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Dear author,
When I run the command: ```snakemake -p -s /data/01/p1/user208/wn/phyloacc-out-08-25-2024.11-57-51/phyloacc-out-08-26-2024.08-31-18/phyloacc-job-files/snakemake/run_phyloacc.smk --config…
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As `varifier` uses `pyfastaq` to parse VCF it is unable to parse BCF format.
I know this is probably a big-ish change but I would suggest switching to using an API such as [`cyvcf2`](https://github…
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The BCF specification does not explicitly state what is the maximum header size, but htslib implementation assumes a 4 byte integer https://github.com/samtools/htslib/blob/develop/vcf.c#L909-L913
T…
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Hope this is the right place to be asking about this. I read with interest [this thread](https://sourceforge.net/p/vcftools/mailman/message/31748286/) from 2013 about the possibility of introducing do…
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Hi ! I got this error :
```
benjamin@MacBook-Pro-de-Benjamin ~ % git clone https://github.com/Illumina/ExpansionHunterDenovo.git
Clonage dans 'ExpansionHunterDenovo'...
remote: Enumerating obje…
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Hello,
in order to run:
bcftools view -T mylist.txt file.bcf -Ou -o filteredfile.bcf
can you please show me how a first few lines of "mylist.txt" should look like?
Thanks
Ana
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Hello.
I tried compressing a large BCF file I use as a reference and it seems something goes wrong because decompressed file is different (much larger) than input file.
I use the following comma…
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Hi, thanks for htslib and how responsive developers have always been. Apologies in advance for the long text below.
While exploring potential speedups setting `bcf1_t.max_unpack` as documented in v…
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Hey there! Just wondering if you know about https://github.com/IfcOpenShell/IfcOpenShell/tree/v0.6.0/src/bcf and https://github.com/IfcOpenShell/IfcOpenShell/tree/v0.6.0/src/foundationserver and wheth…
Moult updated
3 years ago
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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("…