1 Beta release 0.1.12a (2 December, 2010)
2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
4 This is another bug fix release:
6 * Fixed a memory violation in mpileup, which causes segfault. Release
7 0.1.9 and above are affected.
9 * Fixed a memory violation in the indel caller, which does not causes
10 segfault, but may potentially affect deletion calls in an unexpected
11 way. Release 0.1.10 and above are affected.
13 * Fixed a bug in computing r-square in bcftools. Few are using this
14 functionality and it only has minor effect.
16 * Fixed a memory leak in bam_fetch().
18 * Fixed a bug in writing meta information to the BAM index for the last
19 sequence. This bug is invisible to most users, but it is a bug anyway.
21 * Fixed a bug in bcftools which causes false "DP4=0,0,0,0" annotations.
23 (0.1.12: 2 December 2010, r862)
27 Beta release 0.1.11 (21 November, 2010)
28 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
30 This is mainly a bug fix release:
32 * Fixed a bug in random retrieval (since 0.1.8). It occurs when reads
33 are retrieved from a small region containing no reads.
35 * Fixed a bug in pileup (since 0.1.9). The bug causes an assertion
36 failure when the first CIGAR operation is a deletion.
38 * Improved fault tolerence in remote access.
40 One minor feature has been implemented in bcftools:
42 * Added a reference-free variant calling mode. In this mode, a site is
43 regarded as a variat iff the sample(s) contains two or more alleles;
44 the meaning of the QUAL field in the VCF output is changed
45 accordingly. Effectively, the reference allele is irrelevant to the
46 result in the new mode, although the reference sequence has to be
47 used in realignment when SAMtools computes genotype likelihoods.
49 In addition, since 0.1.10, the `pileup' command has been deprecated by
50 `mpileup' which is more powerful and more accurate. The `pileup' command
51 will not be removed in the next few releases, but new features will not
54 (0.1.11: 21 November 2010, r851)
58 Beta Release 0.1.10 (16 November, 2010)
59 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
61 This release is featured as the first major improvement to the indel
62 caller. The method is similar to the old one implemented in the pileup
63 command, but the details are handled more carefully both in theory and
64 in practice. As a result, the new indel caller usually gives more
65 accurate indel calls, though at the cost of sensitivity. The caller is
66 implemented in the mpileup command and is invoked by default. It works
67 with multiple samples.
69 Other notable changes:
71 * With the -r option, the calmd command writes the difference between
72 the original base quality and the BAQ capped base quality at the BQ
73 tag but does not modify the base quality. Please use -Ar to overwrite
74 the original base quality (the 0.1.9 behavior).
76 * Allow to set a maximum per-sample read depth to reduce memory. In
77 0.1.9, most of memory is wasted for the ultra high read depth in some
78 regions (e.g. the chr1 centromere).
80 * Optionally write per-sample read depth and per-sample strand bias
83 * Compute equal-tail (Bayesian) credible interval of site allele
84 frequency at the CI95 VCF annotation.
86 * Merged the vcfutils.pl varFilter and filter4vcf for better SNP/indel
89 (0.1.10: 16 November 2010, r829)
93 Beta Release 0.1.9 (27 October, 2010)
94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
96 This release is featured as the first major improvement to the samtools'
97 SNP caller. It comes with a revised MAQ error model, the support of
98 multi-sample SNP calling and the computation of base alignment quality
101 The revised MAQ error model is based on the original model. It solves an
102 issue of miscalling SNPs in repetitive regions. Althought such SNPs can
103 usually be filtered at a later step, they mess up unfiltered calls. This
104 is a theoretical flaw in the original model. The revised MAQ model
105 deprecates the orginal MAQ model and the simplified SOAPsnp model.
107 Multi-sample SNP calling is separated in two steps. The first is done by
108 samtools mpileup and the second by a new program, bcftools, which is
109 included in the samtools source code tree. Multi-sample SNP calling also
110 works for single sample and has the advantage of enabling more powerful
111 filtration. It is likely to deprecate pileup in future once a proper
112 indel calling method is implemented.
