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comparison SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/NEWS @ 0:74f5ea818cea

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author ryanmorin
date Wed, 12 Oct 2011 19:50:38 -0400
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1 Beta Release 0.1.6 (2 September, 2009)
2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3
4 Notable changes:
5
6 * In tview, do not show a blank screen when no reads mapped to the
7 corresponding region.
8
9 * Implemented native HTTP support in the BGZF library. Samtools is now
10 able to directly open a BAM file on HTTP. HTTP proxy is also
11 supported via the "http_proxy" environmental variable.
12
13 * Samtools is now compitable with the MinGW (win32) compiler and the
14 PDCurses library.
15
16 * The calmd (or fillmd) command now calculates the NM tag and replaces
17 MD tags if they are wrong.
18
19 * The view command now recognizes and optionally prints FLAG in HEXs or
20 strings to make a SAM file more friendly to human eyes. This is a
21 samtools-C extension, not implemented in Picard for the time
22 being. Please type `samtools view -?' for more information.
23
24 * BAM files now have an end-of-file (EOF) marker to facilitate
25 truncation detection. A warning will be given if an on-disk BAM file
26 does not have this marker. The warning will be seen on BAM files
27 generated by an older version of samtools. It does NO harm.
28
29 * New key bindings in tview: `r' to show read names and `s' to show
30 reference skip (N operation) as deletions.
31
32 * Fixed a bug in `samtools merge -n'.
33
34 * Samtools merge now optionally copies the header of a user specified
35 SAM file to the resultant BAM output.
36
37 * Samtools pileup/tview works with a CIGAR with the first or the last
38 operation is an indel.
39
40 * Fixed a bug in bam_aux_get().
41
42
43 Changes in other utilies:
44
45 * Fixed wrong FLAG in maq2sam.
46
47
48 (0.1.6: 2 September 2009, r453)
49
50
51
52 Beta Release 0.1.5 (7 July, 2009)
53 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
54
55 Notable changes:
56
57 * Support opening a BAM alignment on FTP. Users can now use "tview" to
58 view alignments at the NCBI ftp site. Please read manual for more
59 information.
60
61 * In library, propagate errors rather than exit or complain assertion
62 failure.
63
64 * Simplified the building system and fixed compiling errors caused by
65 zlib<1.2.2.1.
66
67 * Fixed an issue about lost header information when a SAM is imported
68 with "view -t".
69
70 * Implemented "samtool.pl varFilter" which filters both SNPs and short
71 indels. This command replaces "indelFilter".
72
73 * Implemented "samtools.pl pileup2fq" to generate FASTQ consensus from
74 pileup output.
75
76 * In pileup, cap mapping quality at 60. This helps filtering when
77 different aligners are in use.
78
79 * In pileup, allow to output variant sites only.
80
81 * Made pileup generate correct calls in repetitive region. At the same
82 time, I am considering to implement a simplified model in SOAPsnp,
83 although this has not happened yet.
84
85 * In view, added '-u' option to output BAM without compression. This
86 option is preferred when the output is piped to other commands.
87
88 * In view, added '-l' and '-r' to get the alignments for one library or
89 read group. The "@RG" header lines are now partially parsed.
90
91 * Do not include command line utilities to libbam.a.
92
93 * Fixed memory leaks in pileup and bam_view1().
94
95 * Made faidx more tolerant to empty lines right before or after FASTA >
96 lines.
97
98
99 Changes in other utilities:
100
101 * Updated novo2sam.pl by Colin Hercus, the key developer of novoalign.
102
103
104 This release involves several modifications to the key code base which
105 may potentially introduce new bugs even though we have tried to minimize
106 this by testing on several examples. Please let us know if you catch
107 bugs.
108
109 (0.1.5: 7 July 2009, r373)
110
111
112
113 Beta Release 0.1.4 (21 May, 2009)
114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
115
116 Notable changes:
117
118 * Added the 'rmdupse' command: removing duplicates for SE reads.
119
120 * Fixed a critical bug in the indel caller: clipped alignments are not
121 processed correctly.
122
123 * Fixed a bug in the tview: gapped alignment may be incorrectly
124 displayed.
125
126 * Unified the interface to BAM and SAM I/O. This is done by
127 implementing a wrapper on top of the old APIs and therefore old APIs
128 are still valid. The new I/O APIs also recognize the @SQ header
129 lines.
130
131 * Generate the MD tag.
132
133 * Generate "=" bases. However, the indel caller will not work when "="
134 bases are present.
135
136 * Enhanced support of color-read display (by Nils Homer).
