1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
|
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: Goby
Upstream-Contact: goby-framework@googlegroups.com
Source: https://github.com/CampagneLaboratory/goby3/releases
Files-Excluded: */*.jar
goby-distribution/data
models
testsupport/*/lib
test-data/bam/Example.bam
test-data/bam/Example-sorted.bam
test-data/bam/Example2.bam
test-data/seq-var-test/seq-var-reads-gsnap.html
Comment: We remove jar files that are bundled with the source.
Also we remove a html file with very long lines that is unused.
Finally, we remove very large test data files. Some tests must be
deactivated, but they were succeeding before.
Files: *
Copyright: 2009-2017 Institute for Computational Biomedicine
License: GPL-3+
Files: cpp/*
Copyright: 2009 Peter Adolphs
2008 Thomas Porschberg <thomas@randspringer.de>
License: FSFAP
Files: cpp/m4/ax_boost_date_time.m4
Copyright: 2008 Thomas Porschberg <thomas@randspringer.de>
2008 Michael Tindal
License: FSFAP
Files: cpp/m4/ax_boost_filesystem.m4
Copyright: 2009 Thomas Porschberg <thomas@randspringer.de>
2009 Roman Rybalko <libtorrent@romanr.info>
2009 Michael Tindal
License: FSFAP
Files: cpp/m4/ax_boost_program_options.m4
Copyright: 2009 Thomas Porschberg <thomas@randspringer.de>
License: FSFAP
Files: cpp/m4/ax_boost_system.m4
Copyright: 2008 Thomas Porschberg <thomas@randspringer.de>
2008 Michael Tindal
2008 Daniel Casimiro <dan.casimiro@gmail.com>
License: FSFAP
Files: cpp/src/*
Copyright: 2009-2012 Institute for Computational Biomedicine
License: LGPL-3+
Files: cpp/src/Makefile.am
Copyright: 2009-2017 Institute for Computational Biomedicine
License: GPL-3+
Files: cpp/src/goby/ICBFileInputStream.cc
cpp/src/goby/ICBFileInputStream.h
Copyright: 2008 Google Inc.
License: BSD-3-clause
Files: cpp/src/kseq.h
Copyright: 2008 Genome Research Ltd (GRL).
License: Expat
Files: goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticCoder.java
Copyright: 2002-2011 Sebastiano Vigna
2009-2012 Institute for Computational Biomedicine
License: LGPL-3+ and GPL-3+
Files: goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoder.java
Copyright: 2002-2011 Sebastiano Vigna
2012 Fabien Campagne
License: LGPL-3+
Files: goby-distribution/src/main/java/org/campagnelab/goby/GobyVersion.java
goby-distribution/src/main/java/org/campagnelab/goby/alignments/AbstractAlignmentReader.java
goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignedSequence.java
goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentPositionComparator.java
goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReaderImpl.java
goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentStats.java
goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentTooManyHitsReader.java
goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentTooManyHitsWriter.java
goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentWriterImpl.java
goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java
goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatSortedAlignmentReader.java
goby-distribution/src/main/java/org/campagnelab/goby/alignments/IterateAlignments.java
goby-distribution/src/main/java/org/campagnelab/goby/alignments/IterateSortedAlignments.java
goby-distribution/src/main/java/org/campagnelab/goby/alignments/LastParser.java
goby-distribution/src/main/java/org/campagnelab/goby/alignments/Merge.java
goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionFacadeAlignmentReader.java
goby-distribution/src/main/java/org/campagnelab/goby/alignments/ScanReferenceSequence.java
goby-distribution/src/main/java/org/campagnelab/goby/alignments/filters/*
goby-distribution/src/main/java/org/campagnelab/goby/baseinfo/*
goby-distribution/src/main/java/org/campagnelab/goby/compression/FastBufferedMessageChunksReader.java
goby-distribution/src/main/java/org/campagnelab/goby/compression/MessageChunksReader.java
goby-distribution/src/main/java/org/campagnelab/goby/compression/MessageChunksWriter.java
goby-distribution/src/main/java/org/campagnelab/goby/counts/*
goby-distribution/src/main/java/org/campagnelab/goby/exception/*
goby-distribution/src/main/java/org/campagnelab/goby/modes/AbstractCommandLineMode.java
