Htseq

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

2014-02-27

- added parser classes for BED and Wiggle format

Patch versions:

- 0.6.1p1 (2014-04-13)

- Fixed incorrect version tag

- 0.6.1p2 (2014-08-09)

- some improvements to documentation

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

2014-02-26

- Several changes and improvements to htseq-count:

- BAM files can now be read natively. (New option ``--format``)

- Paired-end SAM files can be used also if sorted by position. No need any mroe to sort by name. (New option ``--order``.)

- Documentation extended by a FAQ section.

- Default for ``--minaqual`` is now 10. (was: 0)

- New chapter in documentation, with more information on counting reads.

- New function ``pair_SAM_alignments_with_buffer`` to implement pairing for position-sorted SAM files.

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

2013-02-20

Various bugs fixed, including

- GFF_Reader interpreted the constructor's "end_included" flag
in the wrong way, hence the end position of intervals of
GFF features was off by 1 base pair before

- htseq-count no longer warns about missing chromosomes, as this
warning was often misleading. Also, these reads are no properly
included in the "no_feature" count.

- default for "max_qual" in "htseq-qa" is now 41, to accommodate newer
Illumina FASTQ files

- BAM_Reader used to incorrectly label single-end reads as paired-end


Patch versions:

* v0.5.4p1 (2013-02-22):

- changed default for GFF_Reader to end_included=True, which is actually the
correct style for Ensemble GTF files. Now the behavious should be as it
was before.

* v0.5.4p2 (2013-04-18):

- fixed issue blocking proper built on Windows

* v0.5.4p3 (2013-04-29):

- htseq-count now correctly skips over "M0" cigar operations

* v0.5.4p4 (2013-08-28):

- added ``.get_original_line()`` function to ``VariantCall``
- firex a bug with reads not being read as paired if they were not
flagged as proper pair

* v0.5.4p5 (2013-10-02/2013-10-10):

- parsing of GFF attribute field no longer fails on quoted semicolons
- fixed issue with get_line_number_string

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

2011-06-29

- added the '--stranded=reverse' option to htseq-count


Patch versions:

* v0.5.3p1 (2011-07-15):

- fix a bug in pair_sam_Alignment (many thanks for Justin Powell for
finding the bug and suggesting a patch)

* v0.5.3p2 (2011-09-15)

- fixed a bug (and a documentation bug) in trim_left/right_end_with_quals

* v0.5.3p3 (2011-09-15)

- p2 was built improperly

* v0.5.3p5 (2012-05-29)

- added 'to_line' function to VariantCall objects and 'meta_info' function to VCF_Reader objects to print VCF-lines / -headers respectively

* v0.5.3p5b (2012-06-01)
- added 'flag' field to SAM_Alignment objects and fixed 'get_sam_line' function of those

* v0.5.3p6 (2012-06-11)
- fixed mix-up between patches p3, p4 and p5

* v0.5.3p7 (2012-06-13)
- switched global pysam import to on-demand version

* v0.5.3p9ur1 (2012-08-31)
- corrected get_sam_line: tab isntead of space between optional fields

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

2011-06-24

- added the '--maxqual' option to htseq-qa

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

2011-05-03

- added steps method to GenomicArray

Patch versions:

* v0.5.1p1 (2011-05-11):

- fixed a bug in step_vector.h causing linkage failure under GCC 4.2

* v0.5.1p2 (2011-05-12):

- fixed pickling

* v0.5.1p3 (2011-05-22):

- fixed quality plot in htseq-qa (top pixel row, for quality score 40, was cut off)