r402: updated NEWS (prepare for the 0.7.5 release)

NEWS

@@ -1,3 +1,54 @@
+Release 0.7.5 (28 May, 2013)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Changes in all components:
+
+ * Improved error checking. Patches probived by Rob Davies.
+
+ * Updated README.
+
+ * Bugfix: return code is zero upon errors.
+
+Changes in BWA-MEM:
+
+ * Changed the way a chimeric alignment is reported (conforming to the upcoming
+   SAM spec v1.5). With 0.7.5, if the read has a chimeric alignment, the paired
+   or the top hit uses soft clipping and is marked with neither 0x800 nor 0x100
+   bits. All the other hits part of the chimeric alignment will use hard
+   clipping and be marked with 0x800 if option "-M" is not in use, or marked
+   with 0x100 otherwise.
+
+ * Other hits part of a chimeric alignment are now reported in the SA tag,
+   conforming to the SAM spec v1.5.
+
+ * Better method for resolving an alignment bridging two or more short
+   reference sequences. The current strategy maps the query to the reference
+   sequence that covers the middle point of the alignment. For most
+   applications, this change has no effects.
+
+Changes in BWA-backtrack:
+
+ * Added a magic number to .sai files. This prevents samse/sampe from reading
+   corrupted (e.g. a .sai file containing LSF log) or incompatible .sai
+   generated by a different version of bwa.
+
+ * Bugfix: alignments in the XA:Z: tag were wrong.
+
+ * Keep track of #ins and #del during backtracking. This simplifies the code
+   and reduces errors in rare corner cases. I should have done this in the
+   early days of bwa.
+
+In addition, if you use BWA-MEM or the fastmap command of BWA, please cite:
+
+ - Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs
+   with BWA-MEM. arXiv:1303.3997v2 [q-bio.GN].
+
+Thank you.
+
+(0.7.5: 28 May 2013, r402)
+
+
+
 Release 0.7.4 (23 April, 2013)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

README.md

@@ -50,7 +50,7 @@ in forums such as [BioStar][8] and [SEQanswers][9].
  [20080505][11]]. (if you use the BWA-SW algorithm)
 
 * Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs
- with BWA-MEM. [arXiv:1303.3997v1][12] [q-bio.GN]. (if you use the BWA-MEM
+ with BWA-MEM. [arXiv:1303.3997v2][12] [q-bio.GN]. (if you use the BWA-MEM
  algorithm or the **fastmap** command, or want to cite the whole BWA package)
 
 Please note that the last reference is a preprint hosted at [arXiv.org][13]. I