diff --git a/NEWS b/NEWS index 7474726..788ae40 100644 --- a/NEWS +++ b/NEWS @@ -1,3 +1,34 @@ +Release 0.7.3 (15 March, 2013) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Changes to BWA-MEM: + + * Bugfix: pairing score is inaccurate when option -A does not take the default + value. This is a very minor issue even if it happens. + + * Bugfix: occasionally wrong CIGAR. This happens when in the alignment there + is a 1bp deletion and a 1bp insertion which are close to the end of the + reads, and there are no other substitutions or indels. BWA-MEM would not do + a gapped alignment due to the bug. + + * New feature: output other non-overlapping alignments in the XP tag such that + we can see the entire picture of alignment from one SAM line. XP gives the + position, CIGAR, NM and mapQ of each aligned subsequence of the query. + +BWA-MEM has been used to align ~300Gbp 100-700bp SE/PE reads. SNP/indel calling +has also been evaluated on part of these data. BWA-MEM generally gives better +pre-filtered SNP calls than BWA. No significant issues have been observed since +0.7.2, though minor improvements or bugs (e.g. the bug fixed in this release) +are still possible. If you find potential issues, please send bug reports to + (free registration required). + +In addition, more detailed description of the BWA-MEM algorithm can be found at +. + +(0.7.3: 15 March 2013, r366) + + + Release 0.7.2 (9 March, 2013) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff --git a/bwa.1 b/bwa.1 index f01dce1..a02aebe 100644 --- a/bwa.1 +++ b/bwa.1 @@ -1,4 +1,4 @@ -.TH bwa 1 "13 March 2013" "bwa-0.7.3" "Bioinformatics tools" +.TH bwa 1 "15 March 2013" "bwa-0.7.3" "Bioinformatics tools" .SH NAME .PP bwa - Burrows-Wheeler Alignment Tool @@ -580,7 +580,7 @@ XS Suboptimal alignment score XF Support from forward/reverse alignment XE Number of supporting seeds _ -XP Alt primary hits; format: /(chr,pos,CIGAR;mapQ,NM;)+/ +XP Alt primary hits; format: /(chr,pos,CIGAR,mapQ,NM;)+/ .TE .PP diff --git a/main.c b/main.c index 4761bc9..a03c49f 100644 --- a/main.c +++ b/main.c @@ -3,7 +3,7 @@ #include "utils.h" #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.7.2-r365-beta" +#define PACKAGE_VERSION "0.7.3-r366" #endif int bwa_fa2pac(int argc, char *argv[]);