./biology/biolibc, Low-level high-performance bioinformatics library

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Branch: CURRENT, Version: 0.2.5, Package name: biolibc-0.2.5, Maintainer: bacon

Biolibc is a library of fast, memory-efficient, low-level functions for
processing biological data. Like libc, it consists of numerous disparate,
general-purpose functions which could be used by a wide variety of
applications. These include functions for streaming common file formats such
as SAM and VCF, string functions specific to bioinformatics, etc.

Master sites:

Filesize: 138.111 KB

Version history: (Expand)

CVS history: (Expand)


   2023-08-12 16:49:18 by Jason Bacon | Files touched by this commit (4) 
Log message:
biology/biolibc: Update to 0.2.5

Make header files C++ compatible (extern C)
bl_chrom_name_cmp(): Support names with embedded digits, e.g. chr2p
bl_gff_extract_attribute(): Improve performance
gff -> gff3 to distinguish from past and future GFF specs
Silence some compiler warnings

Changes: https://github.com/auerlab/biolibc/releases
   2023-06-14 20:41:24 by Jason Bacon | Files touched by this commit (4) 
Log message:
biology/biolibc: Update to 0.2.4.3

Add extern "C" to support use from C++ apps
   2022-12-28 16:27:18 by Jason Bacon | Files touched by this commit (20) 
Log message:
Change MAINTAINER= to OWNER= on mission-critical packages
   2022-12-11 22:14:37 by Jason Bacon | Files touched by this commit (4) 
Log message:
biology/biolibc: Update to 0.2.4

Minor enhancements

Changes:    https://github.com/auerlab/biolibc/releases
   2022-06-11 21:42:39 by Jason Bacon | Files touched by this commit (4) 
Log message:
biology/biolibc: Update to 0.2.3

Expand use of tsv_read_field_malloc() to improve memory efficiency
Add SAM bit flag constants
Import SAM-GFF compare functions from diffanal
Updates for libxtend DSV API changes
Numerous minor bug fixes and enhancements
Changes: https://github.com/auerlab/biolibc/releases
   2022-03-15 22:06:32 by Jason Bacon | Files touched by this commit (4) 
Log message:
biology/biolibc: Update to 0.2.2

Numerous bug fixes and enhancements
Serveral new functions
3 new classes
Cleaned up some API slop
Changes: https://github.com/auerlab/biolibc/tags
   2021-12-14 19:58:57 by Jason Bacon | Files touched by this commit (5) 
Log message:
biology/biolibc: Update to 0.2.1

Add orf.c with start/stop codon locators
Standardize BED and GFF APIs
Implement VCF input filtering
Eliminate mutator macros mirroring mutator functions
Numerous minor bug fixes and enhancements

Changes: https://github.com/auerlab/biolibc/releases/tag/0.2.1
   2021-10-26 12:03:45 by Nia Alarie | Files touched by this commit (73) 
Log message:
biology: Replace RMD160 checksums with BLAKE2s checksums

All checksums have been double-checked against existing RMD160 and
SHA512 hashes