bio-bwa 0.2.0
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- data/.document +5 -0
- data/Gemfile +15 -0
- data/Gemfile.lock +28 -0
- data/LICENSE.txt +35 -0
- data/README.rdoc +33 -0
- data/Rakefile +56 -0
- data/VERSION +1 -0
- data/bio-bwa.gemspec +152 -0
- data/doc/Bio.html +93 -0
- data/doc/Bio/BWA.html +2884 -0
- data/doc/Bio/BWA/Library.html +229 -0
- data/doc/_index.html +119 -0
- data/doc/class_list.html +36 -0
- data/doc/css/common.css +1 -0
- data/doc/css/full_list.css +53 -0
- data/doc/css/style.css +310 -0
- data/doc/file.LICENSE.html +88 -0
- data/doc/file.README.html +119 -0
- data/doc/file_list.html +41 -0
- data/doc/frames.html +13 -0
- data/doc/index.html +119 -0
- data/doc/js/app.js +203 -0
- data/doc/js/full_list.js +149 -0
- data/doc/js/jquery.js +154 -0
- data/doc/method_list.html +171 -0
- data/doc/top-level-namespace.html +88 -0
- data/ext/COPYING +674 -0
- data/ext/ChangeLog +3864 -0
- data/ext/NEWS +555 -0
- data/ext/README +29 -0
- data/ext/bamlite.c +155 -0
- data/ext/bamlite.h +94 -0
- data/ext/bntseq.c +303 -0
- data/ext/bntseq.h +80 -0
- data/ext/bwa.1 +562 -0
- data/ext/bwape.c +807 -0
- data/ext/bwase.c +686 -0
- data/ext/bwase.h +27 -0
- data/ext/bwaseqio.c +222 -0
- data/ext/bwt.c +250 -0
- data/ext/bwt.h +105 -0
- data/ext/bwt_gen/Makefile +23 -0
- data/ext/bwt_gen/QSufSort.c +496 -0
- data/ext/bwt_gen/QSufSort.h +40 -0
- data/ext/bwt_gen/bwt_gen.c +1547 -0
- data/ext/bwt_gen/bwt_gen.h +105 -0
- data/ext/bwt_lite.c +94 -0
- data/ext/bwt_lite.h +29 -0
- data/ext/bwtaln.c +345 -0
- data/ext/bwtaln.h +150 -0
- data/ext/bwtgap.c +264 -0
- data/ext/bwtgap.h +38 -0
- data/ext/bwtindex.c +186 -0
- data/ext/bwtio.c +77 -0
- data/ext/bwtmisc.c +269 -0
- data/ext/bwtsw2.h +51 -0
- data/ext/bwtsw2_aux.c +650 -0
- data/ext/bwtsw2_chain.c +107 -0
- data/ext/bwtsw2_core.c +594 -0
- data/ext/bwtsw2_main.c +100 -0
- data/ext/cs2nt.c +191 -0
- data/ext/is.c +218 -0
- data/ext/khash.h +506 -0
- data/ext/kseq.h +208 -0
- data/ext/ksort.h +269 -0
- data/ext/kstring.c +35 -0
- data/ext/kstring.h +46 -0
- data/ext/kvec.h +90 -0
- data/ext/main.c +63 -0
- data/ext/main.h +29 -0
- data/ext/mkrf_conf.rb +49 -0
- data/ext/qualfa2fq.pl +27 -0
- data/ext/simple_dp.c +162 -0
- data/ext/simpletest.c +23 -0
- data/ext/solid2fastq.pl +111 -0
- data/ext/stdaln.c +1072 -0
- data/ext/stdaln.h +162 -0
- data/ext/utils.c +82 -0
- data/ext/utils.h +54 -0
- data/lib/bio-bwa.rb +7 -0
- data/lib/bio/bwa.rb +312 -0
- data/lib/bio/bwa/library.rb +42 -0
- data/test/data/testdata.fa +602 -0
- data/test/data/testdata.long.fa +175 -0
- data/test/data/testdata.short.fa +2 -0
- data/test/helper.rb +18 -0
- data/test/test_bio-bwa_basic.rb +62 -0
- data/test/test_bio-bwa_make_index.rb +42 -0
- data/test/test_bio-bwa_run_aln.rb +49 -0
- data/test/test_bio-bwa_sam_conversion.rb +49 -0
- metadata +218 -0
@@ -0,0 +1,175 @@
|
|
1
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+
>NM_204276
|
2
|
+
GCGCCGCGGGAGCGCGCAGTTCGGTGTGGCTGTGCCGTGCCCGCGGGGAGCCCCGCGCTT
|
3
|
+
GGGGCGATGCTGCGGTCCCGGAGCGCTCCCGGGGGCCGGAGGGAGGTTTGCCAACAAGTG
|
4
|
+
TTCCAGTGAGATAAAAAAATGGCTTACAAATCTGGGAAAAGACCTACTTTCTTTGAAGTA
|
5
|
+
TTTAAGGCGCATTGTAGCGATTCAGACTTGGGGCCTGTAAGTCTTGACTGGTTTGAAGAG
|
6
|
+
CTCAGCTCAGAAGCACCTCCGTATGAGCCTAAGTTGTTAGGAGAACCTGAGGGTCCCATT
|
7
|
+
GGATGGTTTGATCAAACTTTTAAAACTCCAAAGGCAAAATCTTCTACGGACAGCCAGTTG
|
8
|
+
GCATCAACTCCACTGATTTTTAAAGAACAGAATACAATGCCGCCTTTTTCTTCTCCTGGA
|
9
|
+
AAAGAATTGGATCAGAAAAAAATGGAAACAAGCAGAGAGAATTTGCTAAGTCCAAGTATG
|
10
|
+
GCAGGAAGAAAGACAGATCAAGAAAATCAAATACTCGCTTCTCCTCATGGTATCTGCCAC
|
11
|
+
AACTACACTGCTGCTAGTCCAGCTATTGTAAGGAATCCTTGCAGAACACCACAGGGAAGT