114 BAQ is the Phred-scaled probability of a read base being wrongly
115 aligned. Capping base quality by BAQ has been shown to be very effective
116 in suppressing false SNPs caused by misalignments around indels or in
117 low-complexity regions with acceptable compromise on computation
118 time. This strategy is highly recommended and can be used with other SNP
121 In addition to the three major improvements, other notable changes are:
123 * Changes to the pileup format. A reference skip (the N CIGAR operator)
124 is shown as '<' or '>' depending on the strand. Tview is also changed
127 * Accelerated pileup. The plain pileup is about 50% faster.
129 * Regional merge. The merge command now accepts a new option to merge
130 files in a specified region.
132 * Fixed a bug in bgzip and razip which causes source files to be
133 deleted even if option -c is applied.
135 * In APIs, propogate errors to downstream callers and make samtools
136 return non-zero values once errors occur.
138 (0.1.9: 27 October 2010, r783)
142 Beta Release 0.1.8 (11 July, 2010)
143 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
145 Notable functional changes:
147 * Added the `reheader' command which replaces a BAM header with a new
148 header. This command is much faster than replacing header by
149 BAM->SAM->BAM conversions.
151 * Added the `mpileup' command which computes the pileup of multiple
154 * The `index' command now stores the number of mapped and unmapped
155 reads in the index file. This information can be retrieved quickly by
156 the new `idxstats' command.
158 * By default, pileup used the SOAPsnp model for SNP calling. This
159 avoids the floating overflow in the MAQ model which leads to spurious
160 calls in repetitive regions, although these calls will be immediately
161 filtered by varFilter.
163 * The `tview' command now correctly handles CIGARs like 7I10M and
164 10M1P1I10M which cause assertion failure in earlier versions.
166 * Tview accepts a region like `=10,000' where `=' stands for the
167 current sequence name. This saves typing for long sequence names.
169 * Added the `-d' option to `pileup' which avoids slow indel calling
170 in ultradeep regions by subsampling reads locally.
172 * Added the `-R' option to `view' which retrieves alignments in read
173 groups listed in the specified file.
175 Performance improvements:
177 * The BAM->SAM conversion is up to twice faster, depending on the
178 characteristic of the input.
180 * Parsing SAM headers with a lot of reference sequences is now much
183 * The number of lseek() calls per query is reduced when the query
184 region contains no read alignments.
188 * Fixed an issue in the indel caller that leads to miscall of indels.
189 Note that this solution may not work well when the sequencing indel
190 error rate is higher than the rate of SNPs.
192 * Fixed another issue in the indel caller which may lead to incorrect
195 * Fixed a bug in `sort' when option `-o' is applied.
197 * Fixed a bug in `view -r'.
199 APIs and other changes:
201 * Added iterator interfaces to random access and pileup. The callback
202 interfaces directly call the iterator interfaces.
204 * The BGZF blocks holding the BAM header are indepedent of alignment
205 BGZF blocks. Alignment records shorter than 64kB is guaranteed to be
206 fully contained in one BGZF block. This change is fully compatible
207 with the old version of samtools/picard.
209 Changes in other utilities:
211 * Updated export2sam.pl by Chris Saunders.
213 * Improved the sam2vcf.pl script.
215 * Added a Python version of varfilter.py by Aylwyn Scally.
217 (0.1.8: 11 July 2010, r613)
221 Beta Release 0.1.7 (10 November, 2009)
222 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
226 * Improved the indel caller in complex scenariors, in particular for
227 long reads. The indel caller is now able to make reasonable indel
228 calls from Craig Venter capillary reads.
230 * Rewrote single-end duplicate removal with improved
231 performance. Paired-end reads are not touched.
233 * Duplicate removal is now library aware. Samtools remove potential
234 PCR/optical dupliates inside a library rather than across libraries.
236 * SAM header is now fully parsed, although this functionality is not
237 used in merging and so on.
239 * In samtools merge, optionally take the input file name as RG-ID and
240 attach the RG tag to each alignment.
242 * Added FTP support in the RAZF library. RAZF-compressed reference
243 sequence can be retrieved remotely.
245 * Improved network support for Win32.
247 * Samtools sort and merge are now stable.
