3 of the VCF specification, there is a field reserved for sample level filtering `FT`: ##FORMAT= I think it makes more sense for this field to have variable...
Specifies that the number of values is the sample ploidy (i.e. the number of GT entries). One possible example use case is to specify the frequency of alleles (or haplotypes):...
I've noticed a few instances where the SynDip truth sets asserts heterozygous calls that are actually different representations of the same haplotype. For example, in `chr1:2106223-2107071` of `full.38.vcf.gz` we have...
Using [`bron_kerbosch_all_cliques`](https://www.boost.org/doc/libs/1_72_0/boost/graph/bron_kerbosch_all_cliques.hpp) results in an unused variable warning ``` /usr/local/include/boost/graph/bron_kerbosch_all_cliques.hpp:227:41: error: unused variable 'j' [-Werror,-Wunused-variable] typename Container::iterator i, j; ^ /usr/local/include/boost/graph/bron_kerbosch_all_cliques.hpp:289:13: note: in instantiation of function template specialization 'boost::detail::extend_clique' requested...
Hi, I'm trying to use Pisces to call a tumour-only sample. I'm using the following command: ```shell $ dotnet Pisces.dll -bam tumour.bam \ -CallMNVs false -g hs37d5 -gVCF false \...