4 Notable functional changes:
6 * Added the `reheader' command which replaces a BAM header with a new
7 header. This command is much faster than replacing header by
8 BAM->SAM->BAM conversions.
10 * Added the `mpileup' command which computes the pileup of multiple
13 * The `index' command now stores the number of mapped and unmapped
14 reads in the index file. This information can be retrieved quickly by
15 the new `idxstats' command.
17 * By default, pileup used the SOAPsnp model for SNP calling. This
18 avoids the floating overflow in the MAQ model which leads to spurious
19 calls in repetitive regions, although these calls will be immediately
20 filtered by varFilter.
22 * The `tview' command now correctly handles CIGARs like 7I10M and
23 10M1P1I10M which cause assertion failure in earlier versions.
25 * Added the `-d' option to `pileup' which avoids slow indel calling
26 in ultradeep regions by subsampling reads locally.
28 * Added the `-R' option to `view' which retrieves alignments in read
29 groups listed in the specified file.
31 Performance improvements:
33 * The BAM->SAM conversion is up to twice faster, depending on the
34 characteristic of the input.
36 * Parsing SAM headers with a lot of reference sequences is now much
39 * The number of lseek() calls per query is reduced when the query
40 region contains no read alignments.
44 * Fixed an issue in the indel caller that leads to miscall of indels.
45 Note that this solution may not work well when the sequencing indel
46 error rate is higher than the rate of SNPs.
48 * Fixed another issue in the indel caller which may lead to incorrect
51 * Fixed a bug in `view -r'.
53 APIs and other changes:
55 * Added iterator interfaces to random access and pileup. The callback
56 interfaces directly call the iterator interfaces.
58 * The BGZF blocks holding the BAM header are indepedent of alignment
59 BGZF blocks. Alignment records shorter than 64kB is guaranteed to be
60 fully contained in one BGZF block. This change is fully compatible
61 with the old version of samtools/picard.
63 Changes in other utilities:
65 * Updated export2sam.pl by Chris Saunders.
67 * Improved the sam2vcf.pl script.
69 * Added a Python version of varfilter.py by Aylwyn Scally.
75 Beta Release 0.1.7 (10 November, 2009)
76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
80 * Improved the indel caller in complex scenariors, in particular for
81 long reads. The indel caller is now able to make reasonable indel
82 calls from Craig Venter capillary reads.
84 * Rewrote single-end duplicate removal with improved
85 performance. Paired-end reads are not touched.
87 * Duplicate removal is now library aware. Samtools remove potential
88 PCR/optical dupliates inside a library rather than across libraries.
90 * SAM header is now fully parsed, although this functionality is not
91 used in merging and so on.
93 * In samtools merge, optionally take the input file name as RG-ID and
94 attach the RG tag to each alignment.
96 * Added FTP support in the RAZF library. RAZF-compressed reference
97 sequence can be retrieved remotely.
99 * Improved network support for Win32.
101 * Samtools sort and merge are now stable.
103 Changes in other utilities:
105 * Implemented sam2vcf.pl that converts the pileup format to the VCF
108 * This release of samtools is known to work with the latest
109 Bio-Samtools Perl module.
111 (0.1.7: 10 November 2009, r510)
115 Beta Release 0.1.6 (2 September, 2009)
116 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
120 * In tview, do not show a blank screen when no reads mapped to the
121 corresponding region.
123 * Implemented native HTTP support in the BGZF library. Samtools is now
124 able to directly open a BAM file on HTTP. HTTP proxy is also
125 supported via the "http_proxy" environmental variable.
127 * Samtools is now compitable with the MinGW (win32) compiler and the
130 * The calmd (or fillmd) command now calculates the NM tag and replaces
131 MD tags if they are wrong.
133 * The view command now recognizes and optionally prints FLAG in HEXs or
134 strings to make a SAM file more friendly to human eyes. This is a
135 samtools-C extension, not implemented in Picard for the time
136 being. Please type `samtools view -?' for more information.
138 * BAM files now have an end-of-file (EOF) marker to facilitate
139 truncation detection. A warning will be given if an on-disk BAM file
140 does not have this marker. The warning will be seen on BAM files
141 generated by an older version of samtools. It does NO harm.
143 * New key bindings in tview: `r' to show read names and `s' to show
144 reference skip (N operation) as deletions.
146 * Fixed a bug in `samtools merge -n'.
148 * Samtools merge now optionally copies the header of a user specified
149 SAM file to the resultant BAM output.
151 * Samtools pileup/tview works with a CIGAR with the first or the last
152 operation is an indel.
154 * Fixed a bug in bam_aux_get().
157 Changes in other utilies:
159 * Fixed wrong FLAG in maq2sam.
162 (0.1.6: 2 September 2009, r453)
166 Beta Release 0.1.5 (7 July, 2009)
167 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
171 * Support opening a BAM alignment on FTP. Users can now use "tview" to
172 view alignments at the NCBI ftp site. Please read manual for more
175 * In library, propagate errors rather than exit or complain assertion
178 * Simplified the building system and fixed compiling errors caused by
181 * Fixed an issue about lost header information when a SAM is imported
184 * Implemented "samtool.pl varFilter" which filters both SNPs and short
185 indels. This command replaces "indelFilter".
187 * Implemented "samtools.pl pileup2fq" to generate FASTQ consensus from
190 * In pileup, cap mapping quality at 60. This helps filtering when
191 different aligners are in use.
193 * In pileup, allow to output variant sites only.
195 * Made pileup generate correct calls in repetitive region. At the same
196 time, I am considering to implement a simplified model in SOAPsnp,
197 although this has not happened yet.
