[med-svn] [python-pbcore] 01/05: Fix compatibility with pysam 0.9.0

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository python-pbcore.

commit 859bb13dc3b4dc3fbb0fc2a2929fe0190bbdc4f2
Author: Afif Elghraoui <afif at ghraoui.name>
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 <afif at debian.org>  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 <afif at debian.org>
+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

-- 
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