1 Beta Release 0.1.5 (7 July, 2009)
2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
6 * Support opening a BAM alignment on FTP. Users can now use "tview" to
7 view alignments at the NCBI ftp site. Please read manual for more
10 * In library, propagate errors rather than exit or complain assertion
13 * Simplified the building system and fixed compiling errors caused by
16 * Fixed an issue about lost header information when a SAM is imported
19 * Implemented "samtool.pl varFilter" which filters both SNPs and short
20 indels. This command replaces "indelFilter".
22 * Implemented "samtools.pl pileup2fq" to generate FASTQ consensus from
25 * In pileup, cap mapping quality at 60. This helps filtering when
26 different aligners are in use.
28 * In pileup, allow to output variant sites only.
30 * Made pileup generate correct calls in repetitive region. At the same
31 time, I am considering to implement a simplified model in SOAPsnp,
32 although this has not happened yet.
34 * In view, added '-u' option to output BAM without compression. This
35 option is preferred when the output is piped to other commands.
37 * In view, added '-l' and '-r' to get the alignments for one library or
38 read group. The "@RG" header lines are now partially parsed.
40 * Do not include command line utilities to libbam.a.
42 * Fixed memory leaks in pileup and bam_view1().
44 * Made faidx more tolerant to empty lines right before or after FASTA >
48 Changes in other utilities:
50 * Updated novo2sam.pl by Colin Hercus, the key developer of novoalign.
53 This release involves several modifications to the key code base which
54 may potentially introduce new bugs even though we have tried to minimize
55 this by testing on several examples. Please let us know if you catch
58 (0.1.5: 7 July 2009, r373)
62 Beta Release 0.1.4 (21 May, 2009)
63 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
67 * Added the 'rmdupse' command: removing duplicates for SE reads.
69 * Fixed a critical bug in the indel caller: clipped alignments are not
72 * Fixed a bug in the tview: gapped alignment may be incorrectly
75 * Unified the interface to BAM and SAM I/O. This is done by
76 implementing a wrapper on top of the old APIs and therefore old APIs
77 are still valid. The new I/O APIs also recognize the @SQ header
80 * Generate the MD tag.
82 * Generate "=" bases. However, the indel caller will not work when "="
85 * Enhanced support of color-read display (by Nils Homer).
87 * Implemented the GNU building system. However, currently the building
88 system does not generate libbam.a. We will improve this later. For
89 the time being, `make -f Makefile.generic' is preferred.
91 * Fixed a minor bug in pileup: the first read in a chromosome may be
94 * Fixed bugs in bam_aux.c. These bugs do not affect other components as
95 they were not used previously.
97 * Output the 'SM' tag from maq2sam.
99 (0.1.4: 21 May 2009, r297)
103 Beta Release 0.1.3 (15 April, 2009)
104 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
106 Notable changes in SAMtools:
108 * SAMtools is more consistent with the specification: a) '*' in the
109 QUAL field is allowed; b) the field separator is TAB only and SPACE
110 is treated as a character in a field; c) empty header is allowed.
112 * Implemented GLFv3 support in pileup.
114 * Fixed a severe bug in fixmate: strand information is wrongly
117 * Fixed a bug in alignment retrieval: alignments bridging n*16384bp are
118 not correctly retrieved sometimes.
120 * Fixed a bug in rmdup: segfault if unmapped reads are present.
122 * Move indel_filter.pl to samtools.pl and improved the filtering by
123 checking the actual number of alignments containing indels. The indel
124 pileup line is also changed a little to make this filtration easier.
126 * Fixed a minor bug in indexing: the bin number of an unmapped read is
129 * Added `flagstat' command to show statistics on the FLAG field.
131 * Improved indel caller by setting the maximum window size in local
134 Changes in other utilities:
136 * Fixed a bug in maq2sam: a tag name is obsolete.
138 * Improvement to wgsim: a) added support for SOLiD read simulation; b)
139 show the number of substitutions/indels/errors in read name; c)
140 considerable code clean up.
142 * Various converters: improved functionality in general.
144 * Updated the example SAM due to the previous bug in fixmate.
146 (0.1.3: 15 April 2009, r227)
150 Beta Release 0.1.2 (28 January, 2008)
151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
153 Notable changes in SAMtools:
155 * Implemented a Bayesian indel caller. The new caller generate scores
156 and genotype and is potentially more accurate than Maq's indel
157 caller. The pileup format is also changed accordingly.
159 * Implemented rmdup command: remove potential PCR duplicates. Note that
160 this command ONLY works for FR orientation and requires ISIZE is
163 * Added fixmate command: fill in mate coordinates, ISIZE and mate
164 related flags from a name-sorted alignment.
166 * Fixed a bug in indexing: reads bridging 16x kbp were not retrieved.
168 * Allow to select reads shown in the pileup output with a mask.
170 * Generate GLFv2 from pileup.
172 * Added two more flags for flagging PCR/optical duplicates and for QC
175 * Fixed a bug in sort command: name sorting for large alignment did not
178 * Allow to completely disable RAZF (using Makefile.lite) as some people
179 have problem to compile it.
181 * Fixed a bug in import command when there are reads without
184 * Fixed a bug in tview: clipping broke the alignment viewer.
186 * Fixed a compiling error when _NO_CURSES is applied.
188 * Fixed a bug in merge command.
190 Changes in other utilities:
192 * Added wgsim, a paired-end reads simulator. Wgsim was adapted from
193 maq's reads simulator. Colin Hercus further improved it to allow
196 * Added wgsim_eval.pl, a script that evaluates the accuracy of
197 alignment on reads generated by wgsim.
199 * Added soap2sam.pl, a SOAP2->SAM converter. This converter does not
200 work properly when multiple hits are output.
202 * Added bowtie2sam.pl, a Bowtie->SAM converter. Only the top hit will
203 be retained when multiple hits are present.
205 * Fixed a bug in export2sam.pl for QC reads.
207 * Support RG tag at MAQ->SAM converter.
209 * Added novo2sam.pl, a NovoAlign->SAM converter. Multiple hits and
210 indel are not properly handled, though.
212 * Added zoom2sam.pl, a ZOOM->SAM converter. It only works with the
213 default Illumina output.
215 (0.1.2: 28 January 2008; r116)
219 Beta Release 0.1.1 (22 December, 2008)
220 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
222 The is the first public release of samtools. For more information,
223 please check the manual page `samtools.1' and the samtools website
224 http://samtools.sourceforge.net