1 Beta Release 0.1.7 (10 November, 2009)
2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
6 * Improved the indel caller in complex scenariors, in particular for
7 long reads. The indel caller is now able to make reasonable indel
8 calls from Craig Venter capillary reads.
10 * Rewrote single-end duplicate removal with improved
11 performance. Paired-end reads are not touched.
13 * Duplicate removal is now library aware. Samtools remove potential
14 PCR/optical dupliates inside a library rather than across libraries.
16 * SAM header is now fully parsed, although this functionality is not
17 used in merging and so on.
19 * In samtools merge, optionally take the input file name as RG-ID and
20 attach the RG tag to each alignment.
22 * Added FTP support in the RAZF library. RAZF-compressed reference
23 sequence can be retrieved remotely.
25 * Improved network support for Win32.
27 * Samtools sort and merge are now stable.
29 Changes in other utilities:
31 * Implemented sam2vcf.pl that converts the pileup format to the VCF
34 * This release of samtools is known to work with the latest
35 Bio-Samtools Perl module.
37 (0.1.7: 10 November 2009, r510)
41 Beta Release 0.1.6 (2 September, 2009)
42 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
46 * In tview, do not show a blank screen when no reads mapped to the
49 * Implemented native HTTP support in the BGZF library. Samtools is now
50 able to directly open a BAM file on HTTP. HTTP proxy is also
51 supported via the "http_proxy" environmental variable.
53 * Samtools is now compitable with the MinGW (win32) compiler and the
56 * The calmd (or fillmd) command now calculates the NM tag and replaces
57 MD tags if they are wrong.
59 * The view command now recognizes and optionally prints FLAG in HEXs or
60 strings to make a SAM file more friendly to human eyes. This is a
61 samtools-C extension, not implemented in Picard for the time
62 being. Please type `samtools view -?' for more information.
64 * BAM files now have an end-of-file (EOF) marker to facilitate
65 truncation detection. A warning will be given if an on-disk BAM file
66 does not have this marker. The warning will be seen on BAM files
67 generated by an older version of samtools. It does NO harm.
69 * New key bindings in tview: `r' to show read names and `s' to show
70 reference skip (N operation) as deletions.
72 * Fixed a bug in `samtools merge -n'.
74 * Samtools merge now optionally copies the header of a user specified
75 SAM file to the resultant BAM output.
77 * Samtools pileup/tview works with a CIGAR with the first or the last
78 operation is an indel.
80 * Fixed a bug in bam_aux_get().
83 Changes in other utilies:
85 * Fixed wrong FLAG in maq2sam.
88 (0.1.6: 2 September 2009, r453)
92 Beta Release 0.1.5 (7 July, 2009)
93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
97 * Support opening a BAM alignment on FTP. Users can now use "tview" to
98 view alignments at the NCBI ftp site. Please read manual for more
101 * In library, propagate errors rather than exit or complain assertion
104 * Simplified the building system and fixed compiling errors caused by
107 * Fixed an issue about lost header information when a SAM is imported
110 * Implemented "samtool.pl varFilter" which filters both SNPs and short
111 indels. This command replaces "indelFilter".
113 * Implemented "samtools.pl pileup2fq" to generate FASTQ consensus from
116 * In pileup, cap mapping quality at 60. This helps filtering when
117 different aligners are in use.
119 * In pileup, allow to output variant sites only.
121 * Made pileup generate correct calls in repetitive region. At the same
122 time, I am considering to implement a simplified model in SOAPsnp,
123 although this has not happened yet.
125 * In view, added '-u' option to output BAM without compression. This
126 option is preferred when the output is piped to other commands.
128 * In view, added '-l' and '-r' to get the alignments for one library or
129 read group. The "@RG" header lines are now partially parsed.
131 * Do not include command line utilities to libbam.a.
133 * Fixed memory leaks in pileup and bam_view1().
135 * Made faidx more tolerant to empty lines right before or after FASTA >
139 Changes in other utilities:
141 * Updated novo2sam.pl by Colin Hercus, the key developer of novoalign.
144 This release involves several modifications to the key code base which
145 may potentially introduce new bugs even though we have tried to minimize
146 this by testing on several examples. Please let us know if you catch
149 (0.1.5: 7 July 2009, r373)
153 Beta Release 0.1.4 (21 May, 2009)
154 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
158 * Added the 'rmdupse' command: removing duplicates for SE reads.
