prada: pyPRADA_1.2/tools/samtools-0.1.16/NEWS comparison

comparison pyPRADA_1.2/tools/samtools-0.1.16/NEWS @ 0:acc2ca1a3ba4

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+Beta Release 0.1.16 (21 April, 2011)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Notable changes in samtools:
+* Support the new SAM/BAM type `B' in the latest SAM spec v1.4.
+* When the output file of `samtools merge' exists, do not overwrite it unless
+a new command-line option `-f' is applied.
+* Bugfix: BED support is not working when the input BED is not sorted.
+* Bugfix: some reads without coordinates but given on the reverse strand are
+lost in merging.
+Notable changes in bcftools:
+* Code cleanup: separated max-likelihood inference and Bayesian inference.
+* Test Hardy-Weinberg equilibrium with a likelihood-ratio test.
+* Provided another association test P-value by likelihood-ratio test.
+* Use Brent's method to estimate the site allele frequency when EM converges
+slowly. The resulting ML estimate of allele frequnecy is more accurate.
+* Added the `ldpair' command, which computes r^2 between SNP pairs given in
+an input file.
+Also, the `pileup' command, which has been deprecated by `mpileup' since
+version 0.1.10, will be dropped in the next release. The old `pileup' command
+is substandard and causing a lot of confusion.
+(0.1.16: 21 April 2011, r963:234)
+Beta Release 0.1.15 (10 April, 2011)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Noteable changes:
+* Allow to perform variant calling or to extract information in multiple
+regions specified by a BED file (`samtools mpileup -l', `samtools view -L'
+and `bcftools view -l').
+* Added the `depth' command to samtools to compute the per-base depth with a
+simpler interface. File `bam2depth.c', which implements this command, is the
+recommended example on how to use the mpileup APIs.
+* Estimate genotype frequencies with ML; perform chi^2 based Hardy-Weinberg
+test using this estimate.
+* For `samtools view', when `-R' is specified, drop read groups in the header
+that are not contained in the specified file.
+* For `samtools flagstat', separate QC-pass and QC-fail reads.
+* Improved the command line help of `samtools mpileup' and `bcftools view'.
+* Use a global variable to control the verbose level of samtools stderr
+output. Nonetheless, it has not been full utilized.
+* Fixed an issue in association test which may report false associations,
+possibly due to floating point underflow.
+(0.1.15: 10 April 2011, r949:203)
+Beta release 0.1.14 (21 March, 2011)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+This release implements a method for testing associations for case-control
+data. The method does not call genotypes but instead sums over all genotype
+configurations to compute a chi^2 based test statistics. It can be potentially
+applied to comparing a pair of samples (e.g. a tumor-normal pair), but this
+has not been evaluated on real data.
+Another new feature is to make X chromosome variant calls when female and male
+samples are both present. The user needs to provide a file indicating the
+ploidy of each sample (see also manual bcftools/bcftools.1).
+Other notable changes:
+* Added `bcftools view -F' to parse BCF files generated by samtools r921 or
+older which encodes PL in a different way.
+* Changed the behavior of `bcftools view -s'. Now when a list of samples is
+provided, the samples in the output will be reordered to match the ordering
+in the sample list. This change is mainly designed for association test.
+* Sped up `bcftools view -v' for target sequencing given thousands of samples.
+Also added a new option `view -d' to skip loci where only a few samples are
+covered by reads.
+* Dropped HWE test. This feature has never been implemented properly. An EM
+should be much better. To be implemented in future.
+* Added the `cat' command to samtools. This command concatenate BAMs with
+identical sequence dictionaries in an efficient way. Modified from bam_cat.c
+written by Chris Saunders.
+* Added `samtools view -1' to write BAMs at a low compression level but twice
+faster to create. The `sort' command generates temporary files at a low
+compression level as well.
+* Added `samtools mpileup -6' to accept "BAM" with Illumina 1.3+ quality
+strings (strictly speaking, such a file is not BAM).
+* Added `samtools mpileup -L' to skip INDEL calling in regions with
+excessively high coverage. Such regions dramatically slow down mpileup.