|
12
|
+
AATATACCTGGACCATATGGAAGCTTGTTTTGCACACCAAAATTCTTGGAGATCCCAACT
|
13
|
+
CCGAAACGGATTTCTGAAAGTCTGGGAGCAGAAGTGGATCCAGAAATGTCCTGGACAAGT
|
14
|
+
TCTTTAGCTACTCCTCCTACACTTGGTGTGACAGTGATAATAGCTAGAGAGAATGATTCT
|
15
|
+
ATTTCTGGAGCAAAGCAGCAGGATGAAAGAGCTGAGATAGTTTTGCACAACTTTTTATCT
|
16
|
+
GAAGATGATGGATATACTGCAAAGAATGATACAAGTCTGCTGTCCATACCAGAGACGGTA
|
17
|
+
AAACTAAATGCTAGAGATGACATAAAAGATCTTGAGTCAGAAGTGTTAGATGGTTTATTT
|
18
|
+
GGTGAGACAAATAGCTTTGAGGATTCATTCAACTTGCCTGCTGAATCCAGTGGAATTCTG
|
19
|
+
TTGTCGCCACGTGCTCTGGATGCAATAGAGAAATGTGAAATAAAAATAGATGAAGCACAA
|
20
|
+
GAAAAGAGTGATGTTCTTTCAGAGCAACATAGGAGAAGAAAGTCTACCATTTCACAGGAG
|
21
|
+
GTGAAAGCTGCTAACTGGACTGAAAAAAGCTGCTGTGTTGAAGTGAAGGATTCTATAATC
|
22
|
+
CAGAACACCAATGAAGATATCATGGATAGTAAAGACAACTGCTTACTAGGGCGTGAAAAG
|
23
|
+
GAATTGGAGTATCTTAGGATTGCAGGAAACTTGCAAGATAATAGAACACAGAAATCATCT
|
24
|
+
GTGAATGAGAAGCTTGTGAAAGATGTGCTGTCTTCATCAAGCCAGTGGTCTCAGCTGAAC
|
25
|
+
TTGTCTGGTCTTGATGTAACTCATCTGGAAATGTCTATATGTAGCTCTCCACAGTCTGAC
|
26
|
+
TCATGTAGAGAGAAAGGTTTAGAAGAGAAGTCAGTACTGATGACCAAGGATGATGCTGTA
|
27
|
+
GAAACATCTTTACTGAATACTTCAGGCTTGAGAAATGCACAGGAGCTCTCAAGTGCCAGT
|
28
|
+
TTGTCAGAAAATGGCAGTGATACGAAAATATCTAAAAACAACCCAATGTCAGAAATAACT
|
29
|
+
CCAGTAAAACCTGTGTGTGCAAGTCCGAAGTTGGTAAAAGGATATGCACATGAGGAGGTT
|
30
|
+
TCCGGAATGAGCTTTTTAAACTGTAGTTCTTTTTTAATTGAAAGTACAAATGTCATGGAG
|
31
|
+
TATTCTGTAGTCTACAACAGCACTTTTTCCACGCATTTAAAAGCAACTTCGCAATCTGTG
|
32
|
+
GTAACTGATGTTCTTTCTCACCCTCTTATATGTAGTGCTGCATCTCCAGATAATTGCAGT
|
33
|
+
GACCTACATTTAAGAAATAGTGAAAAAACTCTTAGGAAATCTAACTTTAAAAGCCTAAAT
|
34
|
+
ATGTTATCCAGATTGAGGAAGAAATCCAAGAGATTTATTTATACAATAAATAATACTTTA
|
35
|
+
GTGTATCAGGAAGAAAATGTGCAGAAAGAAGTAACCTCTGAATCACCTGATAATCCTGTA
|
36
|
+
TTAACACATTTGGAATCTGATTTACATGAATTTAAAGATTGTCAGGTGGCCACAGATGGT
|
37
|
+
AACCAAGACTGCTTGCTTTCGGCTGAGAGGCAATCAAATATCAAAGAAAATAATTTAAAC
|
38
|
+
ACTCTTACCATAAAGGTAGATATAATGGATAACTCATCTGATAATTCTGTCAACAATAGG
|
39
|
+
CTGAAACAAGAGCTGAGTGAGTCAGGGAAAAATGCAAGAGAGTATCAACCTGCTACCTCA
|
40
|
+
TTTAAATGCTTAAAAGCTTCTCATACTGAGAGTGAAGACACAACAGATTGTTTAAACAGT
|
41
|
+
GGAAGAATTTCAAATATAAAACATAAGGTACTAACTTCGGCATACCTAATGGCAAGAAGG
|
42
|
+
CATTCCAGATTGTTTCCTGAAGACTGTTGCTTAAGGAAAGGCAAGAATGATACATATACC
|
43
|
+
GTTTCTAATGTGAACAGTCGAGCTGCTGTACCTCGGAGCCCTAAAGGACAGCCTCCACAG
|
44
|
+
TCCTCTCCTAGTTGTAGTGATTGCTTGATTGATATGCGCCATGGCACTGCGTTTGTGACA
|
45
|
+
AACAGCAAGTTCAATAATACTTTGAGTCACATCAAGTTTGGCATGAACAGAGTCAGTAGT
|
46
|
+
AACTCTTGCAATAAAATATCGGCTGATAAAAGACGTGCTTCAGATCAGTTGTCAGTAGCT
|
47
|
+
GAATGTAGGGAAATAGTTGCACCTTTGGGAATAAACTGCTTAGAAAACAATAGTACTAGC
|
48
|
+
TTAAAACAACGGGGAAAAGAAGATGTAGATGAAAATCAAGAAACACTCTCTATTAAAAGC
|
49
|
+
AGTGAAAACCCTCAAGCAGCTGCTTGGAATAACGAATCTATAGAGGTTGCTGAAGAATTC
|
50
|
+
TTGGATTGTATAGATAATTCTTTGAATGAAGTAGTTTCTGAAGAAGATAGACAAGTAGCA
|
51
|
+
CCTGTGTATTTCAACACAAAGCCAATTGAAAGCCTAGAACATAAAGGGAAATCATCAGGA
|
52
|
+
GATCTTAACGCATGCAGTTCAAGTTTGAGCTTTGGTGGCTTCCAGACTGCTTCCAATAAG
|
53
|
+
CAGATTAAATTCTCAGAAAGCAGCATAGCGAAAGGCAAAATGCTGTTCAAAGATATTGAA
|
54
|
+
AATGAATTCTTTGAAGCCTCTTCCATGGAAAGAGTCAGAAATTTTTCAAATCGAGTTCAA
|
55
|
+
AAGGAGAATATATTTTCCTCAGATTTGGAAAGCAAAACAGGCAGTACTTCATCTGGTTTG
|
56
|
+
CAGACAAGGTGTATGCAATATATTCCACGTAAAGTTGATTTATGTAAAAACTCGCCTAGA
|
57
|
+
AATCAACTATCTGTGCAAGAACCAAATCAGTCTTTGACAGCAAGCCAAGAAGCTGAAATT
|
58
|
+
GCTGAACTTTCTAATATCTTGGAAGAAACGGGTAGCCAGTTTGAATTCACACAATTTAGA
|
59
|
+
AAGCAAAGTAACATGATACAAAGTCACATTCAGCAGTTTGGAGCAACGAATGTGGAAAAT
|
60
|
+
GCTTCTGAAGCAGGGGAAGATACTAATTTCTATAGCACTCTTAAATCTGAAAATCATGTA
|
61
|
+
ATAAATGACGAGTATTGCAGTAAGttgaaaaatgaaaatgaatgtaaaatggtagaatat
|
62
|
+
gaaaaagaagacacagtggtttttcataaaaataaaagaaaaGTTACTTTTACTAACTTG
|
63
|
+
GACAGAAATGAAAGTAGAATATCCAGCCATGAGAGCTGTCCGGTACCTTTACGGGACAGC
