Released bwa-0.7.6-r432

NEWS

@@ -1,3 +1,59 @@
+Release 0.7.6 (31 Januaray, 2014)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Changes in BWA-MEM:
+
+ * Changed the way mapping quality is estimated. The new method tends to give
+   the same alignment a higher mapping quality. On paired-end reads, the change
+   is minor as with pairing, the mapping quality is usually high. For short
+   single-end reads, the difference is considerable.
+
+ * Improved load balance when many threads are spawned. However, bwa-mem is
+   still not very thread efficient, probably due to the frequent heap memory
+   allocation. Further improvement is a little difficult and may affect the
+   code stability.
+
+ * Allow to use different clipping penalties for 5'- and 3'-ends. This helps
+   when we do not want to clip one end.
+
+ * Print the @PG line, including the command line options.
+
+ * Improved the band width estimate: a) fixed a bug causing the band
+   width extimated from extension not used in the final global alignment; b)
+   try doubled band width if the global alignment score is smaller.
+   Insufficient band width leads to wrong CIGAR and spurious mismatches/indels.
+
+ * Added a new option -D to fine tune a heuristic on dropping suboptimal hits.
+   Reducing -D increases accuracy but decreases the mapping speed. If unsure,
+   leave it to the default.
+
+ * Bugfix: for a repetitive single-end read, the reported hit is not randomly
+   distributed among equally best hits.
+
+ * Bugfix: missing paired-end hits due to unsorted list of SE hits.
+
+ * Bugfix: incorrect CIGAR caused by a defect in the global alignment.
+
+ * Bugfix: incorrect CIGAR caused by failed SW rescue.
+
+ * Bugfix: alignments largely mapped to the same position are regarded to be
+   distinct from each other, which leads to underestimated mapping quality.
+
+ * Added the MD tag.
+
+There are no changes to BWA-backtrack in this release. However, it has a few
+known issues yet to be fixed. If you prefer BWA-track, It is still advised to
+use bwa-0.6.x.
+
+While I developed BWA-MEM, I also found a few issues with BWA-SW. It is now
+possible to improve BWA-SW with the lessons learned from BWA-MEM. However, as
+BWA-MEM is usually better, I will not improve BWA-SW until I find applications
+where BWA-SW may excel.
+
+(0.7.6: 31 January 2014, r432)
+
+
+
 Release 0.7.5a (30 May, 2013)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

README.md

@@ -28,7 +28,8 @@ different sub-commands: **aln/samse/sampe** for BWA-backtrack,
 BWA is released under [GPLv3][1]. The latest souce code is [freely
 available][2] at github. 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.
+and copy the single executable `bwa` to the destination you want. The only
+dependency of BWA is [zlib][14].
 
 ###Seeking helps
 
@@ -71,3 +72,4 @@ do not have plan to submit it to a peer-reviewed journal in the near future.
 [11]: http://www.ncbi.nlm.nih.gov/pubmed/20080505
 [12]: http://arxiv.org/abs/1303.3997
 [13]: http://arxiv.org/
+[14]: http://zlib.net/

bwa.1

@@ -1,4 +1,4 @@
-.TH bwa 1 "24 May 2013" "bwa-0.7.5" "Bioinformatics tools"
+.TH bwa 1 "31 January 2014" "bwa-0.7.6" "Bioinformatics tools"
 .SH NAME
 .PP
 bwa - Burrows-Wheeler Alignment Tool
@@ -158,7 +158,7 @@ Number of threads [1]
 Minimum seed length. Matches shorter than
 .I INT
 will be missed. The alignment speed is usually insensitive to this value unless
-it significantly deviates 20. [19]
+it significantly deviates from 20. [19]
 .TP
 .BI -w \ INT
 Band width. Essentially, gaps longer than
@@ -210,12 +210,13 @@ Gap extension penalty. A gap of length k costs O + k*E (i.e.
 .B -O
 is for opening a zero-length gap). [1]
 .TP
-.BI -L \ INT
+.BI -L \ INT[,INT]
 Clipping penalty. When performing SW extension, BWA-MEM keeps track of the best
 score reaching the end of query. If this score is larger than the best SW score
 minus the clipping penalty, clipping will not be applied. Note that in this
 case, the SAM AS tag reports the best SW score; clipping penalty is not
-deducted. [5]
+deduced. If two numbers are provided, the first is for 5'-end clipping and
+second for 3'-end clipping. [5]
 .TP
 .BI -U \ INT
 Penalty for an unpaired read pair. BWA-MEM scores an unpaired read pair as
@@ -250,10 +251,6 @@ transfer read meta information (e.g. barcode) to the SAM output. Note that the
 FASTA/Q comment (the string after a space in the header line) must conform the SAM
 spec (e.g. BC:Z:CGTAC). Malformated comments lead to incorrect SAM output.
 .TP
-.B -H
-Use hard clipping 'H' in the SAM output. This option may dramatically reduce
-the redundancy of output when mapping long contig or BAC sequences.
-.TP
 .B -M
 Mark shorter split hits as secondary (for Picard compatibility).
 .TP
@@ -569,6 +566,7 @@ NM	Edit distance
 MD	Mismatching positions/bases
 AS	Alignment score
 BC	Barcode sequence
+SA	Supplementary alignments
 _
 X0	Number of best hits
 X1	Number of suboptimal hits found by BWA

main.c

@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.5a-r431"
+#define PACKAGE_VERSION "0.7.6-r432"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);