+* Updated `misc/export2sam.pl', provided by Chris Saunders from Illumina Inc.
+(0.1.14: 21 March 2011, r933:170)
+Beta release 0.1.13 (1 March, 2011)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+The most important though largely invisible modification is the change of the
+order of genotypes in the PL VCF/BCF tag. This is to conform the upcoming VCF
+spec v4.1. The change means that 0.1.13 is not backward compatible with VCF/BCF
+generated by samtools older than r921 inclusive.  VCF/BCF generated by the new
+samtools will contain a line `##fileformat=VCFv4.1' as well as the samtools
+version number.
+Single Individual Haplotyping (SIH) is added as an experimental feature. It
+originally aims to produce haploid consensus from fosmid pool sequencing, but
+also works with short-read data. For short reads, phased blocks are usually too
+short to be useful in many applications, but they can help to rule out part of
+SNPs close to INDELs or between copies of CNVs.
+Other notable changes in samtools:
+* Construct per-sample consensus to reduce the effect of nearby SNPs in INDEL
+calling. This reduces the power but improves specificity.
+* Improved sorting order checking in indexing. Now indexing is the preferred way
+to check if a BAM is sorted.
+* Added a switch `-E' to mpileup and calmd. This option uses an alternative way
+to apply BAQ, which increases sensistivity, especially to MNPs, at the cost of
+a little loss in specificity.
+* Added `mpileup -A' to allow to use reads in anomalous pairs in SNP calling.
+* Added `mpileup -m' to allow fine control of the collection of INDEL candidates.
+* Added `mpileup -S' to compute per-sample strand bias P-value.
+* Added `mpileup -G' to exclude read groups in variant calling.
+* Fixed segfault in indel calling related to unmapped and refskip reads.
+* Fixed an integer overflow in INDEL calling. This bug produces wrong INDEL
+genotypes for longer short INDELs, typically over 10bp.
+* Fixed a bug in tview on big-endian machines.
+* Fixed a very rare memory issue in bam_md.c
+* Fixed an out-of-boundary bug in mpileup when the read base is `N'.
+* Fixed a compiling error when the knetfile library is not used. Fixed a
+library compiling error due to the lack of bam_nt16_nt4_table[] table.
+Suppress a compiling warning related to the latest zlib.
+Other notable changes in bcftools:
+* Updated the BCF spec.
+* Added the `FQ' VCF INFO field, which gives the phred-scaled probability
+of all samples being the same (identical to the reference or all homozygous
+variants). Option `view -f' has been dropped.
+* Implementated of "vcfutils.pl vcf2fq" to generate a consensus sequence
+similar to "samtools.pl pileup2fq".
+* Make sure the GT FORMAT field is always the first FORMAT to conform the VCF
+spec. Drop bcf-fix.pl.
+* Output bcftools specific INFO and FORMAT in the VCF header.
+* Added `view -s' to call variants from a subset of samples.
+* Properly convert VCF to BCF with a user provided sequence dictionary. Nonetheless,
+custom fields are still unparsed and will be stored as a missing value.
+* Fixed a minor bug in Fisher's exact test; the results are rarely changed.
+(0.1.13: 1 March 2011, r926:134)
+Beta release 0.1.12a (2 December, 2010)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+This is another bug fix release:
+* Fixed a memory violation in mpileup, which causes segfault. Release
+0.1.9 and above are affected.
+* Fixed a memory violation in the indel caller, which does not causes
+segfault, but may potentially affect deletion calls in an unexpected
+way. Release 0.1.10 and above are affected.
+* Fixed a bug in computing r-square in bcftools. Few are using this
+functionality and it only has minor effect.
+* Fixed a memory leak in bam_fetch().
+* Fixed a bug in writing meta information to the BAM index for the last
+sequence. This bug is invisible to most users, but it is a bug anyway.
+* Fixed a bug in bcftools which causes false "DP4=0,0,0,0" annotations.
+(0.1.12: 2 December 2010, r862)
+Beta release 0.1.11 (21 November, 2010)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+This is mainly a bug fix release:
+* Fixed a bug in random retrieval (since 0.1.8). It occurs when reads
+are retrieved from a small region containing no reads.