|
64
|
+
TTTTCTAATTTTGTAGGATTTACTTCAGCTGGAGGTAAAAAAATAAATATTTGTAAGGCA
|
65
|
+
GCTTTGACCAGATCTGCAGAGCTTTTCAAGGACTTGGATGATGATAACTTTTTGTTTAAA
|
66
|
+
TCTTCTGGAACTAATACCAGATGCTGCAATTCAGATGGGCATGTATCTTCTAACTGGAAT
|
67
|
+
TTTCTCAGATGCCAGACAAAAGAAGATGAAGGAGGAATACTTTGTGTTCCAAACATAAAA
|
68
|
+
AGCGTAGGTCCCATTTCCCACCATTCAGAGAAAAAATATGCAGAAAATATTAGTTCACCA
|
69
|
+
TGTAAGGAAAATACAGAAAACTGGACAGAAATATTAAGTGATAATGTTGATTTCAGTTGT
|
70
|
+
ACTAATGGTGGATATTCTGCCTCTGGAATGAGAAACAGTCCGTCATCCTTTAAAAAACCT
|
71
|
+
CACCAGAACTGTAAAAATTCTGATCAGTTTCTGAATCAAGGAAACAGCGAAGTTGAAGGT
|
72
|
+
TGTTTGCAAGAAGACACTTCATATCTGATTTGTCTAGGAGATAATATTACTAGTGCAGAA
|
73
|
+
GAACATGATTTAAATGTTTCAGATGAAATGGAAAACCTGTCCCCTAATCAGAAAGAAGAC
|
74
|
+
AGAAAGCAGGAAGATGAGCATTTGCTGCTAAACCGTCAAGCTGCAGACACTGATGCTGTA
|
75
|
+
TCCATTTCTGATTCATCGTTCCGTAGTTCTCTACGTGATCTCAACGTACAATGTGGGGAA
|
76
|
+
AGAGATACAGATGTTTCAGAGAAATCTAGTAAACAAAAGACAAATAGTGTCAGTGTGGAA
|
77
|
+
GGAGAAGACTCCACCTATAAGAACCTGTTTGTGAGTGAAAGTGAGATTAAAATAGGCTCT
|
78
|
+
AACCAACGTCATCAAGTACCTTCCGAGCAAGAGATGGATGTTGACAAAAACAAAGTTAAG
|
79
|
+
GGAACTTATCTGACTGGTTTCTGTACTGCTAGTGGCAAGAAAATAACAATTGCTGATGGA
|
80
|
+
TTTTTGGCTAAAGCTGAAGAGTTTTTTTCAGAAAATAATGTTGATTTAGGAAAAGATGAT
|
81
|
+
AATGATTGTTTTGAGGACTGCTTAAGAAAATGTAATAAAAGCTATGTTAAAGACCGTGAC
|
82
|
+
TTATGTATGGACAGTACTGCTCATTGTGATGCAGATGTACTTAATTTTAAAGATAAGCTT
|
83
|
+
ATTCCTCAAGAACCTGGGGACCGACTAAAGCAGACAATAGAGGAGAGTCCCATTATACAA
|
84
|
+
GCTGTTAATCATGACAGCATTAAAGTGGGTGCATTTATTAATGTGGATGAAGATTGTGAA
|
85
|
+
AGAAATTTGGCAGCTCCATGTGCAAATAAGGAAGCTTATGTCAGACCTGGAAAGTCAGAA
|
86
|
+
GTAGAATCTCTTCCTGTACATGGGAACAATTCTTTAAGTAGAACTCTTTTGCTTGAAGAC
|
87
|
+
AGAAAACAGTTTGCAGAGAGAGATGTGGAATACTCAGCAACAAAGAGGGATAATTCAGAA
|
88
|
+
AGCAAACCTGACTCTTCTCTGAAGTGTGCTACATCTCTGCATTTAACAAAGGTGTCGAGT
|
89
|
+
CACCTTGCAGATAATTCTGTGCCTGGTGGTATTATTCAGACTGTATCTGCTGAGGATAGT
|
90
|
+
TGCAAGTCTAATCAGTCCTTCCTCTTACCTCGTGGTAGTGTTCCAAGAAGTACCTCACCT
|
91
|
+
TATCTGAACTGCGGCAATAAGGAGATTGACTTAAAACGTTTAAATGAACCTTGTTCCAAT
|
92
|
+
ACAGACAGTTTCACAAATACTGTAGATAATGCTCACCAAGAACAGTCTGAATTTGATCTT
|
93
|
+
CCTGAAGATGAAACTAATTTAACCTGCTTACAGGAAACATCACTTAATGCTGAAAGTCAA
|
94
|
+
AAGAGTGATCTGAAACAAGTGTTCAGTACAGCAAAAGGTAAAGCAGTCTCTGTTTCAGAA
|
95
|
+
AGTGCATTAGCAAGCATCAGACAAATGTTTCAAACAGACTGTGATGCATCTGTAAAATCT
|
96
|
+
GAAATTGAGACTAAATCAGGAACTAATCAAACAGCAATTGCTGGAAGTTCATCTTTCAGC
|
97
|
+
ATTCATGCTGGGGGTCCTGGTTTTGCTACATTTTTAGATACTAGAAAAAGTGAGATGAAT
|
98
|
+
GTGGCTGCACCTCATTTTATTAATGGAAATGGGAATCTTATTGAAAACAATCACCAAGGC
|
99
|
+
GCAAACATGTTTGCAGATGCAGATTCTGTTCCAGGTTTTCAGATGCAATGCTTTGAGCAG
|
100
|
+
AAGAGTAAGCTTTTAGGACACTTTCCTGTGCCAGATAAGCAGATGGAGCAGTCAGGTCCT
|
101
|
+
TCAGGCAACCTTGGGTTTTTCAGTACGGCAAGTGGGAAGCCTGTGCAACTATCAGAAGAG
|
102
|
+
TCGCTAAAGAAAGCTAGACAGCTCTTTTCTGAAATGGAAGGTAGCCATTCATCAGGGCTA
|
103
|
+
CAAGATGCACATTTGCTTGAAGACGTTGAGAAATCCACAAACCATGGTGAAGTATTTCCT
|
104
|
+
AGAGAAATGCAGCTACTGCTGCCAAGAGGGAAGGAGAATGCCAGCACGGATAAGATTTCA
|
105
|
+
AGTCCTGCTTTGGGGTTCAGCACTGCAAGTGGAAAGCAAGTGACCATCTCTGAAAGTGCC
|
106
|
+
TATCAGAAAGCAAAGGCAATTTTAAAGGAAGCAGATGGCTTTTTAAGCAGTGAGCTTGGT
|
107
|
+
GTTACAAATGAACTTTGTGAAATTAAAGAGAGTGGTCAACATGCAGAATATTTAACTGGT
|
108
|
+
AAAGTAATTTCAGAATCCAAAACTGAAAAAAGCTGCAGTGAGGAGCTTGACTTGAAAAGC
|
109
|
+
ATTCACCCTGAAAAAATGAAGTCTTTGCCAAGCACTCACCGTGTCAAAATTACTGAGTAT
|
110
|
+
GTACCACATAGTAAGAGAAACAGCCAGTCAGCACCATTTAAAAATAGCTTTGAGCAAGAA
|
111
|
+
GAGACCAGATTTTTCAGAAAAGGAGAGCTGAATCTGGGGATAAAAGCAGAGTCTGAATCA
|
112
|
+
GATTTATGCAGTGCTACATCTAAAGCAGAAATAAACATTTTCCAAACTCCAAAAGACTAC
|
113
|
+
TTGAAAACAGAGGCTGTAGAAAGTGCAAAAGCCTTTATGGAAGATGATCTTTCGGATTCT
|
114
|
+
GGAGTCCAGGTCAAGTCTGCACAGTCCTTTGGCAAAATGTCAGATAACTTTCAAAACAAG
|
115
|
+