249 Changes in other utilities:
251 * Implemented sam2vcf.pl that converts the pileup format to the VCF
254 * This release of samtools is known to work with the latest
255 Bio-Samtools Perl module.
257 (0.1.7: 10 November 2009, r510)
261 Beta Release 0.1.6 (2 September, 2009)
262 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
266 * In tview, do not show a blank screen when no reads mapped to the
267 corresponding region.
269 * Implemented native HTTP support in the BGZF library. Samtools is now
270 able to directly open a BAM file on HTTP. HTTP proxy is also
271 supported via the "http_proxy" environmental variable.
273 * Samtools is now compitable with the MinGW (win32) compiler and the
276 * The calmd (or fillmd) command now calculates the NM tag and replaces
277 MD tags if they are wrong.
279 * The view command now recognizes and optionally prints FLAG in HEXs or
280 strings to make a SAM file more friendly to human eyes. This is a
281 samtools-C extension, not implemented in Picard for the time
282 being. Please type `samtools view -?' for more information.
284 * BAM files now have an end-of-file (EOF) marker to facilitate
285 truncation detection. A warning will be given if an on-disk BAM file
286 does not have this marker. The warning will be seen on BAM files
287 generated by an older version of samtools. It does NO harm.
289 * New key bindings in tview: `r' to show read names and `s' to show
290 reference skip (N operation) as deletions.
292 * Fixed a bug in `samtools merge -n'.
294 * Samtools merge now optionally copies the header of a user specified
295 SAM file to the resultant BAM output.
297 * Samtools pileup/tview works with a CIGAR with the first or the last
298 operation is an indel.
300 * Fixed a bug in bam_aux_get().
303 Changes in other utilies:
305 * Fixed wrong FLAG in maq2sam.
308 (0.1.6: 2 September 2009, r453)
312 Beta Release 0.1.5 (7 July, 2009)
313 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
317 * Support opening a BAM alignment on FTP. Users can now use "tview" to
318 view alignments at the NCBI ftp site. Please read manual for more
321 * In library, propagate errors rather than exit or complain assertion
324 * Simplified the building system and fixed compiling errors caused by
327 * Fixed an issue about lost header information when a SAM is imported
330 * Implemented "samtool.pl varFilter" which filters both SNPs and short
331 indels. This command replaces "indelFilter".
333 * Implemented "samtools.pl pileup2fq" to generate FASTQ consensus from
336 * In pileup, cap mapping quality at 60. This helps filtering when
337 different aligners are in use.
339 * In pileup, allow to output variant sites only.
341 * Made pileup generate correct calls in repetitive region. At the same
342 time, I am considering to implement a simplified model in SOAPsnp,
343 although this has not happened yet.
345 * In view, added '-u' option to output BAM without compression. This
346 option is preferred when the output is piped to other commands.
348 * In view, added '-l' and '-r' to get the alignments for one library or
349 read group. The "@RG" header lines are now partially parsed.
351 * Do not include command line utilities to libbam.a.
353 * Fixed memory leaks in pileup and bam_view1().
355 * Made faidx more tolerant to empty lines right before or after FASTA >
359 Changes in other utilities:
361 * Updated novo2sam.pl by Colin Hercus, the key developer of novoalign.
364 This release involves several modifications to the key code base which
365 may potentially introduce new bugs even though we have tried to minimize
366 this by testing on several examples. Please let us know if you catch
369 (0.1.5: 7 July 2009, r373)
373 Beta Release 0.1.4 (21 May, 2009)
374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
378 * Added the 'rmdupse' command: removing duplicates for SE reads.
380 * Fixed a critical bug in the indel caller: clipped alignments are not
383 * Fixed a bug in the tview: gapped alignment may be incorrectly
386 * Unified the interface to BAM and SAM I/O. This is done by
387 implementing a wrapper on top of the old APIs and therefore old APIs
388 are still valid. The new I/O APIs also recognize the @SQ header
391 * Generate the MD tag.
393 * Generate "=" bases. However, the indel caller will not work when "="
396 * Enhanced support of color-read display (by Nils Homer).
398 * Implemented the GNU building system. However, currently the building
399 system does not generate libbam.a. We will improve this later. For
400 the time being, `make -f Makefile.generic' is preferred.