+* Fixed a bug in pileup (since 0.1.9). The bug causes an assertion
+failure when the first CIGAR operation is a deletion.
+* Improved fault tolerence in remote access.
+One minor feature has been implemented in bcftools:
+* Added a reference-free variant calling mode. In this mode, a site is
+regarded as a variat iff the sample(s) contains two or more alleles;
+the meaning of the QUAL field in the VCF output is changed
+accordingly. Effectively, the reference allele is irrelevant to the
+result in the new mode, although the reference sequence has to be
+used in realignment when SAMtools computes genotype likelihoods.
+In addition, since 0.1.10, the `pileup' command has been deprecated by
+`mpileup' which is more powerful and more accurate. The `pileup' command
+will not be removed in the next few releases, but new features will not
+be added.
+(0.1.11: 21 November 2010, r851)
+Beta Release 0.1.10 (16 November, 2010)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+This release is featured as the first major improvement to the indel
+caller. The method is similar to the old one implemented in the pileup
+command, but the details are handled more carefully both in theory and
+in practice. As a result, the new indel caller usually gives more
+accurate indel calls, though at the cost of sensitivity. The caller is
+implemented in the mpileup command and is invoked by default. It works
+with multiple samples.
+Other notable changes:
+* With the -r option, the calmd command writes the difference between
+the original base quality and the BAQ capped base quality at the BQ
+tag but does not modify the base quality. Please use -Ar to overwrite
+the original base quality (the 0.1.9 behavior).
+* Allow to set a maximum per-sample read depth to reduce memory. In
+0.1.9, most of memory is wasted for the ultra high read depth in some
+regions (e.g. the chr1 centromere).
+* Optionally write per-sample read depth and per-sample strand bias
+P-value.
+* Compute equal-tail (Bayesian) credible interval of site allele
+frequency at the CI95 VCF annotation.
+* Merged the vcfutils.pl varFilter and filter4vcf for better SNP/indel
+filtering.
+(0.1.10: 16 November 2010, r829)
+Beta Release 0.1.9 (27 October, 2010)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+This release is featured as the first major improvement to the samtools'
+SNP caller.  It comes with a revised MAQ error model, the support of
+multi-sample SNP calling and the computation of base alignment quality
+(BAQ).
+The revised MAQ error model is based on the original model. It solves an
+issue of miscalling SNPs in repetitive regions. Althought such SNPs can
+usually be filtered at a later step, they mess up unfiltered calls. This
+is a theoretical flaw in the original model. The revised MAQ model
+deprecates the orginal MAQ model and the simplified SOAPsnp model.
+Multi-sample SNP calling is separated in two steps. The first is done by
+samtools mpileup and the second by a new program, bcftools, which is
+included in the samtools source code tree. Multi-sample SNP calling also
+works for single sample and has the advantage of enabling more powerful
+filtration. It is likely to deprecate pileup in future once a proper
+indel calling method is implemented.
+BAQ is the Phred-scaled probability of a read base being wrongly
+aligned. Capping base quality by BAQ has been shown to be very effective
+in suppressing false SNPs caused by misalignments around indels or in
+low-complexity regions with acceptable compromise on computation
+time. This strategy is highly recommended and can be used with other SNP
+callers as well.
+In addition to the three major improvements, other notable changes are:
+* Changes to the pileup format. A reference skip (the N CIGAR operator)
+is shown as '<' or '>' depending on the strand. Tview is also changed
+accordingly.
+* Accelerated pileup. The plain pileup is about 50% faster.
+* Regional merge. The merge command now accepts a new option to merge
+files in a specified region.
+* Fixed a bug in bgzip and razip which causes source files to be
+deleted even if option -c is applied.
+* In APIs, propogate errors to downstream callers and make samtools
+return non-zero values once errors occur.
+(0.1.9: 27 October 2010, r783)
+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)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+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

Mercurial > repos > siyuan > prada

comparison pyPRADA_1.2/tools/samtools-0.1.16/NEWS @ 0:acc2ca1a3ba4