CCCTTTGGGAAGAGACACTTGGATGAAAAAGACTCACATGGAGAACCTCCAATTAAAAGA
|
116
|
+
CAGCTACTGCTTGAATTTGAGAAGATGAAGATTCCCCCCAAATCTGTGAAACCTTTGAAA
|
117
|
+
AGCACTCCTGATGGCATTTTCAAAGACAGAAGAAAATTTATGTACCACGTCCCTTTAAAA
|
118
|
+
CCAGTAACTTGTCGACCTTTGGGGACTACTAAGGAACGACAAGAAGTCAGGAACCCTACA
|
119
|
+
CTTACTCTTCCTGATCAAGACTTGAAAGGATTTAAATCTATACCTGCCGTTTTTCAGCAC
|
120
|
+
TGTGCCCTACGGCAGTCTTCAAGTGGTGCTTCAGGGCTTTTTACTCCACATAAGGCCGTG
|
121
|
+
GCCAAGGATAGCGAGGAAACAAGAAGTTTGTGCAAGTCAGGCAAAGCTGTTAAAACTTTT
|
122
|
+
GTTCCACCCTTCAAAACCAAGCTGACACTTTCTACAGGTGAACAAGGCGGCAGCAAGAGA
|
123
|
+
TGTCACTCACCAATCAGAAACAGTGTGATGGAGGAGAGGGAATTAAATCAAATCCCAGTT
|
124
|
+
GAACAAAATAGTGCTGAAGCTCGGGATCACCAGTCCTGCATCCTGCATGCAGCGGTCACT
|
125
|
+
GACATAGAAAATGACAATTTAGTTACAAGCAACATGATGGCAAATCTCCACTGTGCTAGA
|
126
|
+
GATCTACAGGAAATGAGAATTAAAAAGAAATATAGGCAAAATATTAGCCCACAGCCAGGC
|
127
|
+
AGCCTTTATGTCACTAAAACATCTGCAAGAAATAGAATCTCTTTGAAAACTGCAGTTGAA
|
128
|
+
GAGGAAACACCCAGTTTTCATTCTACAGAAAAGCTTTACACATACGGAGTTTCAAAACAT
|
129
|
+
TGCATACAAGTTAACAGCACAAATGCAGAATCATTTCAGTTTCTCATTGAAGAATTTTTC
|
130
|
+
AGTAAGGAGTATTTATTAGCAGGAAATGGGATACAACTTGCTGATGGAGGATGGCTGATA
|
131
|
+
CCTACAGATGAGGGAAAGGCTGGAAAAAAGGAATTTTACAGGGCTCTCTGCGATACTCCT
|
132
|
+
GGTGTGGATCCCAAGCTAATAACAGAGGCCTGGGTTTACAATCATTATAGGTGGATTGTA
|
133
|
+
TGGAAACTGGCAGCCATGGAAGTGTGTTTTCCACATAAATTTGCTAACAGATGCTTGACA
|
134
|
+
CCAGAAACAGTACTGTTGCAGTTGAAATATAGGTATGACTTGGAAATCGATAAAAGTAAA
|
135
|
+
CGATCAGCAATCAAAAAAATAACAGAGAGAGATGATGCAGCAGGTAAAACACTTGTGCTG
|
136
|
+
TGTGTTTCTAAAGTCCTATCACTGAACACTGCTGTATCTCCTAGTAATAGTAATAACAAC
|
137
|
+
ACGGAAGGTGAAAAAGCAGCAGCAATAATTGAAGTTACTGATGGCTGGTATGGGATTAGA
|
138
|
+
GCTCTTTTGGATCCACCTCTCAAAGCTTTCTTACATAGAAGAAGGCTGACTGTTGGTCAG
|
139
|
+
AAGATCATAGTGCATGGAGCAGAACTTATTGGCTCTCCAAATGGATGTACGCCACTGGAA
|
140
|
+
GCCCCAGATTCCCTTATGCTAAAGATTGCAGCAAACAGCACGCGATGCGCACGGTGGTAC
|
141
|
+
ACAAAGCTGGGATTTCATCGGGACCCCAGACCTTTCCCTTTGCCTCTGTCATCACTTTAC
|
142
|
+
AGTGAGGGTGGTACAGTGGGCTGCATTGATGTGGTTGTCCAAAGAACTTATCCTATTCAG
|
143
|
+
TGGATGGAAAAGACATCAGCTGGCTCATATGTGTTTCGTAACAGCCGAGCTGAAGAAAGG
|
144
|
+
GAAGCTGCCAAGCATGCGGAGGATCAACAAAAGAAACTGGAAGCTCTATTTGCAAAAATT
|
145
|
+
CAAGCAGAATTTGAAAAGCACGAAGAGAGAAATTGCAGAAGAGCACCAAGGTCACGCATA
|
146
|
+
GTCACAAGGCAGCAAATCCATAATTTGCAAGATGGTGCAGAACTTTATGAAGCAATTCAG
|
147
|
+
AATGCAGCTGATCCCAGTTATATGGAGGGATATCTCAGTGAAGATCAGTTAAAAGCTCTG
|
148
|
+
AATGCTCACAAGCAGCTGATGAACGATAAAAAACAAACTCGGATACGGGAAGAATTCAAG
|
149
|
+
AAGGCTGTCGAGTCTGCAGAACAGGAAAAACATGGTTTTTCCAAAAGGGATGTGTCTACT
|
150
|
+
GTATGGAAATTATTTGTGATAGACTATAGAAAGCAAGAAAAACATAGAGGAGTGATCCTG
|
151
|
+
AGTATCTGGCGTCCACTGCTGGATGTGTGTTCACTGCTGAAGGAAGGCAGTCGGTACAGA
|
152
|
+
ATCTGCCAGCTGTCAACATCGCAGTCCAAAGGAAGATCAGACTCAACTAACGTACAGTTA
|
153
|
+
TCAGCAACAAAGAAAACTCGGTATCTACAACTATCAGTCTCACAGAAGATGCTGCAGCAG
|
154
|
+
AttttttttCCAAGAAAGGCTCTCAAATTCACCAGCCTGTTGGATCCTTCTTATCAGCCA
|
155
|
+
CCATGTGCCGAAGTTGATGTAGTTGGAGTTGTAATATCCATTAGCAGGACAGGATTCTCT
|
156
|
+
AACATGGTTTATTTATCTGATGAAAGCTATAATCTTGTGGCAATAAAAATCTGGGCAGAT
|
157
|
+
CTCCGGCATTTTGCTATCGAAGATATCGTTGTCCGCTGTTCGTTCATTGCTGCAAGCAAC
|
158
|
+
CTTCAGTGGCAGTCTGAATTCAGATCAGAAATTCCTGTGCTGTTGGCCGGAGATCTTTCT
|
159
|
+
GCATTCTCAGCTAGCCCAAAGGAAAACCATCTTCAAGAGAAGTTTAATGAACTGCGAAGG
|
160
|
+
ATGATAGAGAATGTGGACTCCTTTTGCTCTGATGCAGAAAGTAAATTGATGAATTTGCTA
|
161
|
+
CAAAGAAATTGCTCACTTACACCCATTTTACCTAAGAGATGTGGTTTGGAATGCTCTTCT
|
162
|
+
CCTTCCTGCAACTCAGGCCTTTATGCAGAAGATAGAAGTTCGATCTCTTCCAAAATTGAA
|
163
|
+
ACGAAGCATCCAAGCCCCTTGTCAGCTAGCACACCAAATACAAAGCTTTTCCCACAAGGC
|
164
|
+
TCAGCAATAACGCCTTCATCTGCTGTAAGTAGTGAGAACCATCCCAGAAACAGCAAAAAG
|
165
|
+
AGAAAAGCAGTGGACTTCCTCAGCTGCATACCTGCCCCTCCACCACTGACACCGCTCTGT
|
166
|
+
