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Setting VariantRecord pos or stop raises error #640

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msto opened this issue Mar 9, 2018 · 3 comments · Fixed by bioconda/bioconda-recipes#13093
Closed

Setting VariantRecord pos or stop raises error #640

msto opened this issue Mar 9, 2018 · 3 comments · Fixed by bioconda/bioconda-recipes#13093

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@msto
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msto commented Mar 9, 2018 •
edited

Hi,

On pysam 0.14, installed via conda, setting the pos or stop of a VariantRecord raises the following error:

Assertion failed: (!inf->vptr_free), function bcf_update_info, file vcf.c, line 3342.
Abort trap: 6

I tried looking into what might be causing this, but I'm unable to replicate when installing from source with pip install -e. It's only occurring when I try to use the pre-compiled version from bioconda. Any idea what might be causing this? Thanks!

EDIT: the error occurs when building with python setup.py install as well
@mvdbeek
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mvdbeek commented May 19, 2018 •
edited

I'm seeing the same issue, and using the provided manylinux wheels solves the issue, so maybe that's more of a bioconda problem ?

mvdbeek added a commit to mvdbeek/pysam that referenced this issue Jan 15, 2019
@mvdbeek
Fix external libraries when building against shared htslib
8c432f3 
This is attempting to fix
pysam-developers#640, under the
assumption this is the same issue as in
brentp/cyvcf2#91 and that it can be fixed
as in
brentp/cyvcf2@1ea5805
mvdbeek added a commit to mvdbeek/bioconda-recipes that referenced this issue Jan 15, 2019
@mvdbeek
Remove htslib/samtools/bcftools dependencies
c07bc3a 
This fixes pysam-developers/pysam#640
which is an issue with the bioconda build of pysam.
Removing those dependencies will make pysam use the bundled
subset of htslib.
A side-effect of this is that pysam and samtools/bcftools/htslib
versions are now independent and can no be mixed at will.
@mvdbeek mvdbeek mentioned this issue Jan 15, 2019
Merged
5 tasks
mvdbeek added a commit to mvdbeek/bioconda-recipes that referenced this issue Jan 15, 2019
@mvdbeek
Remove htslib/samtools/bcftools dependencies
3d0a54c 
This fixes pysam-developers/pysam#640
which is an issue with the bioconda build of pysam.
Removing those dependencies will make pysam use the bundled
subset of htslib.
A side-effect of this is that pysam and samtools/bcftools/htslib
versions are now independent and can no be mixed at will.
mvdbeek added a commit to mvdbeek/bioconda-recipes that referenced this issue Jan 15, 2019
@mvdbeek
Remove htslib/samtools/bcftools dependencies
2fbd896 
This fixes pysam-developers/pysam#640
which is an issue with the bioconda build of pysam.
Removing those dependencies will make pysam use the bundled
subset of htslib.
A side-effect of this is that pysam and samtools/bcftools/htslib
versions are now independent and can no be mixed at will.
mvdbeek added a commit to mvdbeek/bioconda-recipes that referenced this issue Jan 15, 2019
@mvdbeek
Remove htslib/samtools/bcftools dependencies
0438d8c 
This fixes pysam-developers/pysam#640
which is an issue with the bioconda build of pysam.
Removing those dependencies will make pysam use the bundled
subset of htslib.
A side-effect of this is that pysam and samtools/bcftools/htslib
versions are now independent and can no be mixed at will.
@kyleabeauchamp
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Looks like the problem is discuss upstream as well: samtools/htslib#813

mvdbeek added a commit to mvdbeek/bioconda-recipes that referenced this issue Jun 13, 2019
@mvdbeek
Remove htslib/samtools/bcftools dependencies
9028a7b 
This fixes pysam-developers/pysam#640
which is an issue with the bioconda build of pysam.
Removing those dependencies will make pysam use the bundled
subset of htslib.
A side-effect of this is that pysam and samtools/bcftools/htslib
versions are now independent and can no be mixed at will.
dpryan79 pushed a commit to bioconda/bioconda-recipes that referenced this issue Aug 15, 2019
@mvdbeek @dpryan79
Remove htslib/samtools/bcftools dependencies (#13093)
c0a8903 
* Remove htslib/samtools/bcftools dependencies

This fixes pysam-developers/pysam#640
which is an issue with the bioconda build of pysam.
Removing those dependencies will make pysam use the bundled
subset of htslib.
A side-effect of this is that pysam and samtools/bcftools/htslib
versions are now independent and can no be mixed at will.

* Bring recipe up to standards

* Update meta.yaml

* Remove HTSLIB env variables
@jmarshall jmarshall mentioned this issue Sep 2, 2019
Closed
@jmarshall
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This has been fixed since pysam 0.16.0 (when used with HTSlib 1.10 — which fixed the underlying problem — or later).

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Remove htslib/samtools/bcftools dependencies mvdbeek/bioconda-recipes
4 participants
@msto @jmarshall @kyleabeauchamp @mvdbeek