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commit 9ad012c5b63ac5837f2a9b60c00c8a06977cc365 Author: Afif Elghraoui <[email protected]> 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 <[email protected]> +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 -- 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
