X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=NEWS;h=149c090c08bc9724d677dce8a66ddf62a83da66b;hb=9f30c9ba76e0266e896f1199b41e0e7ddf6bd648;hp=e3468f17f2a8454167eefee8c27173b0ee78f3ce;hpb=646ba487102664734fb7d57778cb50cb050b2d8c;p=samtools.git

diff --git a/NEWS b/NEWS
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+++ b/NEWS
@@ -1,3 +1,105 @@
+Beta Release 0.1.5 (7 July, 2009)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes:
+
+ * Support opening a BAM alignment on FTP. Users can now use "tview" to
+   view alignments at the NCBI ftp site. Please read manual for more
+   information.
+
+ * In library, propagate errors rather than exit or complain assertion
+   failure.
+
+ * Simplified the building system and fixed compiling errors caused by
+   zlib<1.2.2.1.
+
+ * Fixed an issue about lost header information when a SAM is imported
+   with "view -t".
+
+ * Implemented "samtool.pl varFilter" which filters both SNPs and short
+   indels. This command replaces "indelFilter".
+
+ * Implemented "samtools.pl pileup2fq" to generate FASTQ consensus from
+   pileup output.
+
+ * In pileup, cap mapping quality at 60. This helps filtering when
+   different aligners are in use.
+
+ * In pileup, allow to output variant sites only.
+
+ * Made pileup generate correct calls in repetitive region. At the same
+   time, I am considering to implement a simplified model in SOAPsnp,
+   although this has not happened yet.
+
+ * In view, added '-u' option to output BAM without compression. This
+   option is preferred when the output is piped to other commands.
+
+ * In view, added '-l' and '-r' to get the alignments for one library or
+   read group. The "@RG" header lines are now partially parsed.
+
+ * Do not include command line utilities to libbam.a.
+
+ * Fixed memory leaks in pileup and bam_view1().
+
+ * Made faidx more tolerant to empty lines right before or after FASTA >
+   lines.
+
+
+Changes in other utilities:
+
+ * Updated novo2sam.pl by Colin Hercus, the key developer of novoalign.
+
+
+This release involves several modifications to the key code base which
+may potentially introduce new bugs even though we have tried to minimize
+this by testing on several examples. Please let us know if you catch
+bugs.
+
+(0.1.5: 7 July 2009, r373)
+
+
+
+Beta Release 0.1.4 (21 May, 2009)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes:
+
+ * Added the 'rmdupse' command: removing duplicates for SE reads.
+
+ * Fixed a critical bug in the indel caller: clipped alignments are not
+   processed correctly.
+
+ * Fixed a bug in the tview: gapped alignment may be incorrectly
+   displayed.
+
+ * Unified the interface to BAM and SAM I/O. This is done by
+   implementing a wrapper on top of the old APIs and therefore old APIs
+   are still valid. The new I/O APIs also recognize the @SQ header
+   lines.
+
+ * Generate the MD tag.
+
+ * Generate "=" bases. However, the indel caller will not work when "="
+   bases are present.
+
+ * Enhanced support of color-read display (by Nils Homer).
+
+ * Implemented the GNU building system. However, currently the building
+   system does not generate libbam.a. We will improve this later. For
+   the time being, `make -f Makefile.generic' is preferred.
+
+ * Fixed a minor bug in pileup: the first read in a chromosome may be
+   skipped.
+
+ * Fixed bugs in bam_aux.c. These bugs do not affect other components as
+   they were not used previously.
+
+ * Output the 'SM' tag from maq2sam.
+
+(0.1.4: 21 May 2009, r297)
+
+
+
 Beta Release 0.1.3 (15 April, 2009)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~