From 5370bb23a3f9b263aa8c41e9610ad937094863bd Mon Sep 17 00:00:00 2001 From: Heng Li Date: Fri, 8 Mar 2013 14:14:42 -0500 Subject: [PATCH] Updated NEWS; added stddef.h for size_t I thought size_t is defined in stdlib.h, but it is not always. --- NEWS | 50 +++++++++++++++++++++++++++++++++++++++++++------- bwt.h | 1 + 2 files changed, 44 insertions(+), 7 deletions(-) diff --git a/NEWS b/NEWS index 35202f1..c94b28e 100644 --- a/NEWS +++ b/NEWS @@ -1,3 +1,39 @@ +Release 0.7.1 (8 March, 2013) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Changes to BWA-MEM: + + * Bugfix: rare segmentation fault caused by a partial hit to the end of the + last sequence. + + * Bugfix: occasional mis-pairing given an interleaved fastq. + + * Bugfix: wrong mate information when the mate is unmapped. SAM generated by + BWA-MEM can now be validated with Picard. + + * Improved the performance and accuracy for ultra-long query sequences. + Short-read alignment is not affected. + +Changes to other components: + + * In BWA-backtrack and BWA-SW, replaced the code for global alignment, + Smith-Waterman and SW extension. The performance and accuracy of the two + algorithms stay the same. + + * Added an experimental subcommand to merge overlapping paired ends. The + algorithm is very conservative: it may miss true overlaps but rarely makes + mistakes. + +An important note is that like BWA-SW, BWA-MEM may output multiple primary +alignments for a read, which may cause problems to some tools. For aligning +sequence reads, it is advised to use `-M' to flag extra hits as secondary. This +option is not the default because multiple primary alignments are theoretically +possible in sequence alignment. + +(0.7.1: 8 March 2013, r347) + + + Beta Release 0.7.0 (28 Feburary, 2013) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -16,14 +52,14 @@ In addition to the algorithmic improvements, BWA-MEM also implements a few handy features in practical aspects: 1. BWA-MEM automatically switches between local and glocal (global wrt reads; - local wrt reference) alignment. It reports the end-to-end glocal alignment - if the glocal alignment is not much worse than the optimal local alignment. - Glocal alignment reduces reference bias. + local wrt reference) alignment. It reports the end-to-end glocal alignment + if the glocal alignment is not much worse than the optimal local alignment. + Glocal alignment reduces reference bias. 2. BWA-MEM automatically infers pair orientation from a batch of single-end alignments. It allows more than one orientations if there are sufficient - supporting reads. This feature has not been tested on reads from Illumina - jumping library yet. (EXPERIMENTAL) + supporting reads. This feature has not been tested on reads from Illumina + jumping library yet. (EXPERIMENTAL) 3. BWA-MEM optionally takes one interleaved fastq for paired-end mapping. It is possible to convert a name-sorted BAM to an interleaved fastq on the fly @@ -37,8 +73,8 @@ handy features in practical aspects: files without replying on bash features. 6. BWA-MEM provides a few basic APIs for single-end mapping. The `example.c' - program in the source code directory implements a full single-end mapper in - 50 lines of code. + program in the source code directory implements a full single-end mapper in + 50 lines of code. The BWA-MEM algorithm is in the beta phase. It is not advised to use BWA-MEM for production use yet. However, when the implementation becomes stable after a diff --git a/bwt.h b/bwt.h index e7b0f97..c36bf9b 100644 --- a/bwt.h +++ b/bwt.h @@ -29,6 +29,7 @@ #define BWA_BWT_H #include +#include // requirement: (OCC_INTERVAL%16 == 0); please DO NOT change this line because some part of the code assume OCC_INTERVAL=0x80 #define OCC_INTV_SHIFT 7