| Port details |
- biolibc Low-level high-performance bioinformatics library
- 0.2.6.4 biology
 =2      0.2.6.4Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2021-03-21 15:10:53
- Last Update: 2024-05-19 13:40:24
- Commit Hash: 93db8fd
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: BSD2CLAUSE
- WWW:
- https://github.com/auerlab/biolibc
- Description:
- 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.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- biolibc>0:biology/biolibc
- To install the port:
- cd /usr/ports/biology/biolibc/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/biolibc
- pkg install biolibc
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: biolibc
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1716122167
SHA256 (auerlab-biolibc-0.2.6-4-g723ac84_GH0.tar.gz) = d467c954b3d7ffaafe1dea36006113bf7b412285fdc07e71c504fd5b5db5ae64
SIZE (auerlab-biolibc-0.2.6-4-g723ac84_GH0.tar.gz) = 147951
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Library dependencies:
-
- libxtend.so : devel/libxtend
- This port is required by:
- for Libraries
-
- biology/ad2vcf
- biology/biolibc-tools
- biology/fasda
- biology/fastq-trim
- biology/peak-classifier
- biology/vcf-split
- biology/vcf2hap
Configuration Options:- No options to configure
- Options name:
- biology_biolibc
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
0.2.6.4
19 May 2024 13:40:24
 |
Jason W. Bacon (jwb) |
biology/biolibc: Update to 0.2.6.4
bl_sam_copy(): Make sure all fields are properly initialized |
0.2.6_1
23 Jan 2024 14:51:25
|
Muhammad Moinur Rahman (bofh) |
biology/biolibc: Impelled to share/man
Approved by: portmgr (blanket) |
0.2.6
28 Oct 2023 11:21:35
|
Jason W. Bacon (jwb) |
biology/biolibc: Update to 0.2.6
Updates for libxtend 0.2.0 API
Add full list of functions to biolibc(3) man page
Other documentation improvements
Changes: https://github.com/auerlab/biolibc/releases |
0.2.5
11 Aug 2023 20:35:11
|
Jason W. Bacon (jwb) |
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 |
0.2.4.3
10 Jun 2023 12:15:29
|
Jason W. Bacon (jwb) |
biology/biolibc: Update to 0.2.4.3
Add extern "C" to support use from C++ apps |
0.2.4
11 Dec 2022 20:06:23
|
Jason W. Bacon (jwb) |
biology/biolibc: Update to 0.2.4
Minor enhancements
Changes: https://github.com/auerlab/biolibc/releases |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
Remove WWW entries moved into port Makefiles
Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.
This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.
Approved by: portmgr (tcberner) |
0.2.3
07 Sep 2022 21:10:59
|
Stefan Eßer (se) |
Add WWW entries to port Makefiles
It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.
Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.
There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above  ) |
0.2.3
11 Jun 2022 14:26:56
|
Jason W. Bacon (jwb) |
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/tags |
0.2.2
15 Mar 2022 21:35:22
|
Jason W. Bacon (jwb) |
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 |
0.2.1
14 Dec 2021 19:45:31
|
Jason W. Bacon (jwb) |
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 |
0.2.0.11
17 Sep 2021 16:33:57
|
Jason W. Bacon (jwb) |
biology/biolibc: Update to 0.2.0.11
Regenerate man pages with improved auto-c2man
Adds missing return value sections and improves formatting |
0.2.0.1
02 Sep 2021 23:10:21
|
Jason W. Bacon (jwb) |
biology/biolibc: Update to 0.2.0.1
Fix regression: Replace BL_BED_SET_STRAND() macro with
bl_bed_set_strand(), which performs sanity checks |
0.2.0
28 Aug 2021 01:21:02
|
Jason W. Bacon (jwb) |
biology/biolibc: Update to 0.2.0
Major API overhaul
New classes for FASTA and FASTQ
Generate accessor and mutator functions for all classes
Generate man pages for all functions and macros
Export delimiter-separated-value class to libxtend |
0.1.3
11 Jun 2021 15:38:27
|
Jason W. Bacon (jwb) |
biology/biolibc: Remove comment used to silence portlint |
0.1.3
11 Jun 2021 15:05:18
|
Jason W. Bacon (jwb) |
biology/biolibc: Update to 0.1.3
Changes: https://github.com/auerlab/biolibc/releases |
0.1.1
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
0.1.1
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
0.1.1
21 Mar 2021 15:10:17
 |
jwb |
biology/biolibc: Low-level high-performance bioinformatics library
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. |
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