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minor changes to docs
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AndreasHeger committed Apr 29, 2015
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29 changes: 18 additions & 11 deletions doc/release.rst
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Expand Up @@ -6,28 +6,35 @@ Release 0.8.3
=============

* samtools command now accept the "catch_stdout" option.
* get_aligned_pairs now works for soft-clipped reads

* get_aligned_pairs now works for soft-clipped reads.

* query_position is now None when a PileupRead is not aligned
to a particular position.

* AlignedSegments are now comparable and hashable.

Release 0.8.2.1
===============

* Installation bugfix release
* Installation bugfix release.

Release 0.8.2
=============

* Pysam now wraps htslib 1.2.1 and samtools version 1.2
* Added CRAM file support to pysam
* Pysam now wraps htslib 1.2.1 and samtools version 1.2.

* Added CRAM file support to pysam.

* New alignment info interface.
* opt() and setTag are deprecated, use get_tag() and set_tag()
instead.
* added has_tag()
* tags is deprecated, use get_tags() and set_tags() instead.

* FastqFile is now FastxFile to reflect that the latter permits
iteration over both fastq- and fasta-formatted files.

* A Cython wrapper for htslib VCF/BCF reader/writer. The wrapper
provides a nearly complete Pythonic interface to VCF/BCF metadata
with reading and writing capability. However, the interface is still
Expand All @@ -37,7 +44,7 @@ Release 0.8.2
Release 0.8.1
=============

* Pysam now wraps htslib and samtools versions 1.1
* Pysam now wraps htslib and samtools versions 1.1.

* Bugfixes, most notable:
* issue #43: uncompressed BAM output
Expand Down Expand Up @@ -89,9 +96,9 @@ Release 0.8.1
as strings, no more bytes.

Other changes:
* AlignmentFile.fetch(reopen) option is now multiple_iterators. The
default changed to not reopen a file unless requested by the user.
* FastaFile.getReferenceLength is now FastaFile.get_reference_length
* AlignmentFile.fetch(reopen) option is now multiple_iterators. The
default changed to not reopen a file unless requested by the user.
* FastaFile.getReferenceLength is now FastaFile.get_reference_length

Backwards incompatible changes

Expand All @@ -109,11 +116,11 @@ Release 0.8.0
=============

* Disabled features
* IteratorColumn.setMask() disabled as htslib does not implement
this functionality?
* IteratorColumn.setMask() disabled as htslib does not implement
this functionality?

* Not implemented yet:
* reading SAM files without header
* reading SAM files without header

Tabix files between version 0.7.8 and 0.8.0 are
not compatible and need to be re-indexed.
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