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
incomplete and preliminary and lacks capability to mutate the
resulting data.

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

* Pysam now wraps htslib and samtools versions 1.1.

* Bugfixes, most notable:

* issue 43: uncompressed BAM output
* issue 42: skip tests requiring network if none available
* issue 19: multiple iterators can now be made to work on the same tabix file
* issue 24: All strings returned from/passed to the pysam API are now unicode in python 3
* issue 5: type guessing for lists of integers fixed

* API changes for consistency. The old API is still present,
but deprecated.
In particular:

* Tabixfile -> TabixFile
* Fastafile -> FastaFile
* Fastqfile -> FastqFile
* Samfile -> AlignmentFile
* AlignedRead -> AlignedSegment
* qname -> query_name
* tid -> reference_id
* pos -> reference_start
* mapq -> mapping_quality
* rnext -> next_reference_id
* pnext -> next_reference_start
* cigar -> cigartuples
* cigarstring -> cigarstring
* tlen -> template_length
* seq -> query_sequence
* qual -> query_qualities, now returns array
* qqual -> query_alignment_qualities, now returns array
* tags -> tags
* alen -> reference_length, reference is always "alignment", so removed
* aend -> reference_end
* rlen -> query_length
* query -> query_alignment_sequence
* qstart -> query_alignment_start
* qend -> query_alignment_end
* qlen -> query_alignment_length
* mrnm -> next_reference_id
* mpos -> next_reference_start
* rname -> reference_id
* isize -> template_length
* blocks -> get_blocks()
* aligned_pairs -> get_aligned_pairs()
* inferred_length -> infer_query_length()
* positions -> get_reference_positions()
* overlap() -> get_overlap()

* All strings are now passed to or received from the pysam API
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

Backwards incompatible changes

* Empty cigarstring now returns None (instead of '')
* Empty cigar now returns None (instead of [])
* When using the extension classes in cython modules, AlignedRead
needs to be substituted with AlignedSegment.
* fancy_str() has been removed
* qual, qqual now return arrays

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

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

* Not implemented yet:
* 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.

While version 0.7.8 and 0.8.0 should be mostly
compatible, there are some notable exceptions:

* tabix iterators will fail if there are comments
in the middle or the end of a file.

* tabix raises always ValueError for invalid intervals.
Previously, different types of errors were raised
(KeyError, IndexError, ValueError) depending on
the type of invalid intervals (missing chromosome,
out-of-range, malformatted interval).

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

* added AlignedRead.setTag method
* added AlignedRead.blocks
* unsetting CIGAR strings is now possible
* empty CIGAR string returns empty list
* added reopen flag to Samfile.fetch()
* various bugfixes

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

* added Fastafile.references, .nreferences and .lengths
* tabix_iterator now uses kseq.h for python 2.7

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

* added inferred_length property
* issue 122: MACOSX getline missing, now it works?
* seq and qual can be set None
* added Fastqfile