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feat: request, make synced_bcf_reader::bcf_sr_add_reader equivalent that accepts htsFile #1862

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brentp opened this issue Dec 3, 2024 · 1 comment · Fixed by #1868
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feat: request, make synced_bcf_reader::bcf_sr_add_reader equivalent that accepts htsFile #1862

brentp opened this issue Dec 3, 2024 · 1 comment · Fixed by #1868
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@vasudeva8

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@brentp
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brentp commented Dec 3, 2024

The header has int bcf_sr_add_reader(bcf_srs_t *files, const char *fname)

It would be nice to have something like: int bcf_sr_add_hreader(bcf_srs_t *files, htsFile *file_ptr)

My used case is code that is detecting the file type (BAM/CRAM/BCF/etc) using an htsFile and then I want to still use bcf_synced_reader if it is a BCF/VCF.
@daviesrob
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I think this should be possible. We'll look into it.

@vasudeva8 vasudeva8 mentioned this issue Dec 23, 2024
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jkbonfield pushed a commit to vasudeva8/htslib that referenced this issue Jan 16, 2025
@vasudeva8 @jkbonfield
Add bcf_sr_add_hreader() interface
0d3bccf 
This is like bcf_sr_add_reader but the caller supplies an existing
open htsFile instead of a filename.

Fixes samtools#1862
jkbonfield pushed a commit that referenced this issue Jan 16, 2025
@vasudeva8 @jkbonfield
Add bcf_sr_add_hreader() interface
dac8f29 
This is like bcf_sr_add_reader but the caller supplies an existing
open htsFile instead of a filename.

Fixes #1862
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update to use htsFile in synced reader (for #1862) vasudeva8/htslib
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@brentp @daviesrob @vasudeva8