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r384: updated NEWS

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Heng Li 2013-04-23 11:25:46 -04:00
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33
NEWS
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@ -1,3 +1,36 @@
Release 0.7.4 (23 April, 2013)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This is a bugfix release. Most of bugs are considered to be minor which only
very rarely.
ccur
* Bugfix: wrong CIGAR when a query sequence bridges three or more target
sequences. This only happens when aligning reads to short assembly contigs.
* Bugfix: leading "D" operator in CIGAR.
* Extend more seeds for better alignment around tandem repeats. This is also
a cause of the leading "D" operator in CIGAR.
* Bugfix: SSE2-SSW may occasionally find incorrect query starting position
around tandem repeat. This will lead to a suboptimal CIGAR in BWA-MEM and
a wrong CIGAR in BWA.
* Bugfix: clipping penalty does not work as is intended when there is a gap
towards the end of a read.
* Fixed an issue caused by a bug in the libc from Mac/Darwin. In Darwin,
fread() is unable to read a data block longer than 2GB due to an integer
overflow bug in its implementation.
Since version 0.7.4, BWA-MEM is considered to reach similar stability to
BWA-backtrack for short-read mapping.
(0.7.4: 23 April, r385)
Release 0.7.3a (15 March, 2013)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

4
main.c
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@ -46,6 +46,10 @@ static int usage()
fprintf(stderr, " bwtupdate update .bwt to the new format\n");
fprintf(stderr, " bwt2sa generate SA from BWT and Occ\n");
fprintf(stderr, "\n");
fprintf(stderr, "Note: To use BWA, you need to first index the genome with `bwa index'. There are\n");
fprintf(stderr, " three alignment algorithms in BWA: `mem', `bwasw' and `aln/samse/sampe'. If\n");
fprintf(stderr, " you are not sure which to use, try `bwa mem' first. Please `man ./bwa.1' for\n");
fprintf(stderr, " for the manual.\n\n");
return 1;
}