minimap2 0.2.30.3 → 1.2.31.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (72) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +48 -63
  3. data/ext/minimap2/Makefile +1 -1
  4. data/ext/minimap2/format.c +12 -2
  5. data/ext/minimap2/hit.c +19 -8
  6. data/ext/minimap2/ksw2_ll_sse.c +2 -2
  7. data/ext/minimap2/minimap.h +2 -1
  8. data/ext/minimap2/pe.c +7 -2
  9. data/ext/ruby_minimap2/extconf.rb +47 -0
  10. data/ext/ruby_minimap2/native_main.c +15 -0
  11. data/ext/ruby_minimap2/ruby_minimap2.c +1134 -0
  12. data/lib/minimap2/aligner.rb +66 -374
  13. data/lib/minimap2/alignment.rb +22 -11
  14. data/lib/minimap2/version.rb +2 -1
  15. data/lib/minimap2.rb +39 -110
  16. metadata +8 -89
  17. data/ext/Rakefile +0 -60
  18. data/ext/cmappy/cmappy.c +0 -134
  19. data/ext/cmappy/cmappy.h +0 -46
  20. data/ext/minimap2/FAQ.md +0 -46
  21. data/ext/minimap2/MANIFEST.in +0 -10
  22. data/ext/minimap2/Makefile.simde +0 -97
  23. data/ext/minimap2/NEWS.md +0 -989
  24. data/ext/minimap2/README.md +0 -428
  25. data/ext/minimap2/code_of_conduct.md +0 -30
  26. data/ext/minimap2/cookbook.md +0 -243
  27. data/ext/minimap2/minimap2.1 +0 -844
  28. data/ext/minimap2/misc/README.md +0 -180
  29. data/ext/minimap2/misc/pafcluster.js +0 -241
  30. data/ext/minimap2/misc/paftools.js +0 -3734
  31. data/ext/minimap2/pyproject.toml +0 -2
  32. data/ext/minimap2/python/README.rst +0 -198
  33. data/ext/minimap2/python/cmappy.h +0 -152
  34. data/ext/minimap2/python/cmappy.pxd +0 -156
  35. data/ext/minimap2/python/mappy.pyx +0 -289
  36. data/ext/minimap2/python/minimap2.py +0 -41
  37. data/ext/minimap2/setup.py +0 -55
  38. data/ext/minimap2/test/MT-human.fa +0 -278
  39. data/ext/minimap2/test/MT-orang.fa +0 -276
  40. data/ext/minimap2/test/q-inv.fa +0 -4
  41. data/ext/minimap2/test/q2.fa +0 -2
  42. data/ext/minimap2/test/t-inv.fa +0 -127
  43. data/ext/minimap2/test/t2.fa +0 -2
  44. data/ext/minimap2/test/x3s-aln.txt +0 -5
  45. data/ext/minimap2/test/x3s-qry.fa +0 -5
  46. data/ext/minimap2/test/x3s-ref.fa +0 -10
  47. data/ext/minimap2/tex/Makefile +0 -21
  48. data/ext/minimap2/tex/bioinfo.cls +0 -930
  49. data/ext/minimap2/tex/blasr-mc.eval +0 -17
  50. data/ext/minimap2/tex/bowtie2-s3.sam.eval +0 -28
  51. data/ext/minimap2/tex/bwa-s3.sam.eval +0 -52
  52. data/ext/minimap2/tex/bwa.eval +0 -55
  53. data/ext/minimap2/tex/eval2roc.pl +0 -33
  54. data/ext/minimap2/tex/graphmap.eval +0 -4
  55. data/ext/minimap2/tex/hs38-simu.sh +0 -10
  56. data/ext/minimap2/tex/minialign.eval +0 -49
