This is an automated email from the git hooks/post-receive script. afif pushed a commit to branch master in repository python-pbcore.
commit 859bb13dc3b4dc3fbb0fc2a2929fe0190bbdc4f2 Author: Afif Elghraoui <[email protected]> Date: Thu Mar 10 22:42:32 2016 -0800 Fix compatibility with pysam 0.9.0 --- debian/changelog | 6 ++++++ debian/control | 2 +- debian/patches/pysam-0.9.0.patch | 20 ++++++++++++++++++++ debian/patches/series | 1 + 4 files changed, 28 insertions(+), 1 deletion(-) diff --git a/debian/changelog b/debian/changelog index b3d194d..d98748b 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +python-pbcore (1.2.7+dfsg-2) UNRELEASED; urgency=medium + + * Fix compatibility with pysam 0.9.0 + + -- Afif Elghraoui <[email protected]> Thu, 10 Mar 2016 21:46:21 -0800 + python-pbcore (1.2.7+dfsg-1) unstable; urgency=medium * Revert "Set watch file to point to pypi rather than github" diff --git a/debian/control b/debian/control index 11f5c2b..7453fd3 100644 --- a/debian/control +++ b/debian/control @@ -10,7 +10,7 @@ Build-Depends: debhelper (>= 9), python-nose, python-h5py (>= 2.0.1), python-numpy (>= 1.7.1), - python-pysam (>= 0.8.4), + python-pysam (>= 0.9.0), python-sphinx Standards-Version: 3.9.6 X-Python-Version: >= 2.7 diff --git a/debian/patches/pysam-0.9.0.patch b/debian/patches/pysam-0.9.0.patch new file mode 100644 index 0000000..b01e3fc --- /dev/null +++ b/debian/patches/pysam-0.9.0.patch @@ -0,0 +1,20 @@ +Description: Fix compatibility with pysam 0.9.0 +Author: Afif Elghraoui <[email protected]> +Forwarded: no +Last-Update: 2016-03-10 +--- python-pbcore.orig/pbcore/io/dataset/utils.py ++++ python-pbcore/pbcore/io/dataset/utils.py +@@ -125,11 +125,11 @@ + shutil.move(tmpname, fname) + + def _indexBam(fname): +- pysam.index(fname) ++ pysam.samtools.index(fname, catch_stdout=False) + return fname + ".bai" + + def _indexFasta(fname): +- pysam.faidx(fname) ++ pysam.samtools.faidx(fname, catch_stdout=False) + return fname + ".fai" + + def _mergeBams(inFiles, outFile): diff --git a/debian/patches/series b/debian/patches/series index df144f3..db4588e 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,3 +1,4 @@ doc-theme.patch enable-build-time-testing.patch remove-unnecessary-cython-dep.patch +pysam-0.9.0.patch -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pbcore.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