TCCATCATTTCTCCATCTTTAAAAAAGGCATTTCAGCCTCCGCGACGTTTGGGCTCACAG
|
167
|
+
CATAGCAAGTTATCAAAAGAAACAAACCCAAACGCTGGTTGTGTCACCCCCAGTAGAAGA
|
168
|
+
CTGAGAGAAGCTGTCCAGCTTCCTGATAATGACCTGGTTGCTGATGAAGAACTTGCAATG
|
169
|
+
ATTAATACACAAGCACTCATAAATACTGTACCGGAAGAAAAGAAGATGGATTATGTAAAT
|
170
|
+
GAAGACAGTACAAGGGCTACTAACTTATCTGGTGATACAAGAGCTACTAATTTATCTCGT
|
171
|
+
GATATGAGGGCTCCTAATTTATCTGGTGATCTTTCATCCAAAAATAGTTCCAGATCTGCT
|
172
|
+
AAGGAAGCAAACAGTTCATTGAAAAGCAGTTCTGAAGGAGCTGATGCTCTCCAGAAGGAC
|
173
|
+
ACAGAGGAACCTGAGGGTTCGTTATCAATCCGCAGAGTGCTGCAAAGGCGCAAATCCCGC
|
174
|
+
AAATGCTACTAGATGCACATGTACAGTACTGTGTATATTTCAAATTTAAATGTTTTTACT
|
175
|
+
TTGTACATTAAAGCCTGATTGTAATAAAGTTACATTACAAAATTCAT
|
data/test/helper.rb
ADDED
@@ -0,0 +1,18 @@
|
|
1
|
+
require 'rubygems'
|
2
|
+
require 'bundler'
|
3
|
+
begin
|
4
|
+
Bundler.setup(:default, :development)
|
5
|
+
rescue Bundler::BundlerError => e
|
6
|
+
$stderr.puts e.message
|
7
|
+
$stderr.puts "Run `bundle install` to install missing gems"
|
8
|
+
exit e.status_code
|
9
|
+
end
|
10
|
+
require 'test/unit'
|
11
|
+
require 'shoulda'
|
12
|
+
|
13
|
+
$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
|
14
|
+
$LOAD_PATH.unshift(File.dirname(__FILE__))
|
15
|
+
require 'bio-bwa'
|
16
|
+
|
17
|
+
class Test::Unit::TestCase
|
18
|
+
end
|
@@ -0,0 +1,62 @@
|
|
1
|
+
|
2
|
+
$:<<"."
|
3
|
+
require 'test/helper'
|
4
|
+
require 'digest/md5'
|
5
|
+
|
6
|
+
class TestBioBwa < Test::Unit::TestCase
|
7
|
+
|
8
|
+
def setup
|
9
|
+
@testdata = File.join("test","data","testdata")
|
10
|
+
end
|
11
|
+
|
12
|
+
def test_1bwa_fa2pac
|
13
|
+
Bio::BWA.fa2pac(:file_in => "#{@testdata}.fa",:prefix => @testdata)
|
14
|
+
md5 = Digest::MD5::hexdigest(File.open("#{@testdata}.pac","rb") {|f| f.read})
|
15
|
+
assert_equal("31ab6686d10cf980b9fc910854a38a7a",md5)
|
16
|
+
end
|
17
|
+
|
18
|
+
|
19
|
+
def test_2pac2bwt
|
20
|
+
out = "#{@testdata}.bwt"
|
21
|
+
Bio::BWA.pac2bwt(:file_in => "#{@testdata}.pac",:file_out => out)
|
22
|
+
md5 = Digest::MD5::hexdigest(File.open(out,"rb") {|f| f.read})
|
23
|
+
assert_equal("3c5e20c123ed8ab961287933e9734e70",md5)
|
24
|
+
end
|
25
|
+
|
26
|
+
def test_4bwtupdate
|
27
|
+
out = File.join("test","data","testdata.bwt")
|
28
|
+
FileUtils.cp out,"#{@testdata}.updated.bwt"
|
29
|
+
Bio::BWA.bwtupdate(:file_in => "#{@testdata}.updated.bwt")
|
30
|
+
md5 = Digest::MD5::hexdigest(File.open("#{@testdata}.updated.bwt","rb") {|f| f.read})
|
31
|
+
assert_equal("4f7ee2b68fade083421d8fd93bf024ec",md5)
|
32
|
+
FileUtils.rm(out)
|
33
|
+
end
|
34
|
+
|
35
|
+
def test_3pac_rev
|
36
|
+
out = File.join("test","data","out.rev.pac")
|
37
|
+
Bio::BWA.pac_rev(:file_in => "#{@testdata}.pac",:file_out => out)
|
38
|
+
md5 = Digest::MD5::hexdigest(File.open(out,"rb") {|f| f.read})
|
39
|
+
assert_equal("879cd21435a314f672c7de6d13977d69",md5)
|
40
|
+
FileUtils.rm(out)
|
41
|
+
end
|
42
|
+
|
43
|
+
def test_5bwt2sa
|
44
|
+
out = File.join("test","data","out.sa")
|
45
|
+
bwt = File.join("test","data","testdata.updated.bwt")
|
46
|
+
Bio::BWA.bwt2sa(:file_in => bwt,:file_out => out)
|
47
|
+
md5 = Digest::MD5::hexdigest(File.open(out,"rb") {|f| f.read})
|
48
|
+
assert_equal("948d0ebf6176f61de3ecdc8c085ae88a",md5)
|
49
|
+
FileUtils.rm(out)
|
50
|
+
FileUtils.rm(bwt)
|
51
|
+
FileUtils.rm("#{@testdata}.pac")
|
52
|
+
FileUtils.rm("#{@testdata}.amb")
|
53
|
+
FileUtils.rm("#{@testdata}.ann")
|
54
|
+
end
|
55
|
+
|
56
|
+
def test_no_method
|
57
|
+
assert_raise NoMethodError do
|
58
|
+
Bio::BWA.fake_method("some_file")
|
59
|
+
end
|
60
|
+
end
|
61
|
+
|
62
|
+
end
|
@@ -0,0 +1,42 @@
|
|
1
|
+
|
2
|
+
$:<<"."