199 * In view, added '-u' option to output BAM without compression. This
200 option is preferred when the output is piped to other commands.
202 * In view, added '-l' and '-r' to get the alignments for one library or
203 read group. The "@RG" header lines are now partially parsed.
205 * Do not include command line utilities to libbam.a.
207 * Fixed memory leaks in pileup and bam_view1().
209 * Made faidx more tolerant to empty lines right before or after FASTA >
213 Changes in other utilities:
215 * Updated novo2sam.pl by Colin Hercus, the key developer of novoalign.
218 This release involves several modifications to the key code base which
219 may potentially introduce new bugs even though we have tried to minimize
220 this by testing on several examples. Please let us know if you catch
223 (0.1.5: 7 July 2009, r373)
227 Beta Release 0.1.4 (21 May, 2009)
228 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
232 * Added the 'rmdupse' command: removing duplicates for SE reads.
234 * Fixed a critical bug in the indel caller: clipped alignments are not
237 * Fixed a bug in the tview: gapped alignment may be incorrectly
240 * Unified the interface to BAM and SAM I/O. This is done by
241 implementing a wrapper on top of the old APIs and therefore old APIs
242 are still valid. The new I/O APIs also recognize the @SQ header
245 * Generate the MD tag.
247 * Generate "=" bases. However, the indel caller will not work when "="
250 * Enhanced support of color-read display (by Nils Homer).
252 * Implemented the GNU building system. However, currently the building
253 system does not generate libbam.a. We will improve this later. For
254 the time being, `make -f Makefile.generic' is preferred.
256 * Fixed a minor bug in pileup: the first read in a chromosome may be
259 * Fixed bugs in bam_aux.c. These bugs do not affect other components as
260 they were not used previously.
262 * Output the 'SM' tag from maq2sam.
264 (0.1.4: 21 May 2009, r297)
268 Beta Release 0.1.3 (15 April, 2009)
269 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
271 Notable changes in SAMtools:
273 * SAMtools is more consistent with the specification: a) '*' in the
274 QUAL field is allowed; b) the field separator is TAB only and SPACE
275 is treated as a character in a field; c) empty header is allowed.
277 * Implemented GLFv3 support in pileup.
279 * Fixed a severe bug in fixmate: strand information is wrongly
282 * Fixed a bug in alignment retrieval: alignments bridging n*16384bp are
283 not correctly retrieved sometimes.
285 * Fixed a bug in rmdup: segfault if unmapped reads are present.
287 * Move indel_filter.pl to samtools.pl and improved the filtering by
288 checking the actual number of alignments containing indels. The indel
289 pileup line is also changed a little to make this filtration easier.
291 * Fixed a minor bug in indexing: the bin number of an unmapped read is
294 * Added `flagstat' command to show statistics on the FLAG field.
296 * Improved indel caller by setting the maximum window size in local
299 Changes in other utilities:
301 * Fixed a bug in maq2sam: a tag name is obsolete.
303 * Improvement to wgsim: a) added support for SOLiD read simulation; b)
304 show the number of substitutions/indels/errors in read name; c)
305 considerable code clean up.
307 * Various converters: improved functionality in general.
309 * Updated the example SAM due to the previous bug in fixmate.
311 (0.1.3: 15 April 2009, r227)
315 Beta Release 0.1.2 (28 January, 2008)
316 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
318 Notable changes in SAMtools:
320 * Implemented a Bayesian indel caller. The new caller generate scores
321 and genotype and is potentially more accurate than Maq's indel
322 caller. The pileup format is also changed accordingly.
324 * Implemented rmdup command: remove potential PCR duplicates. Note that
325 this command ONLY works for FR orientation and requires ISIZE is
328 * Added fixmate command: fill in mate coordinates, ISIZE and mate
329 related flags from a name-sorted alignment.
331 * Fixed a bug in indexing: reads bridging 16x kbp were not retrieved.
333 * Allow to select reads shown in the pileup output with a mask.
335 * Generate GLFv2 from pileup.
337 * Added two more flags for flagging PCR/optical duplicates and for QC
340 * Fixed a bug in sort command: name sorting for large alignment did not
343 * Allow to completely disable RAZF (using Makefile.lite) as some people
344 have problem to compile it.
346 * Fixed a bug in import command when there are reads without
349 * Fixed a bug in tview: clipping broke the alignment viewer.
351 * Fixed a compiling error when _NO_CURSES is applied.
353 * Fixed a bug in merge command.
355 Changes in other utilities:
357 * Added wgsim, a paired-end reads simulator. Wgsim was adapted from
358 maq's reads simulator. Colin Hercus further improved it to allow
361 * Added wgsim_eval.pl, a script that evaluates the accuracy of
362 alignment on reads generated by wgsim.
364 * Added soap2sam.pl, a SOAP2->SAM converter. This converter does not
365 work properly when multiple hits are output.
367 * Added bowtie2sam.pl, a Bowtie->SAM converter. Only the top hit will
368 be retained when multiple hits are present.
370 * Fixed a bug in export2sam.pl for QC reads.
372 * Support RG tag at MAQ->SAM converter.
374 * Added novo2sam.pl, a NovoAlign->SAM converter. Multiple hits and
375 indel are not properly handled, though.
377 * Added zoom2sam.pl, a ZOOM->SAM converter. It only works with the
378 default Illumina output.
380 (0.1.2: 28 January 2008; r116)
384 Beta Release 0.1.1 (22 December, 2008)
385 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
387 The is the first public release of samtools. For more information,
388 please check the manual page `samtools.1' and the samtools website
389 http://samtools.sourceforge.net