160 * Fixed a critical bug in the indel caller: clipped alignments are not
163 * Fixed a bug in the tview: gapped alignment may be incorrectly
166 * Unified the interface to BAM and SAM I/O. This is done by
167 implementing a wrapper on top of the old APIs and therefore old APIs
168 are still valid. The new I/O APIs also recognize the @SQ header
171 * Generate the MD tag.
173 * Generate "=" bases. However, the indel caller will not work when "="
176 * Enhanced support of color-read display (by Nils Homer).
178 * Implemented the GNU building system. However, currently the building
179 system does not generate libbam.a. We will improve this later. For
180 the time being, `make -f Makefile.generic' is preferred.
182 * Fixed a minor bug in pileup: the first read in a chromosome may be
185 * Fixed bugs in bam_aux.c. These bugs do not affect other components as
186 they were not used previously.
188 * Output the 'SM' tag from maq2sam.
190 (0.1.4: 21 May 2009, r297)
194 Beta Release 0.1.3 (15 April, 2009)
195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
197 Notable changes in SAMtools:
199 * SAMtools is more consistent with the specification: a) '*' in the
200 QUAL field is allowed; b) the field separator is TAB only and SPACE
201 is treated as a character in a field; c) empty header is allowed.
203 * Implemented GLFv3 support in pileup.
205 * Fixed a severe bug in fixmate: strand information is wrongly
208 * Fixed a bug in alignment retrieval: alignments bridging n*16384bp are
209 not correctly retrieved sometimes.
211 * Fixed a bug in rmdup: segfault if unmapped reads are present.
213 * Move indel_filter.pl to samtools.pl and improved the filtering by
214 checking the actual number of alignments containing indels. The indel
215 pileup line is also changed a little to make this filtration easier.
217 * Fixed a minor bug in indexing: the bin number of an unmapped read is
220 * Added `flagstat' command to show statistics on the FLAG field.
222 * Improved indel caller by setting the maximum window size in local
225 Changes in other utilities:
227 * Fixed a bug in maq2sam: a tag name is obsolete.
229 * Improvement to wgsim: a) added support for SOLiD read simulation; b)
230 show the number of substitutions/indels/errors in read name; c)
231 considerable code clean up.
233 * Various converters: improved functionality in general.
235 * Updated the example SAM due to the previous bug in fixmate.
237 (0.1.3: 15 April 2009, r227)
241 Beta Release 0.1.2 (28 January, 2008)
242 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
244 Notable changes in SAMtools:
246 * Implemented a Bayesian indel caller. The new caller generate scores
247 and genotype and is potentially more accurate than Maq's indel
248 caller. The pileup format is also changed accordingly.
250 * Implemented rmdup command: remove potential PCR duplicates. Note that
251 this command ONLY works for FR orientation and requires ISIZE is
254 * Added fixmate command: fill in mate coordinates, ISIZE and mate
255 related flags from a name-sorted alignment.
257 * Fixed a bug in indexing: reads bridging 16x kbp were not retrieved.
259 * Allow to select reads shown in the pileup output with a mask.
261 * Generate GLFv2 from pileup.
263 * Added two more flags for flagging PCR/optical duplicates and for QC
266 * Fixed a bug in sort command: name sorting for large alignment did not
269 * Allow to completely disable RAZF (using Makefile.lite) as some people
270 have problem to compile it.
272 * Fixed a bug in import command when there are reads without
275 * Fixed a bug in tview: clipping broke the alignment viewer.
277 * Fixed a compiling error when _NO_CURSES is applied.
279 * Fixed a bug in merge command.
281 Changes in other utilities:
283 * Added wgsim, a paired-end reads simulator. Wgsim was adapted from
284 maq's reads simulator. Colin Hercus further improved it to allow
287 * Added wgsim_eval.pl, a script that evaluates the accuracy of
288 alignment on reads generated by wgsim.
290 * Added soap2sam.pl, a SOAP2->SAM converter. This converter does not
291 work properly when multiple hits are output.
293 * Added bowtie2sam.pl, a Bowtie->SAM converter. Only the top hit will
294 be retained when multiple hits are present.
296 * Fixed a bug in export2sam.pl for QC reads.
298 * Support RG tag at MAQ->SAM converter.
300 * Added novo2sam.pl, a NovoAlign->SAM converter. Multiple hits and
301 indel are not properly handled, though.
303 * Added zoom2sam.pl, a ZOOM->SAM converter. It only works with the
304 default Illumina output.
306 (0.1.2: 28 January 2008; r116)
310 Beta Release 0.1.1 (22 December, 2008)
311 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
313 The is the first public release of samtools. For more information,
314 please check the manual page `samtools.1' and the samtools website
315 http://samtools.sourceforge.net