From 012d54fc4930d3830d9fff1889471c2acfc8c821 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Thu, 15 May 2014 11:48:28 -0400 Subject: [PATCH] Updated release notes --- NEWS | 34 +++++++++++++++++++--------------- README.md | 2 +- 2 files changed, 20 insertions(+), 16 deletions(-) diff --git a/NEWS b/NEWS index d09c322..20ef1ed 100644 --- a/NEWS +++ b/NEWS @@ -1,8 +1,9 @@ Release 0.7.9 (11 May, 2014) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -This release brings several major changes to BWA-MEM. Notably, BWA-MEM -now formally supports PacBio reads. It generally runs faster at a minor cost of +This release brings several major changes to BWA-MEM. Notably, BWA-MEM now +formally supports PacBio read-to-reference alignment and experimentally support +PacBio read-to-read alignment. BWA-MEM also runs faster at a minor cost of accuracy. The speedup is more significant when GRCh38 is in use. More specifically: @@ -12,16 +13,16 @@ specifically: new heuristics to improve PacBio alignment. These changes are not used by default. Users need to add option "-x pacbio" to enable the feature. - * Support PacBio subread-to-subread alignment. The feature is enabled with - option "-x pbread". In this mode, the output only gives the overlapping - region between a pair of reads without detailed alignment. + * Support PacBio subread-to-subread alignment (EXPERIMENTAL). This feature is + enabled with option "-x pbread". In this mode, the output only gives the + overlapping region between a pair of reads without detailed alignment. - * Output alternative hits in the XA tag if there are not so many such hits. - This feature is originally implemented in BWA-backtrack. + * Output alternative hits in the XA tag if there are not so many of them. This + is a BWA-backtrack feature. - * EXPERIMENTAL feature to support mapping to ALT contigs in GRCh38. We prodive - a script to postprocess hits in the XA tag to adjust the mapping quality and - generate new primary alignments to all overlapping ALT contigs. We would NOT + * Support mapping to ALT contigs in GRCh38 (EXPERIMENTAL). We provide a script + to postprocess hits in the XA tag to adjust the mapping quality and generate + new primary alignments to all overlapping ALT contigs. We would NOT recommended this feature for production uses. * Improved alignments to many short reference sequences. Older BWA-MEM may @@ -34,8 +35,8 @@ specifically: * Reduced the maximum seed occurrence from 10000 to 500. Reduced the maximum number of Smith-Waterman mate rescue from 100 to 50. Added a heuristic to lower the mapping quality if a read contains seeds with excessive - occurrences. These changes make BWA-MEM XXX faster for mapping short reads - to GRCh37 and XXX faster to GRCh38. + occurrences. These changes make BWA-MEM faster at a minor cost of accuracy + in highly repetitive regions. * Added an option "-Y" to use soft clipping for supplementary alignments. @@ -43,6 +44,12 @@ specifically: * Bugfix: integer overflow when aligning low query sequences. + * Bugfix: chain score is not computed correctly (almost no practical effect) + + * General code cleanup + + * Added FAQs to README + (0.7.9: 11 May 2014, r777) @@ -1041,6 +1048,3 @@ This is the first release of BWA, Burrows-Wheeler Alignment tool. Please read man page for more information about this software. (0.1.1: 03 June 2008, r349) - - - diff --git a/README.md b/README.md index aa12908..dff245e 100644 --- a/README.md +++ b/README.md @@ -24,7 +24,7 @@ different sub-commands: **aln/samse/sampe** for BWA-backtrack, ##Availability -BWA is released under [GPLv3][1]. The latest souce code is [freely +BWA is released under [GPLv3][1]. The latest source code is [freely available at github][2]. Released packages can [be downloaded][3] at SourceForge. After you acquire the source code, simply use `make` to compile and copy the single executable `bwa` to the destination you want. The only