htslib
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samtools
C library for high-throughput sequencing data formats
An alternative to @mlin's #1369 for consideration. The two implementations differ by: - Using kstring's kgetline3 (a new variant of kgetline2), vs manual newline scanning. - Efficiency (my version has...
Compressing with `-n`/`--text` promotes alignment of BGZF blocks with the uncompressed text lines. BGZF blocks start at the beginning of an input line and end after some subsequent newline (except...
As suggested in #1319, this adds new API functions for iterating through a BAM record's aux fields, inline accessor methods for field tag and type (or code can continue to...
In https://github.com/samtools/samtools/pull/1442#issuecomment-871244137 I wrote: > (I can never remember which option I want to use and have to look it up each time. What I would really like to have...
Text files badly transferred from Windows may occasionally be UTF-16-encoded, and this may not be easily noticed by the user — see for example, [this report of tabix woes](https://www.biostars.org/p/9530170/) (`??#`...
Using tabix version 1.9 on CentOS 7 I am querying a public indexed dataset (gnomad annotations from the Broad institute) using tabix together with a regions file in BED format,...
**Steps to reproduce** 1. Create an input.bam file with ~1.5M `@RG` header lines. it can contain a single read, it does not really matter 2. Create a filter.txt file with...
This request is motivated by https://github.com/samtools/bcftools/issues/1704 and the idea is to extend htslib VCF interface as follows ``` #define VCF_REF 0 #define VCF_SNP 1 #define VCF_MNP 2 // #define VCF_OTHER...
The current mpileup API (`bam_mplp_auto()`) gives access to an array of per-read structures but does not give the possibility to store per-position data. One possible use case would be to...
I don't know if the work done to support Google Cloud Storage and Amazon S3 just "magically works" for Azure blob storage, but I did not find any specific mention...
