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[VCF v4.3 section 1.4.8](https://samtools.github.io/hts-specs/VCFv4.3.pdf#subsubsection.1.4.8) defines `##META` lines. What they are for isn't very well described, but they appear to allow allow the …
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I found that ID column from multi-allelic site from a source file only transferred to the first allele in the target file.
My source annotation file:
```
chr21 5030278 rs1258851236 C G,T . . RS=1…
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Hi,
It would be great with support for zstd compression and decompression of especially FASTQ files, as they can get very big with modern sequencing technologies, and zstd seems more and more like …
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I have a custom hFILE backend over C++ streams that I have written for vg: https://github.com/vgteam/vg/blob/39ac300bb735abf8350e3d2a7ec0356a0742fd56/src/stream/hfile_cppstream.cpp
It has built jus…
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302f14d adds crypto as a dependency for building lumpy_filter, which was removed in OS X 10.11 El Capitan. I'm guessing that it's needed for building htslib, but I'm not 100% sure if crypto is [actual…
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Dear Alaina,
I've been trying to set up the latest version of liftoff in a MacBook (M1) and a linux-based HPC following all your instructions. Both conda and pip liftoff installation fail.
### c…
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This is to allow direct random access to info fields given an index.
Combined with an API that allows you to provide an index instead of a field name, this should allow gamgee to directly jump to th…
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When I follow the readme download to make compile, it reports an error, missing file
configure.ac: error: required file 'config.sub' not found
configure.ac: error: required file 'config.guess' n…
sjads updated
9 months ago
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SAMtools implements `bgzf_useek` that apparently allows seeking bgzf files using offset in uncompressed data. https://github.com/samtools/htslib/blob/84a89da6cf0eb828d39f9a85b82411d58c840e16/htslib/bg…
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Would it be possible to add a few fast-starter examples to htslib? Nothing too complicated,
just perhaps 3-5 smallish example for people to quickly test htslib after they have compiled
or installed …