137
138 * Implemented the GNU building system. However, currently the building
139 system does not generate libbam.a. We will improve this later. For
140 the time being, `make -f Makefile.generic' is preferred.
141
142 * Fixed a minor bug in pileup: the first read in a chromosome may be
143 skipped.
144
145 * Fixed bugs in bam_aux.c. These bugs do not affect other components as
146 they were not used previously.
147
148 * Output the 'SM' tag from maq2sam.
149
150 (0.1.4: 21 May 2009, r297)
151
152
153
154 Beta Release 0.1.3 (15 April, 2009)
155 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
156
157 Notable changes in SAMtools:
158
159 * SAMtools is more consistent with the specification: a) '*' in the
160 QUAL field is allowed; b) the field separator is TAB only and SPACE
161 is treated as a character in a field; c) empty header is allowed.
162
163 * Implemented GLFv3 support in pileup.
164
165 * Fixed a severe bug in fixmate: strand information is wrongly
166 overwritten.
167
168 * Fixed a bug in alignment retrieval: alignments bridging n*16384bp are
169 not correctly retrieved sometimes.
170
171 * Fixed a bug in rmdup: segfault if unmapped reads are present.
172
173 * Move indel_filter.pl to samtools.pl and improved the filtering by
174 checking the actual number of alignments containing indels. The indel
175 pileup line is also changed a little to make this filtration easier.
176
177 * Fixed a minor bug in indexing: the bin number of an unmapped read is
178 wrongly calculated.
179
180 * Added `flagstat' command to show statistics on the FLAG field.
181
182 * Improved indel caller by setting the maximum window size in local
183 realignment.
184
185 Changes in other utilities:
186
187 * Fixed a bug in maq2sam: a tag name is obsolete.
188
189 * Improvement to wgsim: a) added support for SOLiD read simulation; b)
190 show the number of substitutions/indels/errors in read name; c)
191 considerable code clean up.
192
193 * Various converters: improved functionality in general.
194
195 * Updated the example SAM due to the previous bug in fixmate.
196
197 (0.1.3: 15 April 2009, r227)
198
199
200
201 Beta Release 0.1.2 (28 January, 2008)
202 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
203
204 Notable changes in SAMtools:
205
206 * Implemented a Bayesian indel caller. The new caller generate scores
207 and genotype and is potentially more accurate than Maq's indel
208 caller. The pileup format is also changed accordingly.
209
210 * Implemented rmdup command: remove potential PCR duplicates. Note that
211 this command ONLY works for FR orientation and requires ISIZE is
212 correctly set.
213
214 * Added fixmate command: fill in mate coordinates, ISIZE and mate
215 related flags from a name-sorted alignment.
216
217 * Fixed a bug in indexing: reads bridging 16x kbp were not retrieved.
218
219 * Allow to select reads shown in the pileup output with a mask.
220
221 * Generate GLFv2 from pileup.
222
223 * Added two more flags for flagging PCR/optical duplicates and for QC
224 failure.
225
226 * Fixed a bug in sort command: name sorting for large alignment did not
227 work.
228
229 * Allow to completely disable RAZF (using Makefile.lite) as some people
230 have problem to compile it.
231
232 * Fixed a bug in import command when there are reads without
233 coordinates.
234
235 * Fixed a bug in tview: clipping broke the alignment viewer.
236
237 * Fixed a compiling error when _NO_CURSES is applied.
238
239 * Fixed a bug in merge command.
240
241 Changes in other utilities:
242
243 * Added wgsim, a paired-end reads simulator. Wgsim was adapted from
244 maq's reads simulator. Colin Hercus further improved it to allow
245 longer indels.
246
247 * Added wgsim_eval.pl, a script that evaluates the accuracy of
248 alignment on reads generated by wgsim.
249
250 * Added soap2sam.pl, a SOAP2->SAM converter. This converter does not
251 work properly when multiple hits are output.
252
253 * Added bowtie2sam.pl, a Bowtie->SAM converter. Only the top hit will
254 be retained when multiple hits are present.
255
256 * Fixed a bug in export2sam.pl for QC reads.
257
258 * Support RG tag at MAQ->SAM converter.
259
260 * Added novo2sam.pl, a NovoAlign->SAM converter. Multiple hits and
261 indel are not properly handled, though.
262
263 * Added zoom2sam.pl, a ZOOM->SAM converter. It only works with the
264 default Illumina output.
265
266 (0.1.2: 28 January 2008; r116)
267
268
269
270 Beta Release 0.1.1 (22 December, 2008)
271 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
272
273 The is the first public release of samtools. For more information,
274 please check the manual page `samtools.1' and the samtools website
275 http://samtools.sourceforge.net