Multiple stdout htsFile's result in no output

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Assessment

Difficulty
3/5
Estimated time
1-2 days
Newbie friendliness
35/100
Issue type
Bug
Clarity
Mostly clear
Activity status
Stale
Tech stack
c
Domain
bioinformatics

Research direction

Start by compiling and running the minimal example using bcf_open, bcf_hdr_write, and hts_close from htslib/vcf.h, first with and then without the second open. Trace how repeated stdout htsFile instances are handled and verify that closing and reopening stdout still produces the expected VCF output.

Written by the indexing model from the issue text.

Description

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 in no output to stdout. For example, uncommenting the two lines below results in no output to stdout:

#include "htslib/vcf.h"

int main()
{
    auto bcf = bcf_open("-", "[w]");
    // hts_close(bcf);
    // bcf = bcf_open("-", "[w]");
    const auto header = bcf_hdr_init("w");
    bcf_hdr_write(bcf, header);
    hts_close(bcf);
    bcf_hdr_destroy(header);
}
Dominant language
C
Stars
950
Forks
475
Avg merge
3d 13h
Merged PRs (30d)
11

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