Package Details: python-pysam 0.18.0-1

Git Clone URL: (read-only, click to copy)
Package Base: python-pysam
Description: Python interface for the SAM/BAM sequence alignment and mapping format
Upstream URL:
Licenses: MIT
Provides: python-pysam
Submitter: iosonofabio
Maintainer: PumpkinCheshire
Last Packager: PumpkinCheshire
Votes: 11
Popularity: 0.016159
First Submitted: 2013-10-14 17:12
Last Updated: 2021-11-24 08:01

Latest Comments

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iosonofabio commented on 2020-12-25 09:02

Sorry guys, my ssh is somehow broken and I can't seem to be able to push to AUR anymore... so I'll disown this package and someone else can pick it up. sorry about that!

luscinius commented on 2020-12-12 07:27

I think a release bump needs to be done to cause the rebuild now that python 3.9 is in extra.

iosonofabio commented on 2018-09-20 16:18

thanks, the .SRCINFO was inconsistent and slipped through the cracks

dburkhardt commented on 2018-09-20 14:19

Fyi, the package version in the AUR package name is different from the version in the PKGBUILD. Can that be updated?

iosonofabio commented on 2016-05-04 22:42

external htslib fails, I think the is buggy. For now using internal htslib still, but see PKGBUILD if you want to give it a go or report upstream.

wookietreiber commented on 2016-04-22 08:23

pysam can be built with an external htslib dependency (c.f., i.e. one that we provide via aur (c.f.

would you be open to add htslib as a dependency?

this would mean setting the following before running install

export HTSLIB_LIBRARY_DIR=/usr/lib
export HTSLIB_INCLUDE_DIR=/usr/include

this then correctly links to /usr/lib/

Stunts commented on 2015-10-23 12:53

PAtch available here:

iosonofabio commented on 2015-09-02 15:24


iosonofabio commented on 2015-09-02 15:23


I'll fix the dep to cython==0.22 for now.

balwierz commented on 2015-09-01 16:25

Problems building:

pysam/cbcf.c: At top level:
pysam/cbcf.c:47530:67: error: unknown type name ‘htsFormatCategory’
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_htsFormatCategory(htsFormatCategory value) {
pysam/cbcf.c:47556:64: error: unknown type name ‘htsExactFormat’
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_htsExactFormat(htsExactFormat value) {
pysam/cbcf.c:47608:64: error: unknown type name ‘htsCompression’
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_htsCompression(htsCompression value) {