Package Details: samtools 1.10-3

Git Clone URL: https://aur.archlinux.org/samtools.git (read-only, click to copy)
Package Base: samtools
Description: tools for manipulating next-generation sequencing data
Upstream URL: http://www.htslib.org/
Licenses: custom
Submitter: Vrob
Maintainer: viralstitch
Last Packager: viralstitch
Votes: 28
Popularity: 0.74
First Submitted: 2009-11-04 21:48
Last Updated: 2019-12-18 04:55

Latest Comments

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Rhinoceros commented on 2019-12-18 20:56

Oops sorry @viralstitch. Missed it somehow. Thank you!

viralstitch commented on 2019-12-18 15:32

If you've installed samtools-1.10-2, you'll need to upgrade to samtools-1.10-3 before upgrading htslib in order to solve the dependency issue.

Let me know if there are any other issues. Thanks!

Rhinoceros commented on 2019-12-18 08:55

@viralstitch Did you mean to depend on htslib=1.10 or htslib>=1.10? Currently htslib is 1.10.1, so samtools cannot be installed.

viralstitch commented on 2019-12-10 16:15

I think this is an issue with htslib changing its type names. I've updated the package to require htslib=1.10

dschrempf commented on 2019-12-09 09:59

Compilation worked at the third attempt. No idea what has changed, I did a clean build three times ... Sorry for the fuzz.

dschrempf commented on 2019-12-09 09:49

Hi,

With the new update, I am getting the following compilation error:

bam_index.c:117:32: error: unknown type name ‘sam_hdr_t’; did you mean ‘bam_hdr_t’? 117 | int slow_idxstats(samFile fp, sam_hdr_t header) { | ^~~~~~~~~ | bam_hdr_t

Is this a problem of the package, or of samtools?

Thanks!

alexpe87 commented on 2017-11-05 16:01

Ncurses update from today fixed the issue again:

ncurses 6.0+20170902-3 (works)
ncurses 6.0+20170902-2 (does not work)

If your core repo isn't up to date yet, you could manually download the most current ncurses package and install manually with pacman -U <pkgname>.

https://www.archlinux.org/packages/core/x86_64/ncurses/

alexpe87 commented on 2017-11-01 13:10

Hm, looks like ncurses was updated 7 days ago (https://git.archlinux.org/svntogit/packages.git/log/trunk?h=packages/ncurses) and that seems to break the package. I'll have a look.

alienzj commented on 2017-11-01 02:29

make: *** [Makefile:126:bam_tview_curses.o] error 1

Compiled failed!

Hele me, please!
Thanks very much!

wookietreiber commented on 2017-05-20 15:03

updated.