Merge commit 'upstream/0.1.7a.dfsg'

[samtools.git] / NEWS

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+Beta Release 0.1.7 (10 November, 2009)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes:
+
+ * Improved the indel caller in complex scenariors, in particular for
+   long reads. The indel caller is now able to make reasonable indel
+   calls from Craig Venter capillary reads.
+
+ * Rewrote single-end duplicate removal with improved
+   performance. Paired-end reads are not touched.
+
+ * Duplicate removal is now library aware. Samtools remove potential
+   PCR/optical dupliates inside a library rather than across libraries.
+
+ * SAM header is now fully parsed, although this functionality is not
+   used in merging and so on.
+
+ * In samtools merge, optionally take the input file name as RG-ID and
+   attach the RG tag to each alignment.
+
+ * Added FTP support in the RAZF library. RAZF-compressed reference
+   sequence can be retrieved remotely.
+
+ * Improved network support for Win32.
+
+ * Samtools sort and merge are now stable.
+
+Changes in other utilities:
+
+ * Implemented sam2vcf.pl that converts the pileup format to the VCF
+   format.
+
+ * This release of samtools is known to work with the latest
+   Bio-Samtools Perl module.
+
+(0.1.7: 10 November 2009, r510)
+
+
+
+Beta Release 0.1.6 (2 September, 2009)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes:
+
+ * In tview, do not show a blank screen when no reads mapped to the
+   corresponding region.
+
+ * Implemented native HTTP support in the BGZF library. Samtools is now
+   able to directly open a BAM file on HTTP. HTTP proxy is also
+   supported via the "http_proxy" environmental variable.
+
+ * Samtools is now compitable with the MinGW (win32) compiler and the
+   PDCurses library.
+
+ * The calmd (or fillmd) command now calculates the NM tag and replaces
+   MD tags if they are wrong.
+
+ * The view command now recognizes and optionally prints FLAG in HEXs or
+   strings to make a SAM file more friendly to human eyes. This is a
+   samtools-C extension, not implemented in Picard for the time
+   being. Please type `samtools view -?' for more information.
+
+ * BAM files now have an end-of-file (EOF) marker to facilitate
+   truncation detection. A warning will be given if an on-disk BAM file
+   does not have this marker. The warning will be seen on BAM files
+   generated by an older version of samtools. It does NO harm.
+
+ * New key bindings in tview: `r' to show read names and `s' to show
+   reference skip (N operation) as deletions.
+
+ * Fixed a bug in `samtools merge -n'.
+
+ * Samtools merge now optionally copies the header of a user specified
+   SAM file to the resultant BAM output.
+
+ * Samtools pileup/tview works with a CIGAR with the first or the last
+   operation is an indel.
+
+ * Fixed a bug in bam_aux_get().
+
+
+Changes in other utilies:
+
+ * Fixed wrong FLAG in maq2sam.
+
+
+(0.1.6: 2 September 2009, r453)
+
+
+
 Beta Release 0.1.5 (7 July, 2009)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~