[med-svn] [python-pbcore] 03/06: Drop patch applied upstream

[Afif Elghraoui]

This is an automated email from the git hooks/post-receive script.

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

commit a454197eb9aefaa1636748c601b8ed491b12d350
Author: Afif Elghraoui <afif at debian.org>
Date:   Sun Oct 9 10:39:39 2016 -0700

    Drop patch applied upstream
---
 debian/patches/pysam-0.9.0.patch                   | 27 ----------------------
 debian/patches/remove-unnecessary-cython-dep.patch |  2 +-
 debian/patches/series                              |  1 -
 3 files changed, 1 insertion(+), 29 deletions(-)

diff --git a/debian/patches/pysam-0.9.0.patch b/debian/patches/pysam-0.9.0.patch
deleted file mode 100644
index 9b1f8da..0000000
--- a/debian/patches/pysam-0.9.0.patch
+++ /dev/null
@@ -1,27 +0,0 @@
-Description: Fix compatibility with pysam 0.9.0
-Author: Afif Elghraoui <afif at debian.org>
-Forwarded: https://github.com/PacificBiosciences/pbcore/pull/86
-Last-Update: 2016-04-11
---- python-pbcore.orig/pbcore/io/dataset/utils.py
-+++ python-pbcore/pbcore/io/dataset/utils.py
-@@ -127,11 +127,11 @@
-     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):
---- python-pbcore.orig/requirements.txt
-+++ python-pbcore/requirements.txt
-@@ -1,3 +1,3 @@
- numpy >= 1.7.1
- h5py >= 2.0.1
--pysam == 0.8.4
-+pysam >= 0.9.0
diff --git a/debian/patches/remove-unnecessary-cython-dep.patch b/debian/patches/remove-unnecessary-cython-dep.patch
index 9d6b395..79a01c3 100644
--- a/debian/patches/remove-unnecessary-cython-dep.patch
+++ b/debian/patches/remove-unnecessary-cython-dep.patch
@@ -11,4 +11,4 @@ Last-Update: 2015-12-13
 -cython
  numpy >= 1.7.1
  h5py >= 2.0.1
- pysam == 0.8.4
+ pysam >= 0.9.0
diff --git a/debian/patches/series b/debian/patches/series
index 84151f3..8b6f192 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,5 +1,4 @@
 doc-theme.patch
 enable-build-time-testing.patch
 remove-unnecessary-cython-dep.patch
-pysam-0.9.0.patch
 deprecate-dataset.patch

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pbcore.git