|
3
|
+
require 'test/helper'
|
4
|
+
require 'digest/md5'
|
5
|
+
|
6
|
+
class TestBwaIndex < Test::Unit::TestCase
|
7
|
+
|
8
|
+
def setup
|
9
|
+
@testdata = File.join("test","data","testdata")
|
10
|
+
end
|
11
|
+
|
12
|
+
def test_make_index_colorspace
|
13
|
+
out = File.join("test","data","out")
|
14
|
+
Bio::BWA.make_index(:file_in=>"#{@testdata}.fa",:a => 'is',:prefix => "#{out}", :c => true)
|
15
|
+
md5_rbwt = Digest::MD5::hexdigest(File.open("#{out}.rbwt","rb") {|f| f.read})
|
16
|
+
md5_rpac = Digest::MD5::hexdigest(File.open("#{out}.rpac","rb") {|f| f.read})
|
17
|
+
md5_bwt = Digest::MD5::hexdigest(File.open("#{out}.bwt","rb") {|f| f.read})
|
18
|
+
md5_pac = Digest::MD5::hexdigest(File.open("#{out}.pac","rb") {|f| f.read})
|
19
|
+
md5_sa = Digest::MD5::hexdigest(File.open("#{out}.sa","rb") {|f| f.read})
|
20
|
+
assert_equal("6d6fd723604377dc5d6ad6c0f4f1cdf6",md5_rbwt)
|
21
|
+
assert_equal("64838ba5ad44f662266853ebc9451191",md5_rpac)
|
22
|
+
assert_equal("12fb7007102154f4bc428ea01a99a6ea",md5_bwt)
|
23
|
+
assert_equal("8cb0c5f86a5b927c233e3d5268f01f6a",md5_pac)
|
24
|
+
assert_equal("95711a0e5c06419017a02c73d12b99a2",md5_sa)
|
25
|
+
FileUtils.rm Dir.glob(out+".*")
|
26
|
+
end
|
27
|
+
|
28
|
+
def test_make_index
|
29
|
+
Bio::BWA.make_index(:file_in=>"#{@testdata}.fa",:a => 'is',:prefix => "#{@testdata}")
|
30
|
+
md5_bwt = Digest::MD5::hexdigest(File.open("#{@testdata}.bwt","rb") {|f| f.read})
|
31
|
+
md5_pac = Digest::MD5::hexdigest(File.open("#{@testdata}.pac","rb") {|f| f.read})
|
32
|
+
assert_equal("4f7ee2b68fade083421d8fd93bf024ec",md5_bwt)
|
33
|
+
assert_equal("31ab6686d10cf980b9fc910854a38a7a",md5_pac)
|
34
|
+
end
|
35
|
+
|
36
|
+
def test_errors
|
37
|
+
assert_raise ArgumentError do
|
38
|
+
Bio::BWA.make_index(:a => 'is',:prefix => "foo", :c => true)
|
39
|
+
end
|
40
|
+
end
|
41
|
+
|
42
|
+
end
|
@@ -0,0 +1,49 @@
|
|
1
|
+
$:<<"."
|
2
|
+
require 'test/helper'
|
3
|
+
require 'digest/md5'
|
4
|
+
|
5
|
+
class TestBioBwa < Test::Unit::TestCase
|
6
|
+
|
7
|
+
def setup
|
8
|
+
@testdata = File.join("test","data","testdata")
|
9
|
+
end
|
10
|
+
|
11
|
+
def test_short_read_alignment
|
12
|
+
assert_nothing_raised do
|
13
|
+
Bio::BWA.short_read_alignment(:prefix=>"#{@testdata}",:file_in=>"#{@testdata}.fa",:file_out=>"#{@testdata}.sai")
|
14
|
+
end
|
15
|
+
md5 = Digest::MD5::hexdigest(File.open("#{@testdata}.sai","rb") {|f| f.read})
|
16
|
+
assert_equal("56793f4473805683a7d494808c19f79e",md5)
|
17
|
+
end
|
18
|
+
|
19
|
+
def test_long_read_alignment
|
20
|
+
assert_nothing_raised do
|
21
|
+
Bio::BWA.long_read_alignment(:prefix=>"#{@testdata}",:file_in=>"#{@testdata}.fa", :file_out=>"#{@testdata}.bwasw")
|
22
|
+
end
|
23
|
+
md5 = Digest::MD5::hexdigest(File.open("#{@testdata}.bwasw","rb") {|f| f.read})
|
24
|
+
assert_equal("f569b0dfa7482d468bc68eb8151fb117",md5)
|
25
|
+
FileUtils.rm("#{@testdata}.bwasw")
|
26
|
+
end
|
27
|
+
|
28
|
+
def test_simple_SW
|
29
|
+
if RUBY_PLATFORM != 'java' then # the method redirect STDOUT to a file and this test does not pass in JRuby
|
30
|
+
assert_nothing_raised do
|
31
|
+
Bio::BWA.simple_SW(:long_seq=>"#{@testdata}.long.fa",:short_seq=>"#{@testdata}.short.fa",:f => true,:file_out => "#{@testdata}.stdsw")
|
32
|
+
end
|
33
|
+
md5 = Digest::MD5::hexdigest(File.open("#{@testdata}.stdsw","rb") {|f| f.read})
|
34
|
+
assert_equal("cedb41d4ba3581111fbcefec6063dc86",md5)
|
35
|
+
FileUtils.rm("#{@testdata}.stdsw")
|
36
|
+
end
|
37
|
+
end
|
38
|
+
|
39
|
+
def test_errors
|
40
|
+
assert_raise ArgumentError do
|
41
|
+
Bio::BWA.long_read_alignment(:prefix=>"#{@testdata}",:file_out=>"#{@testdata}.fa")
|
42
|
+
end
|
43
|
+
|
44
|
+
assert_raise ArgumentError do
|
45
|
+
Bio::BWA.long_read_alignment(:prefix=>"#{@testdata}",:file_in=>"#{@testdata}.fa", :file_out=>"#{@testdata}.bwasw", :unknown_parameter => "foo")
|
46
|
+
end
|
47
|
+
end
|
48
|
+
|
49
|
+
end
|
@@ -0,0 +1,49 @@
|
|
1
|
+
$:<<"."
