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The tool we use in for calculating optical/technical duplicate reads from the STARsolo BAMs requires a flag of 1024, which is captured in the BAM_FDUP attribute of the htslib.sam.h library used by Tag…
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I am trying to install pysam with:
```
export HTSLIB_CONFIGURE_OPTIONS=--disable-bz2
pip3 install pysam --user
```
And I am still getting the same error:
```
Either configure with --disable-b…
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I have managed to install demuxlet in the past but when trying to install on a another server recently the `make` step gave me an error for demuxlet. I found out that it's linked to an update of htsli…
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Hello, I want to change the sample name of .g.vcf.gz files, and it threw seg fault.
`bcftools reheader -s
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Hi,
are these errors known? First seems to be a missing include path, second is that configure likely did not record path to site-wide htslib installation? I have gcc-4.9.4.
```
>>> Configuring…
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`python setup.py test` or `python setup.py install` gives the error message below. I wanted to test my PR https://github.com/brentp/cyvcf2/pull/98 locally.
```
20 warnings generated.
gcc -Wn…
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Hi,
The segfault is caused for example [by this line](https://github.com/fritzsedlazeck/Sniffles/blob/c02731ad288b32949c583cca2252164b235e5cb6/src/sniffles/sniffles#L192), where pysam tries to open…
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when compiling this new version we run into an error
make[2]: Entering directory '/scratch/jjsmit3/bin/trinityrnaseq-v2.15.0/trinity-plugins/bamsifter'
g++ -std=c++11 -o _sift_bam_max_cov sift_ba…
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Note that the new version of `BEDTools` includes `htslib`. My first quick test build failed, so some changes will be required:
https://github.com/arq5x/bedtools2/releases/tag/v2.28.0
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Hi Sam,
The htslib RPM is available on Fedora rawhide.
https://src.fedoraproject.org/rpms/htslib
For Fedora 31, 30, 29, it is going to be available soon after testing on Bodhi system
https://bod…