[med-svn] [python-pbcore] 04/08: Drop patch applied upstream

[Afif Elghraoui]

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

commit a540761a2554795488594e724b27ada2ed4c75a2
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Sun Dec 13 17:16:10 2015 -0800

    Drop patch applied upstream
---
 debian/patches/fix-pysam-compatibility.patch | 36 ----------------------------
 debian/patches/series                        |  1 -
 2 files changed, 37 deletions(-)

diff --git a/debian/patches/fix-pysam-compatibility.patch b/debian/patches/fix-pysam-compatibility.patch
deleted file mode 100644
index e4ce443..0000000
--- a/debian/patches/fix-pysam-compatibility.patch
+++ /dev/null
@@ -1,36 +0,0 @@
-Description: Fix compatibility with recent pysam release
- Deprecations from several releases ago have been fully
- dropped. This patch updates the interface calls.
-Author: Afif Elghraoui <afif at ghraoui.name>
-Bug: https://github.com/PacificBiosciences/pbcore/issues/24
-Forwarded: https://github.com/PacificBiosciences/pbcore/pull/27
-Last-Update: 2015-11-27
---- python-pbcore.orig/pbcore/io/align/BamIO.py
-+++ python-pbcore/pbcore/io/align/BamIO.py
-@@ -32,7 +32,7 @@
- 
- __all__ = [ "BamReader", "IndexedBamReader" ]
- 
--from pysam import Samfile
-+from pysam import AlignmentFile
- from pbcore.io import FastaTable
- from pbcore.chemistry import decodeTriple, ChemistryLookupError
- 
-@@ -51,7 +51,7 @@
- def requiresBai(method):
-     @wraps(method)
-     def f(bamReader, *args, **kwargs):
--        if not bamReader.peer._hasIndex():
-+        if not bamReader.peer.has_index():
-             raise UnavailableFeature, "this feature requires an standard BAM index file (bam.bai)"
-         else:
-             return method(bamReader, *args, **kwargs)
-@@ -185,7 +185,7 @@
- 
-     def __init__(self, fname, referenceFastaFname=None):
-         self.filename = fname = abspath(expanduser(fname))
--        self.peer = Samfile(fname, "rb", check_sq=False)
-+        self.peer = AlignmentFile(fname, "rb", check_sq=False)
-         self._checkFileCompatibility()
- 
-         self._loadReferenceInfo()
diff --git a/debian/patches/series b/debian/patches/series
index 2c30214..57f5ddc 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,2 @@
 doc-theme.patch
 enable-build-time-testing.patch
-fix-pysam-compatibility.patch

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