Mapping and Assembly with Qualities

File Release Notes and Changelog

Release Name: 0.4.1

Notes:
Beta Release 0.4.1 (7 January, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

I am sorry for the frequent updates these days. I like to set a
milestone for BWA and this release seems to be. For paired end reads,
BWA also does Smith-Waterman alignment for an unmapped read whose mate
can be mapped confidently. With this strategy BWA achieves similar
accuracy to maq. Benchmark is also updated accordingly.

(0.4.1: 7 January 2009, r760)



Beta Release 0.4.0 (6 January, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

In comparison to the release two days ago, this release is mainly tuned
for performance with some tricks I learnt from Bowtie. However, as the
indexing format has also been changed, I have to increase the version
number to 0.4.0 to emphasize that *DATABASE MUST BE RE-INDEXED* with
`bwa index'.

 * Improved the speed by about 20%.

 * Added multi-threading to `bwa aln'.

(0.4.0: 6 January 2009, r756)



Beta Release 0.3.0 (4 January, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

 * Added paired-end support by separating SA calculation and alignment
   output.

 * Added SAM output.

 * Added evaluation to the documentation.

(0.3.0: 4 January 2009, r741)


Changes:
See ChangeLog in the source code package.