goby-distribution/src/main/java/org/campagnelab/goby/modes/AbstractGobyMode.java
goby-distribution/src/main/java/org/campagnelab/goby/modes/ColorSpaceConverter.java
goby-distribution/src/main/java/org/campagnelab/goby/modes/GenericToolsDriver.java
goby-distribution/src/main/java/org/campagnelab/goby/modes/PercentMismatchesQualityFilter.java
goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java
goby-distribution/src/main/java/org/campagnelab/goby/modes/UpgradeMode.java
goby-distribution/src/main/java/org/campagnelab/goby/modes/core/*
goby-distribution/src/main/java/org/campagnelab/goby/modes/dsv/DiscoverVariantIterateSortedAlignments.java
goby-distribution/src/main/java/org/campagnelab/goby/modes/dsv/IterateSortedAlignmentsListImpl.java
goby-distribution/src/main/java/org/campagnelab/goby/readers/*
goby-distribution/src/main/java/org/campagnelab/goby/reads/CompressedRead.java
goby-distribution/src/main/java/org/campagnelab/goby/reads/MultiReads.java
goby-distribution/src/main/java/org/campagnelab/goby/reads/QualityEncoding.java
goby-distribution/src/main/java/org/campagnelab/goby/reads/RandomAccessSequenceCache.java
goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadSet.java
goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsLoader.java
goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsReader.java
goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsWriterImpl.java
goby-distribution/src/main/java/org/campagnelab/goby/reads/SequenceDigests.java
goby-distribution/src/main/java/org/campagnelab/goby/reads/SequenceEncoder.java
goby-distribution/src/test/java/org/campagnelab/goby/alignments/TestPositionSlices.java
Copyright: 2009-2012 Institute for Computational Biomedicine
License: LGPL-3+
Files: goby-distribution/src/main/java/org/campagnelab/goby/counts/CachingCountsArchiveReader.java
goby-distribution/src/main/java/org/campagnelab/goby/counts/CountAdaptiveBinningAdaptor.java
goby-distribution/src/main/java/org/campagnelab/goby/counts/CountBinningAdapterI.java
goby-distribution/src/main/java/org/campagnelab/goby/counts/CountBinningAdaptor.java
goby-distribution/src/main/java/org/campagnelab/goby/counts/CountIndexBuilder.java
goby-distribution/src/main/java/org/campagnelab/goby/counts/CountWriterHelper2.java
goby-distribution/src/main/java/org/campagnelab/goby/counts/CountsAggregatorI.java
goby-distribution/src/main/java/org/campagnelab/goby/counts/CountsWriterI.java
goby-distribution/src/main/java/org/campagnelab/goby/counts/PositionAdapter.java
goby-distribution/src/main/java/org/campagnelab/goby/counts/UnionAlgorithmSkeleton.java
goby-distribution/src/main/java/org/campagnelab/goby/counts/UnionDumpIterator.java
goby-distribution/src/main/java/org/campagnelab/goby/readers/sam/*
goby-distribution/src/main/java/org/campagnelab/goby/readers/vcf/GroupAssociations.java
Copyright: 2009-2017 Institute for Computational Biomedicine
License: GPL-3+
Files: debian/*
Copyright: 2012 Andreas Tille <tille@debian.org>
2020-2021 Pierre Gruet <pgt@debian.org>
License: LGPL-3+
License: GPL-3+
On Debian systems the full text of the GPL-3 can be found in
/usr/share/common-licenses/GPL-3
License: FSFAP
Copying and distribution of this file, with or without modification, are
permitted in any medium without royalty provided the copyright notice
and this notice are preserved. This file is offered as-is, without any
warranty.
License: LGPL-3+
On Debian systems the full text of the LGPL-3 can be found in
/usr/share/common-licenses/LGPL-3
License: BSD-3-clause
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
are met:
1. Redistributions of source code must retain the above copyright
notice, and the entire permission notice in its entirety,
including the disclaimer of warranties.
2. Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
3. The name of the author may not be used to endorse or promote
products derived from this software without specific prior
written permission.
.
THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESS OR IMPLIED
WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
OF THE POSSIBILITY OF SUCH DAMAGE.
License: Expat
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
.
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
|
