Commit 3aa47fe7 authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 0.15.1+ds

parent b31915d1

.gitignore

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@@ -17,6 +17,7 @@ tests/cbcf_data 
tests/tabix_data



samtools/config.h

bcftools/config.g

htslib/config.status

htslib/config.h

htslib/config.log

NEWS

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@@ -5,10 +5,19 @@ http://pysam.readthedocs.io/en/latest/release.html 
Release notes

=============



Release 0.15.1

==============



Bugfix release.



* [#716] raise ValueError if tid is out of range when writing

* [#697] release version using cython 0.28.5 for python 3.7

  compatibility



Release 0.15.0

==============



This release wraps htslib/samtools/bcftools version 1.9.0.

This release wraps htslib (and friends) version 1.9.



* [#673] permit dash in chromosome name of region string

* [#656] Support `text` when opening a SAM file for writing

bcftools/config.h

deleted100644 → 0
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/* empty config.h created by pysam */

/* conservative compilation options */

doc/release.rst

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@@ -2,6 +2,15 @@ 
Release notes

=============



Release 0.15.1

==============



Bugfix release.



* [#716] raise ValueError if tid is out of range when writing

* [#697] release version using cython 0.28.5 for python 3.7

  compatibility



Release 0.15.0

==============

pysam/libcalignmentfile.pyx

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@@ -1713,8 +1713,13 @@ cdef class AlignmentFile(HTSFile): 
        if not self.is_open:

            return 0



        cdef int ret

        if self.header.ptr.n_targets <= read._delegate.core.tid:

            raise ValueError(

                "AlignedSegment refers to reference number {} that "

                "is larger than the number of references ({}) in the header".format(

                    read._delegate.core.tid, self.header.ptr.n_targets))

        

        cdef int ret

        with nogil:

            ret = sam_write1(self.htsfile,

                             self.header.ptr,