Package Details: samtools 1.23.1-1

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: r6eve
Last Packager: r6eve
Votes: 31
Popularity: 0.000000
First Submitted: 2009-11-04 21:48 (UTC)
Last Updated: 2026-03-19 10:21 (UTC)

Dependencies (2)

Sources (1)

Latest Comments

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r6eve commented on 2026-04-13 23:06 (UTC)

@balwierz You don't need to delete them. Feel free to ask any questions.

balwierz commented on 2026-04-13 16:00 (UTC)

Thanks, I found the problem. For some reason I have some old version installed in /usr/local/include/htslib/hts.h by bcftools years ago. I cleaned up and it works fine! (btw version.h had #define SAMTOOLS_VERSION "1.23.1", so it did not help. Shall I delete all my comments?

r6eve commented on 2026-04-13 14:27 (UTC)

@balwierz Could you reproduce the error manually?

# Before run those, please remove all installed htslib.
yay -S htslib  # Or, your favorite pacman wrapper
curl -L -O https://github.com/samtools/samtools/releases/download/1.23.1/samtools-1.23.1.tar.bz2
tar xf samtools-1.23.1.tar.bz2
cd samtools-1.23.1
rm -rf htslib-1.23.1
./configure --prefix=/usr --with-htslib=system
make

If you can reproduce it, could you show me version.h after running make?

balwierz commented on 2026-04-13 09:37 (UTC)

@r6eve: I have htslib 1.23.1-1

r6eve commented on 2026-04-13 03:19 (UTC)

@balwierz I can reproduce it. UMI support is introduced after htlib 1.23, so using older htslib, got that error messages. Please check the version of htslib.

r6eve commented on 2026-04-13 00:10 (UTC)

@balwierz I cannot reproduce the problem. Could you show me the version.h after running make?

balwierz commented on 2026-04-12 16:56 (UTC)

Does not compile:

ive-relocs -flto=auto"' >> version.h
bam_fastq.c: In function ‘set_sam_opts’:
bam_fastq.c:519:25: error: ‘FASTQ_OPT_UMI’ undeclared (first use in this function); did you mean ‘FASTQ_OPT_RNUM’?
  519 |         hts_set_opt(fp, FASTQ_OPT_UMI, state->UMI_tag);
      |                         ^~~~~~~~~~~~~
      |                         FASTQ_OPT_RNUM

viralstitch commented on 2021-07-31 15:54 (UTC)

I'm sorry for not getting back to you sooner. I no longer have time to maintain the package. Anyone is welcome to pick it up.

zethson commented on 2021-07-13 13:18 (UTC)

Installation fails because 7 tests are failing. I would appreciate a fix.

Thanks!

viralstitch commented on 2020-09-23 00:13 (UTC)

Thanks for the comment. I've pushed a pkgrel update with the new checksums. They changed at some point today. These files worked for me this morning.

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