|
2
|
+
require 'test/helper'
|
3
|
+
require 'digest/md5'
|
4
|
+
|
5
|
+
class TestBioBwa < Test::Unit::TestCase
|
6
|
+
|
7
|
+
def setup
|
8
|
+
@testdata = File.join("test","data","testdata")
|
9
|
+
end
|
10
|
+
|
11
|
+
def test_sai_to_sam_single
|
12
|
+
assert_nothing_raised do
|
13
|
+
Bio::BWA.sai_to_sam_single(:prefix=>"#{@testdata}",:sai=>"#{@testdata}.sai",:fastq=>"#{@testdata}.fa",:file_out => "#{@testdata}.sam")
|
14
|
+
end
|
15
|
+
md5 = Digest::MD5::hexdigest(File.open("#{@testdata}.sam","rb") {|f| f.read})
|
16
|
+
assert_equal("5c523ae7bf18656190fa0bcd8944bd14",md5)
|
17
|
+
FileUtils.rm("#{@testdata}.sam")
|
18
|
+
end
|
19
|
+
|
20
|
+
def test_sai_to_sam_paired
|
21
|
+
assert_nothing_raised do
|
22
|
+
Bio::BWA.sai_to_sam_paired(:prefix=>"#{@testdata}",:sai=>["#{@testdata}.sai","#{@testdata}.sai"],:fastq=>["#{@testdata}.fa","#{@testdata}.fa"],:file_out => "#{@testdata}.sampe")
|
23
|
+
end
|
24
|
+
md5 = Digest::MD5::hexdigest(File.open("#{@testdata}.sampe","rb") {|f| f.read})
|
25
|
+
assert_equal("8c3847bade0a19e5de77c274355fe154",md5)
|
26
|
+
FileUtils.rm("#{@testdata}.sampe")
|
27
|
+
end
|
28
|
+
|
29
|
+
def test_zomg_cleanup
|
30
|
+
assert_nothing_raised do
|
31
|
+
list = Dir.glob("#{@testdata}.*")
|
32
|
+
list.delete("#{@testdata}.fa")
|
33
|
+
list.delete("#{@testdata}.long.fa")
|
34
|
+
list.delete("#{@testdata}.short.fa")
|
35
|
+
list.each {|l| FileUtils.rm(l)}
|
36
|
+
end
|
37
|
+
end
|
38
|
+
|
39
|
+
def test_errors
|
40
|
+
assert_raise ArgumentError do
|
41
|
+
Bio::BWA.sai_to_sam_single(:prefix=>"#{@testdata}",:fastq=>"#{@testdata}.fa",:file_out => "#{@testdata}.sam")
|
42
|
+
end
|
43
|
+
|
44
|
+
assert_raise ArgumentError do
|
45
|
+
Bio::BWA.sai_to_sam_paired(:prefix=>"#{@testdata}",:sai=>"#{@testdata}.sai",:fastq=>["#{@testdata}.fa","#{@testdata}.fa"],:file_out => "#{@testdata}.sampe")
|
46
|
+
end
|
47
|
+
end
|
48
|
+
|
49
|
+
end
|
metadata
ADDED
@@ -0,0 +1,218 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: bio-bwa
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
prerelease:
|
5
|
+
version: 0.2.0
|
6
|
+
platform: ruby
|
7
|
+
authors:
|
8
|
+
- Francesco Strozzi
|
9
|
+
autorequire:
|
10
|
+
bindir: bin
|
11
|
+
cert_chain: []
|
12
|
+
|
13
|
+
date: 2011-03-22 00:00:00 +01:00
|
14
|
+
default_executable:
|
15
|
+
dependencies:
|
16
|
+
- !ruby/object:Gem::Dependency
|
17
|
+
name: shoulda
|
18
|
+
requirement: &id001 !ruby/object:Gem::Requirement
|
19
|
+
none: false
|
20
|
+
requirements:
|
21
|
+
- - ">="
|
22
|
+
- !ruby/object:Gem::Version
|
23
|
+
version: "0"
|
24
|
+
type: :development
|
25
|
+
prerelease: false
|
26
|
+
version_requirements: *id001
|
27
|
+
- !ruby/object:Gem::Dependency
|
28
|
+
name: bundler
|
29
|
+
requirement: &id002 !ruby/object:Gem::Requirement
|
30
|
+
none: false
|
31
|
+
requirements:
|
32
|
+
- - ~>
|
33
|
+
- !ruby/object:Gem::Version
|
34
|
+
version: 1.0.0
|
35
|
+
type: :development
|
36
|
+
prerelease: false
|
37
|
+
version_requirements: *id002
|
38
|
+
- !ruby/object:Gem::Dependency
|
39
|
+
name: jeweler
|
40
|
+
requirement: &id003 !ruby/object:Gem::Requirement
|
41
|
+
none: false
|
42
|
+
requirements:
|
43
|
+
- - ~>
|
44
|
+
- !ruby/object:Gem::Version
|
45
|
+
version: 1.5.2
|
46
|
+
type: :development
|
47
|
+
prerelease: false
|
48
|
+
version_requirements: *id003
|
49
|
+
- !ruby/object:Gem::Dependency
|
50
|
+
name: rcov
|
51
|
+
requirement: &id004 !ruby/object:Gem::Requirement
|
52
|
+
none: false
|
53
|
+
requirements:
|
54
|
+
- - ">="
|
55
|
+
- !ruby/object:Gem::Version
|
56
|
+
version: "0"
|
57
|
+
type: :development
|
58
|
+
prerelease: false
|
59
|
+
version_requirements: *id004
|
60
|
+
- !ruby/object:Gem::Dependency
|
61
|
+
name: bio
|
62
|
+
requirement: &id005 !ruby/object:Gem::Requirement
|
63
|
+
none: false
|
64
|
+
requirements:
|
65
|
+
- - ">="
|
66
|
+
- !ruby/object:Gem::Version
|
67
|
+
version: 1.4.1
|
68
|
+
type: :development
|
69
|
+
prerelease: false
|
70
|
+
version_requirements: *id005
|
71
|
+
- !ruby/object:Gem::Dependency
|
72
|
+
name: ffi
|
73
|
+
requirement: &id006 !ruby/object:Gem::Requirement
|
74
|
+
none: false
|
75
|
+
requirements:
|
76
|
+
- - ">="
|
77
|
+
- !ruby/object:Gem::Version
|
78
|
+
version: 1.0.5
|
79
|
+
type: :development
|
80
|
+
prerelease: false
|
81
|
+
version_requirements: *id006
|
82
|
+
description: Ruby binding for BWA mapping software, built using Ruby-FFI library
|
83
|
+
email: francesco.strozzi@gmail.com
|
84
|
+
executables: []
|
85
|
+
|
86
|
+
extensions:
|
87
|
+
- ext/mkrf_conf.rb
|
88
|
+
extra_rdoc_files:
|
89
|
+
- LICENSE.txt
|
90
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- README.rdoc
|
91
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files:
|
92
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- .document
|
93
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- Gemfile
|
94
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- Gemfile.lock
|
95
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- LICENSE.txt
|
96
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- README.rdoc
|
97
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- Rakefile
|
98
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- VERSION
|
99
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- bio-bwa.gemspec
|
100
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- doc/Bio.html
|
101
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- doc/Bio/BWA.html
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102
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- doc/Bio/BWA/Library.html
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103
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- doc/_index.html
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104
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- doc/class_list.html
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105
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- doc/css/common.css
