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Updated NEWS; added stddef.h for size_t

I thought size_t is defined in stdlib.h, but it is not always.
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1 parent 66c9783 commit 5370bb23a3f9b263aa8c41e9610ad937094863bd @lh3 committed Mar 8, 2013
Showing with 44 additions and 7 deletions.
  1. +43 −7 NEWS
  2. +1 −0 bwt.h
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50 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
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1 bwt.h
@@ -29,6 +29,7 @@
#define BWA_BWT_H
#include <stdint.h>
+#include <stddef.h>
// 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

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