search

brentp / hts-nim-tools

useful command-line tools written to showcase hts-nim
https://github.com/brentp/hts-nim
MIT License
49 stars 6 forks source link

Could not import: bam_hdr_destroy #8

Closed pengyu1608 closed 4 years ago

pengyu1608 commented 5 years ago

Hi, when I tried to run the latest hts_nim_tools, it reports: "could not import: bam_hdr_destroy"

I searched it on the web and found the following: "Rename bam_hdr_init/_destroy/_dup() to sam_hdr_init/_destroy/_dup()" in htslib.

https://github.com/samtools/htslib/commit/58b64d83da95f6290baaa76f01d91216312ad16b

Is that the cause? Thanks.

brentp commented 5 years ago

hi, you'll need to use htslib 1.9 (or after 1.9 but before the commit that changed the API). i'll start a branch soon that tracks htslib devel, but i want to make sure it's stable.

cmdcolin commented 4 years ago

I think currently the homebrew/linuxbrew formula might run into this at the moment commit log from homebrew formula says it updated to 1.10 in dec 2019

commit 3eef35543681ae89b0dbfc59c3f507ff01c5a16a
Author: BrewTestBot <homebrew-test-bot@lists.sfconservancy.org>
Date:   Sat Jan 11 20:57:59 2020 +0000

    htslib: update 1.10.2 bottle.

commit b705d726dbeb11c3d7dc783debddfc5dafa65827
Author: Caleb Xu <calebcenter@live.com>
Date:   Sat Jan 11 15:05:15 2020 -0500

    htslib 1.10.2

commit a20d2e27a8a1936110e9bd22d230c0e77210561a
Author: BrewTestBot <homebrew-test-bot@lists.sfconservancy.org>
Date:   Sun Dec 8 23:29:45 2019 +0000

    htslib: update 1.10 bottle.

commit 00147bb8cd4338cd3a587e984fc41477fca63ddc
Author: Jonathan Chang <jchang641@gmail.com>
Date:   Mon Dec 9 10:12:06 2019 +1100

    htslib 1.10
cmdcolin commented 4 years ago

(to be specific I was using mosdepth installed via linuxbrew)

brentp commented 4 years ago

the latest mosdepth tag (v0.2.9) will build with htslib 1.10+ (and hts-nim >= 0.3.0).

I just pushed a fix (08c5296) for this library (08c5296) to work with hts-nim >= 0.3.0.

@pengyu1608 , that should resolve your issue.

@cmdcolin let me know if using the latest mosdepth release resolve your problem.

thanks, -Brent

cmdcolin commented 4 years ago

Thanks! I'll see if I can update the homebrew formula

brentp commented 4 years ago

great! let me know if you encounter any problems.