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106
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- doc/css/full_list.css
|
107
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- doc/css/style.css
|
108
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- doc/file.LICENSE.html
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109
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- doc/file.README.html
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110
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- doc/file_list.html
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111
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- doc/frames.html
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112
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- doc/index.html
|
113
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- doc/js/app.js
|
114
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- doc/js/full_list.js
|
115
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- doc/js/jquery.js
|
116
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- doc/method_list.html
|
117
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- doc/top-level-namespace.html
|
118
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- ext/COPYING
|
119
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- ext/ChangeLog
|
120
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+
- ext/NEWS
|
121
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+
- ext/README
|
122
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+
- ext/bamlite.c
|
123
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- ext/bamlite.h
|
124
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- ext/bntseq.c
|
125
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+
- ext/bntseq.h
|
126
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- ext/bwa.1
|
127
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- ext/bwape.c
|
128
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- ext/bwase.c
|
129
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- ext/bwase.h
|
130
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- ext/bwaseqio.c
|
131
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- ext/bwt.c
|
132
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- ext/bwt.h
|
133
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- ext/bwt_gen/Makefile
|
134
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- ext/bwt_gen/QSufSort.c
|
135
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- ext/bwt_gen/QSufSort.h
|
136
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- ext/bwt_gen/bwt_gen.c
|
137
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- ext/bwt_gen/bwt_gen.h
|
138
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- ext/bwt_lite.c
|
139
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- ext/bwt_lite.h
|
140
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- ext/bwtaln.c
|
141
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- ext/bwtaln.h
|
142
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- ext/bwtgap.c
|
143
|
+
- ext/bwtgap.h
|
144
|
+
- ext/bwtindex.c
|
145
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- ext/bwtio.c
|
146
|
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- ext/bwtmisc.c
|
147
|
+
- ext/bwtsw2.h
|
148
|
+
- ext/bwtsw2_aux.c
|
149
|
+
- ext/bwtsw2_chain.c
|
150
|
+
- ext/bwtsw2_core.c
|
151
|
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- ext/bwtsw2_main.c
|
152
|
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- ext/cs2nt.c
|
153
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+
- ext/is.c
|
154
|
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- ext/khash.h
|
155
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+
- ext/kseq.h
|
156
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- ext/ksort.h
|
157
|
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- ext/kstring.c
|
158
|
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- ext/kstring.h
|
159
|
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- ext/kvec.h
|
160
|
+
- ext/main.c
|
161
|
+
- ext/main.h
|
162
|
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- ext/mkrf_conf.rb
|
163
|
+
- ext/qualfa2fq.pl
|
164
|
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- ext/simple_dp.c
|
165
|
+
- ext/simpletest.c
|
166
|
+
- ext/solid2fastq.pl
|
167
|
+
- ext/stdaln.c
|
168
|
+
- ext/stdaln.h
|
169
|
+
- ext/utils.c
|
170
|
+
- ext/utils.h
|
171
|
+
- lib/bio-bwa.rb
|
172
|
+
- lib/bio/bwa.rb
|
173
|
+
- lib/bio/bwa/library.rb
|
174
|
+
- test/data/testdata.fa
|
175
|
+
- test/data/testdata.long.fa
|
176
|
+
- test/data/testdata.short.fa
|
177
|
+
- test/helper.rb
|
178
|
+
- test/test_bio-bwa_basic.rb
|
179
|
+
- test/test_bio-bwa_make_index.rb
|
180
|
+
- test/test_bio-bwa_run_aln.rb
|
181
|
+
- test/test_bio-bwa_sam_conversion.rb
|
182
|
+
has_rdoc: true
|
183
|
+
homepage: http://github.com/fstrozzi/bioruby-bwa
|
184
|
+
licenses:
|
185
|
+
- MIT/GPLv3
|
186
|
+
post_install_message:
|
187
|
+
rdoc_options: []
|
188
|
+
|
189
|
+
require_paths:
|
190
|
+
- lib
|
191
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
192
|
+
none: false
|
193
|
+
requirements:
|
194
|
+
- - ">="
|
195
|
+
- !ruby/object:Gem::Version
|
196
|
+
hash: -1510626449413692226
|
197
|
+
segments:
|
198
|
+
- 0
|
199
|
+
version: "0"
|
200
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
201
|
+
none: false
|
202
|
+
requirements:
|
203
|
+
- - ">="
|
204
|
+
- !ruby/object:Gem::Version
|
205
|
+
version: "0"
|
206
|
+
requirements: []
|
207
|
+
|
208
|
+
rubyforge_project:
|
209
|
+
rubygems_version: 1.6.2
|
210
|
+
signing_key:
|
211
|
+
specification_version: 3
|
212
|
+
summary: Ruby binding for BWA mapping software
|
213
|
+
test_files:
|
214
|
+
- test/helper.rb
|
215
|
+
- test/test_bio-bwa_basic.rb
|
216
|
+
- test/test_bio-bwa_make_index.rb
|
217
|
+
- test/test_bio-bwa_run_aln.rb
|
218
|
+
- test/test_bio-bwa_sam_conversion.rb
|