--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/NEWS	Wed Oct 12 19:50:38 2011 -0400
@@ -0,0 +1,275 @@
+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)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+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)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes in SAMtools:
+
+ * SAMtools is more consistent with the specification: a) '*' in the
+   QUAL field is allowed; b) the field separator is TAB only and SPACE
+   is treated as a character in a field; c) empty header is allowed.
+
+ * Implemented GLFv3 support in pileup.
+
+ * Fixed a severe bug in fixmate: strand information is wrongly
+   overwritten.
+
+ * Fixed a bug in alignment retrieval: alignments bridging n*16384bp are
+   not correctly retrieved sometimes.
+
+ * Fixed a bug in rmdup: segfault if unmapped reads are present.
+
+ * Move indel_filter.pl to samtools.pl and improved the filtering by
+   checking the actual number of alignments containing indels. The indel
+   pileup line is also changed a little to make this filtration easier.
+
+ * Fixed a minor bug in indexing: the bin number of an unmapped read is
+   wrongly calculated.
+
+ * Added `flagstat' command to show statistics on the FLAG field.
+
+ * Improved indel caller by setting the maximum window size in local
+   realignment.
+
+Changes in other utilities:
+
+ * Fixed a bug in maq2sam: a tag name is obsolete.
+
+ * Improvement to wgsim: a) added support for SOLiD read simulation; b)
+   show the number of substitutions/indels/errors in read name; c)
+   considerable code clean up.
+
+ * Various converters: improved functionality in general.
+
+ * Updated the example SAM due to the previous bug in fixmate.
+
+(0.1.3: 15 April 2009, r227)
+
+
+
+Beta Release 0.1.2 (28 January, 2008)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes in SAMtools:
+
+ * Implemented a Bayesian indel caller. The new caller generate scores
+   and genotype and is potentially more accurate than Maq's indel
+   caller. The pileup format is also changed accordingly.
+
+ * Implemented rmdup command: remove potential PCR duplicates. Note that
+   this command ONLY works for FR orientation and requires ISIZE is
+   correctly set.
+
+ * Added fixmate command: fill in mate coordinates, ISIZE and mate
+   related flags from a name-sorted alignment.
+
+ * Fixed a bug in indexing: reads bridging 16x kbp were not retrieved.
+
+ * Allow to select reads shown in the pileup output with a mask.
+
+ * Generate GLFv2 from pileup.
+
+ * Added two more flags for flagging PCR/optical duplicates and for QC
+   failure.
+
+ * Fixed a bug in sort command: name sorting for large alignment did not
+   work.
+
+ * Allow to completely disable RAZF (using Makefile.lite) as some people
+   have problem to compile it.
+
+ * Fixed a bug in import command when there are reads without
+   coordinates.
+
+ * Fixed a bug in tview: clipping broke the alignment viewer.
+
+ * Fixed a compiling error when _NO_CURSES is applied.
+
+ * Fixed a bug in merge command.
+
+Changes in other utilities:
+
+ * Added wgsim, a paired-end reads simulator. Wgsim was adapted from
+   maq's reads simulator. Colin Hercus further improved it to allow
+   longer indels.
+
+ * Added wgsim_eval.pl, a script that evaluates the accuracy of
+   alignment on reads generated by wgsim.
+
+ * Added soap2sam.pl, a SOAP2->SAM converter. This converter does not
+   work properly when multiple hits are output.
+
+ * Added bowtie2sam.pl, a Bowtie->SAM converter. Only the top hit will
+   be retained when multiple hits are present.
+
+ * Fixed a bug in export2sam.pl for QC reads.
+
+ * Support RG tag at MAQ->SAM converter.
+
+ * Added novo2sam.pl, a NovoAlign->SAM converter. Multiple hits and
+   indel are not properly handled, though.
+
+ * Added zoom2sam.pl, a ZOOM->SAM converter. It only works with the
+   default Illumina output.
+
+(0.1.2: 28 January 2008; r116)
+
+
+
+Beta Release 0.1.1 (22 December, 2008)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The is the first public release of samtools. For more information,
+please check the manual page `samtools.1' and the samtools website
+http://samtools.sourceforge.net
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