comparison SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/NEWS @ 0:74f5ea818cea

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0:74f5ea818cea

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