  57. data/ext/minimap2/tex/minimap2.bib +0 -460
  58. data/ext/minimap2/tex/minimap2.tex +0 -724
  59. data/ext/minimap2/tex/mm2-s3.sam.eval +0 -62
  60. data/ext/minimap2/tex/mm2-update.tex +0 -240
  61. data/ext/minimap2/tex/mm2.approx.eval +0 -12
  62. data/ext/minimap2/tex/mm2.eval +0 -13
  63. data/ext/minimap2/tex/natbib.bst +0 -1288
  64. data/ext/minimap2/tex/natbib.sty +0 -803
  65. data/ext/minimap2/tex/ngmlr.eval +0 -38
  66. data/ext/minimap2/tex/roc.gp +0 -60
  67. data/ext/minimap2/tex/snap-s3.sam.eval +0 -62
  68. data/ext/minimap2.patch +0 -19
  69. data/lib/minimap2/ffi/constants.rb +0 -267
  70. data/lib/minimap2/ffi/functions.rb +0 -239
  71. data/lib/minimap2/ffi/mappy.rb +0 -104
  72. data/lib/minimap2/ffi.rb +0 -27
data/ext/minimap2/test/MT-orang.fa DELETED
@@ -1,276 +0,0 @@
1
- >MT_orang co:Z:comment
2
- GTTTATGTAGCTTATTCTATCCAAAGCAATGCACTGAAAATGTCTCGACGGGCCCACACG
3
- CCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTGAGGTTACACAT
4
- GCAAGCATCCCCGCCCCAGTGAGTCGCCCTCCAAGTCACTCTGACTAAGAGGAGCAAGCA
5
- TCAAGCACGCAACAGCGCAGCTCAAGACGCTCAGCCTAGCCACACCCCCACGGGAGACAG
6
- CAGTGATAAGTCTTTAGCAATAAACGAAAGTTCAACTAAGCTACACTAACCCCAGGGTTG
7
- GTCAACTTCGTGCCAGCCACCGCGGTCACACGATTAGCCCAAGTTAATAGAGATCGGCGT
8
- AGAGAGTGTTTTAGATTCTTTTTCTCCCCAATAAAGCTAAAATTTACCTGAGTTGTAGAA
9
- AACTTAAGCTAATACAAAATAAACTACGAAAGTGGCTTTAATATATCTGAACACACAATA
10
- GCTAAGGCCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACTTTAACAGTTA
11
- AATCAACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGG
12
- CGGTGCTTCATATCCCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTC
13
- ACCACCCCTTGCTCAGCCTATATACCGCCATCTTCAGCAAACCCTGATGAAGGCCACGAA
14
- GTAAGCGCAAGCATCCACATAAAGACGTTAGGTCAAGGTGTAGCCCATGGAGTGGCAAGA
15
- AATGGGCTACATTTTCTACTTCAGAAAACTACGATAGCCCTCATGAAACCTGAGGGTCGA
16
- AGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGAAGCGCG
17
- TACACACCGCCCGTCACCCTCTTCAAGTATATTTCAGGGACTACCTAACTAAAACCCCCA
18
- CGCATCTATATAGAGGAGGCAAGTCGTAACATGGTAAGCGTACTGGAAAGTGCGCTTGGA
19
- CGAACCAGAGGGTAGCTTAACACAAAGCACCCGGCTTACACCTGGGAGATTTCAATTCAA
20
- CCTGGCCCCTCTGAGCTAACCCTAGCCCCAAACCCAACCCACCCTACTACCAACCAACCC
21
- TAACCAAACCATTCACCCAAACAAAGTATAGGCGATAGAAATTACAATCCGGCGCAATAG
22
- ACACAGTACCGTAAGGGAAAGATGAAAAAACACAACCAAGCACAACATAGCAAGGACTAA
23
- CCCCTGTACCTTTTGCATAATGAATTAACTAGAAACAACTTTGCAAGGAGAGCCAAAGCC
24
- AAGACCCCCGAAACCAGACGAGCTACCCATAAACAGCTAAAAGAGCACACCCGTCTATGT
25
- AGCAAAATAGTGGGAAGATTTATGGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGC
26
- TGGTTGTCCAAGACAGAATCTTAGTTCAACTTTAAATTTACTTACAGAACCCCTAATCCC
27
- CTCGTAAATTTAATTGCTAGTCTAAAGAGGAACAGCTCTTTAGACACTAGGAAAAAACCT
