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commit 7c93b9c0d42c415ef3296e6ee4a7d61b6fc34cb8 Author: Afif Elghraoui <a...@ghraoui.name> Date: Sun Dec 6 12:45:11 2015 -0800 Add patch to allow compatibility with pysam 0.8.4 --- debian/patches/series | 1 + debian/patches/update-pysam-interface.patch | 53 +++++++++++++++++++++++++++++ 2 files changed, 54 insertions(+) diff --git a/debian/patches/series b/debian/patches/series index fd4d512..c4f5cd8 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -3,3 +3,4 @@ fix_version.patch add_sphinx_man_pages.patch skip_tests_with_rounding_differences.patch sphinx_1_3.patch +update-pysam-interface.patch diff --git a/debian/patches/update-pysam-interface.patch b/debian/patches/update-pysam-interface.patch new file mode 100644 index 0000000..496a0c4 --- /dev/null +++ b/debian/patches/update-pysam-interface.patch @@ -0,0 +1,53 @@ +Description: Update pysam interface for 0.8.4 + In pysam 0.8.4, interfaces that have been deprecated in + 0.8.1 have been removed. This patch makes the necessary + changes for 0.8.4 compatibility. +Author: Afif Elghraoui <a...@ghraoui.name> +Forwarded: no +Last-Update: 2015-12-06 +--- python-htseq.orig/HTSeq/__init__.py ++++ python-htseq/HTSeq/__init__.py +@@ -940,14 +940,14 @@ + raise + + def __iter__( self ): +- sf = pysam.Samfile(self.filename, "rb") ++ sf = pysam.AlignmentFile(self.filename, "rb") + self.record_no = 0 + for pa in sf: + yield SAM_Alignment.from_pysam_AlignedRead( pa, sf ) + self.record_no += 1 + + def fetch( self, reference = None, start = None, end = None, region = None ): +- sf = pysam.Samfile(self.filename, "rb") ++ sf = pysam.AlignmentFile(self.filename, "rb") + self.record_no = 0 + try: + for pa in sf.fetch( reference, start, end, region ): +@@ -972,14 +972,14 @@ + if not isinstance( iv, GenomicInterval ): + raise TypeError, "Use a HTSeq.GenomicInterval to access regions within .bam-file!" + if self.sf is None: +- self.sf = pysam.Samfile( self.filename, "rb" ) +- if not self.sf._hasIndex(): ++ self.sf = pysam.AlignmentFile( self.filename, "rb" ) ++ if not self.sf.has_index(): + raise ValueError, "The .bam-file has no index, random-access is disabled!" + for pa in self.sf.fetch( iv.chrom, iv.start+1, iv.end ): + yield SAM_Alignment.from_pysam_AlignedRead( pa, self.sf ) + + def get_header_dict( self ): +- sf = pysam.Samfile(self.filename, "rb") ++ sf = pysam.AlignmentFile(self.filename, "rb") + return sf.header + + +@@ -997,7 +997,7 @@ + self.referencelengths = referencelengths + self.text = text + self.header = header +- self.sf = pysam.Samfile( self.filename, mode="wb", template = self.template, referencenames = self.referencenames, referencelengths = self.referencelengths, text = self.text, header = self.header ) ++ self.sf = pysam.AlignmentFile( self.filename, mode="wb", template = self.template, referencenames = self.referencenames, referencelengths = self.referencelengths, text = self.text, header = self.header ) + + @classmethod + def from_BAM_Reader( cls, fn, br ): -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-htseq.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit