+Beta Release 0.1.8 (11 July, 2010)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable functional changes:
+
+ * Added the `reheader' command which replaces a BAM header with a new
+ header. This command is much faster than replacing header by
+ BAM->SAM->BAM conversions.
+
+ * Added the `mpileup' command which computes the pileup of multiple
+ alignments.
+
+ * The `index' command now stores the number of mapped and unmapped
+ reads in the index file. This information can be retrieved quickly by
+ the new `idxstats' command.
+
+ * By default, pileup used the SOAPsnp model for SNP calling. This
+ avoids the floating overflow in the MAQ model which leads to spurious
+ calls in repetitive regions, although these calls will be immediately
+ filtered by varFilter.
+
+ * The `tview' command now correctly handles CIGARs like 7I10M and
+ 10M1P1I10M which cause assertion failure in earlier versions.
+
+ * Tview accepts a region like `=10,000' where `=' stands for the
+ current sequence name. This saves typing for long sequence names.
+
+ * Added the `-d' option to `pileup' which avoids slow indel calling
+ in ultradeep regions by subsampling reads locally.
+
+ * Added the `-R' option to `view' which retrieves alignments in read
+ groups listed in the specified file.
+
+Performance improvements:
+
+ * The BAM->SAM conversion is up to twice faster, depending on the
+ characteristic of the input.
+
+ * Parsing SAM headers with a lot of reference sequences is now much
+ faster.
+
+ * The number of lseek() calls per query is reduced when the query
+ region contains no read alignments.
+
+Bug fixes:
+
+ * Fixed an issue in the indel caller that leads to miscall of indels.
+ Note that this solution may not work well when the sequencing indel
+ error rate is higher than the rate of SNPs.
+
+ * Fixed another issue in the indel caller which may lead to incorrect
+ genotype.
+
+ * Fixed a bug in `sort' when option `-o' is applied.
+
+ * Fixed a bug in `view -r'.
+
+APIs and other changes:
+
+ * Added iterator interfaces to random access and pileup. The callback
+ interfaces directly call the iterator interfaces.
+
+ * The BGZF blocks holding the BAM header are indepedent of alignment
+ BGZF blocks. Alignment records shorter than 64kB is guaranteed to be
+ fully contained in one BGZF block. This change is fully compatible
+ with the old version of samtools/picard.
+
+Changes in other utilities:
+
+ * Updated export2sam.pl by Chris Saunders.
+
+ * Improved the sam2vcf.pl script.
+
+ * Added a Python version of varfilter.py by Aylwyn Scally.
+
+(0.1.8: 11 July 2010, r613)
+
+
+
+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)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+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)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* 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.
* Various converters: improved functionality in general.
-(0.1.3: 15 April 2009, rXXX)
+ * Updated the example SAM due to the previous bug in fixmate.
+
+(0.1.3: 15 April 2009, r227)
projects / samtools.git / blobdiff