28
- TAAAAAGAGAGTAAAAAACACAACACCCATAGTGGGCCCAAAAGCAGCCATCAATTAAGA
29
- AAGCGTTCAAGCTCGACACCTAAACACCAAAAAATACCAAACACAAAACTGAACTCCTTA
30
- CTCCCCATTGGACTAATCTATTGCCCCATAGAAGAAACAATGTTAGTATAAGTAACATGA
31
- AGATATTCTCCCCCGCATAAGTCTACGTCAGACCGAAACATCACACTGACAATTAACGGT
32
- CCAATATGCATAGTTAACAAATAAACTATTATTTTTTCCCCCCGTTAATCCAACACAGGC
33
- ATGCCTATAAGGAAAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTCACCCCGCCTGT
34
- TTACCAAAAACATCACCTCTAGCATTACCAGTATTAGAGGCACCGCCTGCCCGGTGACAT
35
- ACGTTTAACGGCCGCGGTACCCTGACCGTGCAAAGGTAGCATAATCACTTGTTCCTTAAA
36
- TGGGGACTTGTATGAATGGCTTCACGAGGGTTCGACTGTCTCTTACTTTTAACCAGTGAA
37
- ATTGACCTGCCCGTGAAGAGGCGGGCATAACATAACAAGACGAGAAGACCCTATGGAGCT
38
- TCAATTTACCAGTGCAAATAACATACAACAAGCCCACAGGCCCTAAATCACCAAACCTGC
39
- ACTGAAGATTTCGGTTGGGGCGACCTCGGAGCACAACCCAACCTCCGAGAAACACATGTT
40
- AAGACCTCACAAGTCAAAACGAACTTCCACACACAATTGATCCAACAACTTGACCAACGG
41
- AACAAGTTACCCTAGGGATAACAGCGCAATCCTGTTCTAGAGTCCATATCAACAACAGGG
42
- TTTACGACCTCGATGTTGGATCAGGACATCCTAATGGTGCAGCCGCTATTAAAGGTTCGT
43
- TTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGGAGCAATCCAGGTCGGTT
44
- TCTATCTATTTCACATTTCTCCCTGTACGAAAGGACAAGAGAAATGGGGCCTACTTCACA
45
- TAAGCGCCTTTCCCAAACAAATGATATCATCTCAATTTAACACCACACCAACACCCACCC
46
- AAGAAAAGGGCTATGTTAAGATGGCAGAGCCCGGTAACTGCATAAAATTTAAAGCTTTAC
47
- AGTCAGAGGTTCAACTCCTCTTCTTAACAATATGCCCATAATCAACCTCCTACTCCTCAT
48
- TATATCCATCCTAATCGCCATAGCATTTCTAATGCTAACCGAACGAAAAATCCTAGGCCA
49
- CACACAACTACGCAAAGGGCCCAACATTGTGGGCCCCTACGGCTTACTACAACCCTTTGC
50
- CGACGCCCTAAAACTATTCACCAAAGAACCCCTAAAACCCTCCACATCAACCATCACCCT
51
- TTACATTATTTCCCCCGCCCTAGCCCTTACCATTGCCCTCCTACTATGAACCCCCCTCCC
52
- TATGCCCATCCCCCTAATCAACCTCAACTTAGGCCTCCTATTTATCCTAGCCGCGTCAAG
53
- CCTAACCGTCTACTCCATCCTCTGATCAGGATGAGCATCTAACTCAAACTACGCCCTAAT
54
- CGGCGCATTGCGGGCGGTAGCCCAAACGATCTCATACGAAATTACCCTAGCCCTTATCCT
55
- GTTATCAGTACTACTAATAAGCGGCTCTTTTAACCTCTCCGCCCTCATCACAACACAAGA
56
- ACACTCATGACTACTTCTACCATCATGACCTCTAGCCCTAATATGATTTATTTCAACACT
57
- AGCAGAAACCAACCGAGCCCCCTTCGACCTCACCGAAGGAGAATCCGAACTAGTTTCGGG
58
- CTTTAACACTGAATACGCCGCAGGTCCATTCGCCCTATTCTTCATAGCCGAATATACAAA
59
- CATTATCTTAATAAACGCCCTCACCACTATAATTTTCCTAGGAACAACATTCAACATCCA
60
- CTCCCCAGAACTCTACACAACCCTCTTCACCATCAAAACCCTACTCCTAACCTCCCTATT
61
- CCTATGAATTCGATCAACATACCCCCGATTCCGCTACGACCAACTCATGCACCTTCTATG
62
- AAAAAATTTCCTGCCACTCACCCTAGCACTACTAATATGACACATCTCCGTACCCATTGC
63
- AACCTCCGGCATTCCCCCACAAACCTAAGAAATATGTCTGACAAAAGAGTTACTTTGATA
64
- GAGTAAAAAATAGAGGTCTAAATCCCCTTATTTCTAGGATTATGGGAGTTGAACCCACCC
65
- CTGAGAATCCAAAATTCTCCGTGCCACCCATCACACCCTATCCTAAAGTAAGGTCAGCTA
