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r402: updated NEWS (prepare for the 0.7.5 release)

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Heng Li 2013-05-28 11:18:42 -04:00
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51
NEWS
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Release 0.7.5 (28 May, 2013)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Changes in all components:
* Improved error checking. Patches probived by Rob Davies.
* Updated README.
* Bugfix: return code is zero upon errors.
Changes in BWA-MEM:
* Changed the way a chimeric alignment is reported (conforming to the upcoming
SAM spec v1.5). With 0.7.5, if the read has a chimeric alignment, the paired
or the top hit uses soft clipping and is marked with neither 0x800 nor 0x100
bits. All the other hits part of the chimeric alignment will use hard
clipping and be marked with 0x800 if option "-M" is not in use, or marked
with 0x100 otherwise.
* Other hits part of a chimeric alignment are now reported in the SA tag,
conforming to the SAM spec v1.5.
* Better method for resolving an alignment bridging two or more short
reference sequences. The current strategy maps the query to the reference
sequence that covers the middle point of the alignment. For most
applications, this change has no effects.
Changes in BWA-backtrack:
* Added a magic number to .sai files. This prevents samse/sampe from reading
corrupted (e.g. a .sai file containing LSF log) or incompatible .sai
generated by a different version of bwa.
* Bugfix: alignments in the XA:Z: tag were wrong.
* Keep track of #ins and #del during backtracking. This simplifies the code
and reduces errors in rare corner cases. I should have done this in the
early days of bwa.
In addition, if you use BWA-MEM or the fastmap command of BWA, please cite:
- Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs
with BWA-MEM. arXiv:1303.3997v2 [q-bio.GN].
Thank you.
(0.7.5: 28 May 2013, r402)
Release 0.7.4 (23 April, 2013)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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README.md
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@ -50,7 +50,7 @@ in forums such as [BioStar][8] and [SEQanswers][9].
[20080505][11]]. (if you use the BWA-SW algorithm)
* Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs
with BWA-MEM. [arXiv:1303.3997v1][12] [q-bio.GN]. (if you use the BWA-MEM
with BWA-MEM. [arXiv:1303.3997v2][12] [q-bio.GN]. (if you use the BWA-MEM
algorithm or the **fastmap** command, or want to cite the whole BWA package)
Please note that the last reference is a preprint hosted at [arXiv.org][13]. I