Path to this page:
./
biology/samtools,
Tools for manipulating sequence alignment maps
Branch: CURRENT,
Version: 1.21,
Package name: samtools-1.21,
Maintainer: baconSamtools implements various utilities for post-processing alignments in the
SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction
with bcftools), and a simple alignment viewer.
Required to run:[
lang/perl5] [
biology/htslib] [
lang/python37]
Required to build:[
pkgtools/cwrappers]
Master sites:
Filesize: 8934.848 KB
Version history: (Expand)
- (2024-10-12) Updated to version: samtools-1.21
- (2023-08-14) Updated to version: samtools-1.17nb1
- (2023-02-25) Updated to version: samtools-1.17
- (2022-12-13) Updated to version: samtools-1.16.1
- (2022-06-30) Updated to version: samtools-1.15nb2
- (2022-06-28) Updated to version: samtools-1.15nb1
CVS history: (Expand)
2023-08-14 07:25:36 by Thomas Klausner | Files touched by this commit (1247) |
Log message:
*: recursive bump for Python 3.11 as new default
|
2023-02-25 14:52:39 by Jason Bacon | Files touched by this commit (4) |
Log message:
biology/samtools: Update to 1.17
Numerous enhancements and bug fixes
Changes: https://github.com/samtools/samtools/releases
|
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
|
2022-12-13 11:28:01 by Adam Ciarcinski | Files touched by this commit (3) | |
Log message:
samtools: updated to 1.16.1
1.16.1
Bug fixes:
Fixed a bug with the template-coordinate sort which caused incorrect ordering \
when using threads, or processing large files that don't fit completely in \
memory.
Fixed a crash that occurred when trying to use samtools merge in \
template-coordinate mode.
1.16
New work and changes:
samtools reference command added. This subcommand extracts the embedded \
reference out of a CRAM file.
samtools import now adds grouped by query-name to the header.
Made samtools view read error messages more generic. Former error message would \
claim that there was a "truncated file or corrupt BAM index file" with \
no real justification. Also reset errno in stream_view which could lead to \
confusing error messages.
Make samtools view -p also clear mqual, tlen and cigar.
Add bedcov option -c to report read count.
Add UMI/barcode handling to samtools markdup.
Add a new template coordinate sort order to samtools sort and samtools merge. \
This is useful when working with unique molecular identifiers (UMIs).
Rename mpileup --ignore-overlaps to --ignore-overlaps-removal or \
--disable-overlap-removal. The previous name was ambiguous and was often read as \
an option to enable removal of overlapping bases, while in reality this is on by \
default and the option turns off the ability to remove overlapping bases.
The dict command can now read BWA's .alt file and add AH:* tags indicating \
reference sequences that represent alternate loci.
The samtools index command can now accept multiple alignment filenames with the \
new -M option, and will index each of them separately. (Specifying the output \
index filename via out.index or the new -o option is currently only applicable \
when there is only one alignment file to be indexed.)
Allow samtools fastq -T "*". This allows all tags from SAM records to \
be written to fastq headers. This is a counterpart to samtools import -T \
"*".
Bug Fixes:
Re-enable --reference option for samtools depth. The reference is not used but \
this makes the command line usage compatible with older releases.
Fix regex coordinate bug in samtools markdup.
Fix divide by zero in plot-bamstats -m, on unmapped data.
Fix missing RG headers when using samtools merge -r.
Fix a possible unaligned access in samtools reference.
Documentation:
Add documentation on CRAM compression profiles and some of the newer options \
that appear in CRAM 3.1 and above.
Add sclen filter expression keyword documentation.
Extend FILTER EXPRESSION man page section to match the changes made in HTSlib.
Non user-visible changes and build improvements:
Ensure generated test files are ignored (by git) and cleaned (by make testclean)
|
2022-06-30 13:19:02 by Nia Alarie | Files touched by this commit (524) |
Log message:
*: Revbump packages that use Python at runtime without a PKGNAME prefix
|
2022-06-28 13:38:00 by Thomas Klausner | Files touched by this commit (3952) |
Log message:
*: recursive bump for perl 5.36
|
2022-02-27 00:11:43 by Jason Bacon | Files touched by this commit (4) |
Log message:
biology/samtools: Update to 1.15
Several minor enhancements and bug fixes
Changes: https://github.com/samtools/samtools/tags
|
2021-12-17 16:10:06 by Jason Bacon | Files touched by this commit (4) |
Log message:
biology/samtools: Update to 1.14
Numerous fixes and enhancements since 1.12
Changes: https://github.com/samtools/samtools/tags
|