402 * Fixed a minor bug in pileup: the first read in a chromosome may be
405 * Fixed bugs in bam_aux.c. These bugs do not affect other components as
406 they were not used previously.
408 * Output the 'SM' tag from maq2sam.
410 (0.1.4: 21 May 2009, r297)
414 Beta Release 0.1.3 (15 April, 2009)
415 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
417 Notable changes in SAMtools:
419 * SAMtools is more consistent with the specification: a) '*' in the
420 QUAL field is allowed; b) the field separator is TAB only and SPACE
421 is treated as a character in a field; c) empty header is allowed.
423 * Implemented GLFv3 support in pileup.
425 * Fixed a severe bug in fixmate: strand information is wrongly
428 * Fixed a bug in alignment retrieval: alignments bridging n*16384bp are
429 not correctly retrieved sometimes.
431 * Fixed a bug in rmdup: segfault if unmapped reads are present.
433 * Move indel_filter.pl to samtools.pl and improved the filtering by
434 checking the actual number of alignments containing indels. The indel
435 pileup line is also changed a little to make this filtration easier.
437 * Fixed a minor bug in indexing: the bin number of an unmapped read is
440 * Added `flagstat' command to show statistics on the FLAG field.
442 * Improved indel caller by setting the maximum window size in local
445 Changes in other utilities:
447 * Fixed a bug in maq2sam: a tag name is obsolete.
449 * Improvement to wgsim: a) added support for SOLiD read simulation; b)
450 show the number of substitutions/indels/errors in read name; c)
451 considerable code clean up.
453 * Various converters: improved functionality in general.
455 * Updated the example SAM due to the previous bug in fixmate.
457 (0.1.3: 15 April 2009, r227)
461 Beta Release 0.1.2 (28 January, 2008)
462 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
464 Notable changes in SAMtools:
466 * Implemented a Bayesian indel caller. The new caller generate scores
467 and genotype and is potentially more accurate than Maq's indel
468 caller. The pileup format is also changed accordingly.
470 * Implemented rmdup command: remove potential PCR duplicates. Note that
471 this command ONLY works for FR orientation and requires ISIZE is
474 * Added fixmate command: fill in mate coordinates, ISIZE and mate
475 related flags from a name-sorted alignment.
477 * Fixed a bug in indexing: reads bridging 16x kbp were not retrieved.
479 * Allow to select reads shown in the pileup output with a mask.
481 * Generate GLFv2 from pileup.
483 * Added two more flags for flagging PCR/optical duplicates and for QC
486 * Fixed a bug in sort command: name sorting for large alignment did not
489 * Allow to completely disable RAZF (using Makefile.lite) as some people
490 have problem to compile it.
492 * Fixed a bug in import command when there are reads without
495 * Fixed a bug in tview: clipping broke the alignment viewer.
497 * Fixed a compiling error when _NO_CURSES is applied.
499 * Fixed a bug in merge command.
501 Changes in other utilities:
503 * Added wgsim, a paired-end reads simulator. Wgsim was adapted from
504 maq's reads simulator. Colin Hercus further improved it to allow
507 * Added wgsim_eval.pl, a script that evaluates the accuracy of
508 alignment on reads generated by wgsim.
510 * Added soap2sam.pl, a SOAP2->SAM converter. This converter does not
511 work properly when multiple hits are output.
513 * Added bowtie2sam.pl, a Bowtie->SAM converter. Only the top hit will
514 be retained when multiple hits are present.
516 * Fixed a bug in export2sam.pl for QC reads.
518 * Support RG tag at MAQ->SAM converter.
520 * Added novo2sam.pl, a NovoAlign->SAM converter. Multiple hits and
521 indel are not properly handled, though.
523 * Added zoom2sam.pl, a ZOOM->SAM converter. It only works with the
524 default Illumina output.
526 (0.1.2: 28 January 2008; r116)
530 Beta Release 0.1.1 (22 December, 2008)
531 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
533 The is the first public release of samtools. For more information,
534 please check the manual page `samtools.1' and the samtools website
535 http://samtools.sourceforge.net