From 78ed00021f07e6b5e1d531795ecf0289feac13ff Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 23 Apr 2013 11:25:46 -0400 Subject: [PATCH] r384: updated NEWS --- NEWS | 33 +++++++++++++++++++++++++++++++++ main.c | 4 ++++ 2 files changed, 37 insertions(+) diff --git a/NEWS b/NEWS index 0cf0591..42e7c79 100644 --- a/NEWS +++ b/NEWS @@ -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) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff --git a/main.c b/main.c index aee4772..f7616b7 100644 --- a/main.c +++ b/main.c @@ -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; }