htslib
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samtools
C library for high-throughput sequencing data formats
Zstd Support
An undergrad is the lab is looking into how modern compression algorithms work with genomic data. Long story short, it looks like there are justifications to use LZ4, ZSTD, and...
Add option to tabix to interleave multiple bgzipped indexed files, without the need for external resorting. ``` # bgzipped file*.bed.gz files with index. # "Concatenate" indexed bgzipped files so they...
(Put here simply so we don't forget it.) The (now merged) Samtools PR https://github.com/samtools/samtools/pull/516 copies over the `aux_type2size` and `skip_aux` functions as it has a mechanism of iterating through the...
Thanks for maintaining this software. When checking a htslib 1.13 RPM package on Fedora by a lint tool called rpmlint, the following warning was detected. I am not sure how...
I am attempting to read from a BAM file stored in a GCE bucket that is configured as user pay and get the following error: ``` $ samtools view -H...
TODO: Fix the 28-bit limit on CIGAR length size in the internal memory structures. While we have no immediate plans to support reads several Gb long, we do support references...
I have many large (indexed) vcfs of the form `${CHROM}_${CHUNK}vcf.gz` and was looking for a quick way to get the coordinates spanned by the file. I know that given a...
The current default mpielup maximum depth is [8000](https://github.com/samtools/htslib/blob/c3ba3026d6cebc30bb6c50e6171473db3cd8d445/sam.c#L4720), which could be increased.
Greetings, The tarball for release 1.12 [here](https://github.com/samtools/htslib/archive/refs/tags/1.12.tar.gz) is giving me an error on `./configure`. It is missing the cram codecs, and it looks like this is a release that moved...
As noted in PR #1198, autoconf 2.70 is more careful about cross compilation and with this autoconf version using `AC_FUNC_MMAP` implicitly pulls in `AC_CANONICAL_HOST` and the cross-compilation infrastructure. So we...
