[med-svn] [python-pbcore] 06/06: Fix compatibility with pysam 0.8.4

[Afif Elghraoui]

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commit 9ad012c5b63ac5837f2a9b60c00c8a06977cc365
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Fri Nov 27 04:34:36 2015 -0800

    Fix compatibility with pysam 0.8.4
    
    Closes: #805687
---
 debian/patches/fix-pysam-compatibility.patch | 36 ++++++++++++++++++++++++++++
 debian/patches/series                        |  1 +
 2 files changed, 37 insertions(+)

diff --git a/debian/patches/fix-pysam-compatibility.patch b/debian/patches/fix-pysam-compatibility.patch
new file mode 100644
index 0000000..e4ce443
--- /dev/null
+++ b/debian/patches/fix-pysam-compatibility.patch
@@ -0,0 +1,36 @@
+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 57f5ddc..2c30214 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 doc-theme.patch
 enable-build-time-testing.patch
+fix-pysam-compatibility.patch

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