+++ /dev/null
-Description: Fix spelling errors in source distribution
-Author: Afif Elghraoui <afif@ghraoui.name>
-Bug: https://github.com/pysam-developers/pysam/pull/122
-Last-Update: 2015-06-09
----
-This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- python-pysam.orig/pysam/calignmentfile.pyx
-+++ python-pysam/pysam/calignmentfile.pyx
-@@ -1442,7 +1442,7 @@
- .. note::
-
- It is usually not necessary to create an object of this class
-- explicitely. It is returned as a result of call to a
-+ explicitly. It is returned as a result of call to a
- :meth:`AlignmentFile.fetch`.
-
- '''
-@@ -1491,7 +1491,7 @@
- .. note::
-
- It is usually not necessary to create an object of this class
-- explicitely. It is returned as a result of call to a
-+ explicitly. It is returned as a result of call to a
- :meth:`AlignmentFile.fetch`.
-
- """
-@@ -1645,7 +1645,7 @@
-
- .. note::
- It is usually not necessary to create an object of this class
-- explicitely. It is returned as a result of call to a
-+ explicitly. It is returned as a result of call to a
- :meth:`AlignmentFile.fetch`.
-
- """
-@@ -1715,7 +1715,7 @@
-
- .. note::
- It is usually not necessary to create an object of this class
-- explicitely. It is returned as a result of call to a :meth:`AlignmentFile.fetch`.
-+ explicitly. It is returned as a result of call to a :meth:`AlignmentFile.fetch`.
- """
-
- def __init__(self, AlignmentFile samfile, positions, int multiple_iterators=True):
-@@ -3311,7 +3311,7 @@
- section.
-
- *value_type* describes the type of *value* that is to entered
-- into the alignment record.. It can be set explicitely to one
-+ into the alignment record.. It can be set explicitly to one
- of the valid one-letter type codes. If unset, an appropriate
- type will be chosen automatically.
-
-@@ -3421,7 +3421,7 @@
- bytesize, nvalues, values = convertBinaryTagToList(v + 1)
- return values
- else:
-- raise ValueError("unknown auxilliary type '%s'" % auxtype)
-+ raise ValueError("unknown auxiliary type '%s'" % auxtype)
-
- def get_tags(self, with_value_type=False):
- """the fields in the optional aligment section.
-@@ -3504,7 +3504,7 @@
- a list of (tag, value) tuples.
-
- The :term:`value type` of the values is determined from the
-- python type. Optionally, a type may be given explicitely as
-+ python type. Optionally, a type may be given explicitly as
- a third value in the tuple, For example:
-
- x.set_tags([(NM, 2, "i"), (RG, "GJP00TM04", "Z")]
---- python-pysam.orig/pysam/ctabix.pyx
-+++ python-pysam/pysam/ctabix.pyx
-@@ -199,7 +199,7 @@
- +-----------+-----------+------------------------------------------+
-
- Only the first three fields are required. Additional
-- fields are optional, but if one is defined, all the preceeding
-+ fields are optional, but if one is defined, all the preceding
- need to be defined as well.
-
- '''
---- python-pysam.orig/save/pysam_test2.6.py
-+++ python-pysam/save/pysam_test2.6.py
-@@ -355,7 +355,7 @@
-
- If *use_template* is set, the header is copied from infile using the
- template mechanism, otherwise target names and lengths are passed
-- explicitely.
-+ explicitly.
-
- '''
-
---- python-pysam.orig/tests/AlignmentFile_test.py
-+++ python-pysam/tests/AlignmentFile_test.py
-@@ -370,7 +370,7 @@
-
- If *use_template* is set, the header is copied from infile
- using the template mechanism, otherwise target names and
-- lengths are passed explicitely.
-+ lengths are passed explicitly.
-
- The *checkf* is used to determine if the files are
- equal.
---- python-pysam.orig/tests/SamFile_test.py
-+++ python-pysam/tests/SamFile_test.py
-@@ -355,7 +355,7 @@
-
- If *use_template* is set, the header is copied from infile
- using the template mechanism, otherwise target names and
-- lengths are passed explicitely.
-+ lengths are passed explicitly.
-
- '''
-
+++ /dev/null
-From 6efb22b1a3ee4bc57a691f163b456b417da56db3 Mon Sep 17 00:00:00 2001
-From: Andreas Heger <andreas.heger@gmail.com>
-Date: Thu, 3 Sep 2015 21:25:28 +0100
-Subject: [PATCH] change ctypedef enum to typedef enum for cython 0.23
-Bug: https://github.com/pysam-developers/pysam/issues/164
----
- pysam/chtslib.pxd | 6 +++---
- 1 file changed, 3 insertions(+), 3 deletions(-)
-
-diff --git a/pysam/chtslib.pxd b/pysam/chtslib.pxd
-index 2f8c941..299e84a 100644
---- a/pysam/chtslib.pxd
-+++ b/pysam/chtslib.pxd
-@@ -363,7 +363,7 @@ cdef extern from "htslib/hts.h" nogil:
- hFILE *hfile
- void *voidp
-
-- ctypedef enum htsFormatCategory:
-+ cdef enum htsFormatCategory:
- unknown_category
- sequence_data # Sequence data -- SAM, BAM, CRAM, etc
- variant_data # Variant calling data -- VCF, BCF, etc
-@@ -371,14 +371,14 @@ cdef extern from "htslib/hts.h" nogil:
- region_list # Coordinate intervals or regions -- BED, etc
- category_maximum
-
-- ctypedef enum htsExactFormat:
-+ cdef enum htsExactFormat:
- unknown_format
- binary_format
- text_format
- sam, bam, bai, cram, crai, vcf, bcf, csi, gzi, tbi, bed
- format_maximum
-
-- ctypedef enum htsCompression:
-+ cdef enum htsCompression:
- no_compression, gzip, bgzf, custom
- compression_maximum
-
+++ /dev/null
-Author: Andreas Tille <tille@debian.org>
-Last-Update: 2015-07-24
-Forwarded: https://github.com/pysam-developers/pysam/pull/149
-Description: Update depricated command in test suite
- [Andreas]
- samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
- [main] The `pileup' command has been removed. Please use `mpileup' instead.
- [Afif]
- --Simply replacing pileup with mpileup introduced a new error:
- samtools mpileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
- mpileup: invalid option -- 'c'
- Invalid option: '?'
- --See:
- samtools man page, under mpileup: "In the pileup format (without -u or -g),"
- http://www.htslib.org/doc/samtools.html
- https://www.biostars.org/p/42094/
- The solution is to remove the "-c" flag
---- python-pysam.orig/tests/pysam_data/Makefile
-+++ python-pysam/tests/pysam_data/Makefile
-@@ -48,7 +48,7 @@
- samtools index $<
-
- ex1.pileup.gz:ex1.bam ex1.fa
-- samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
-+ samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz
-
- ex2_truncated.bam: ex2.bam
- head -c 124000 ex2.bam > ex2_truncated.bam
projects / python-pysam.git / commitdiff