66
- AATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAATTAAC
67
- CCCTTGGCCCAACCCATCATTTACCCCACCATCTTCACAGGCACGCTCATTACAGCACTG
68
- AGCTCCCACTGATTCTTTGCCTGACTGGGACTAGAAATAAATATACTCGCTTTCATCCCA
69
- GTCCTAACCAAAAAAACAAGCCCCCGCTCCACAGAAGCCGCCATTAAATATTTCCTCACA
70
- CAGGCAACCGCATCCATAATCCTCCTGATAGCCATCCTCTACAACAACATACTTTCCGGA
71
- CAGTGAACCACAACCAACACCACCAACCCATATTCATCTCTAATAATCGTAACCGCCCTA
72
- GCAATGAAGCTAGGAATAGCCCCCTTCCACTTTTGAGTCCCAGAAGTCACCCAAGGAGTC
73
- CCCCTGACATCCGGCTTACTCCTCCTTACATGACAAAAATTAGCCCCCATTTCAATTATA
74
- TACCAAATATCTTCATCGGTAGACACAAACATCCTCCTCACCCTCTCAATTCTATCTATC
75
- CTAGTAGGCGGCTGAGGCGGACTAAACCAAACCCAACTACGCAAAATCCTGGCATACTCC
76
- TCAATCACCCATATAGGATGAATAATAGCAGTACTACCATATAACCCAGACATCACTATC
77
- CTCAACCTAATCATCTACATCATCCTGACAACTACCGCATTCCTAATCCTCGACTTAAAC
78
- TCTAGTGTCACAATCCTAATATTAACCCGCACCTGGAACAAGCTGACATGACTAATACCC
79
- TTAATCCCATCAACCTTATTATCCCTAGGGGGCCTGCCACCACTAACCGGCTTCCTGCCC
80
- AAATGAGCCATCATTGAAGAATTTGCAAAAAATGGCAATCTCATTACCCCCACAATCATG
81
- GCTATTATCACCCTCCTCAACCTCTACTTCTACGTACGCCTAATCTACGCCACCTCAATC
82
- ACACTACTCCCCATATCTAACAACGCAAAAATGAAATGACAGTTCGAAAACACAAAACCC
83
- ACCCCTCTTCTCCCCACACTCACCATTCTTACCACCCTACTCCTACCTATCTCCCCTCTC
84
- ATCCTATCTATCTCATAGAAATTTAGGTTAACACAGACCAAGAGCCTTCAAAGCCCTCAG
85
- CAAGTCACAGCACTTAATTTCTGTAACACTAAGGACTGCAAAGCCCCGCTCTGCATCAAC
86
- TGAACGCAAACCAGCCACTTTAATTAAGCTAAGCCCTCCCTAGACCGATGGGACTTAAAC
87
- CCACAAACATTTAGTTAACAGCTAAACACCCTAATCAATTGGCTTCAGTCCACTTCTCCC
88
- GCCGCGGGGAAAAAGGCGGGAGAAGCCCCGGCAGGCCTTAAAGCTGCTCCTTCGAATTTG
89
- CAATTCAACATGACAATCACCTCGGGGCTGGTAAAAAGAGGTCTAACCCCTGTTCTTAGA
90
- TTTACAGCCTAATGCCTTAACTCGGCCATTTTACCCCCCCCCCCCCTTTTTTTCTCCACT
91
- AATGTTCGCCGACCGCTGGCTATTCTCCACGAACCACAAAGACATCGGGACACTATACCT
92
- GTTATTCGGCGCATGGGCTGGAGTCCTAGGCACTGCCCTAAGCCTCCTCATTCGAGCTGA
93
- ACTGGGCCAACCCGGCAACCTTCTAGGCAATGACCATATCTACAATGTCATCGTCACAGC
94
- TCATGCATTCGTAATAATTTTCTTTATAGTCATACCCATTATAATTGGAGGCTTTGGCAA
95
- CTGACTAGTGCCCCTAATAATCGGCGCCCCCGATATAGCATTCCCGCGCATAAATAATAT
96
- AAGCTTCTGACTCCTCCCCCCCTCCTTTCTCCTACTGCTCGCTTCTGCTACAGTAGAGGC
97
- TGGCGCAGGAACAGGCTGAACAGTCTATCCGCCCCTAGCAGGAAACTACTCTCACCCAGG
98
- AGCCTCTGTAGACTTAACAATCTTCTCTTTACACCTAGCAGGCATTTCCTCTATCCTAGG
99
- AGCTATCAATTTCATCACAACAATTATTAATATAAAACCCCCTGCAATATCCCAATACCA
100
- AACCCCCCTCTTCGTCTGATCAGTCTTGATCACAGCAGTCCTACTTCTCCTTTCCCTCCC
101
- AGTCCTAGCCGCTGGCATCACCATACTACTAACAGATCGCAACCTAAACACCACATTCTT
102
- TGACCCAGCCGGAGGTGGAGATCCCATCCTATATCAGCACCTATTCTGATTTTTTGGCCA
103
- CCCTGAAGTCTACATTCTCATCCTGCCGGGTTTCGGCATAATCTCCCACATCGTAACACA
104
- CTATTCCGGAAAAGAAGAGCCATTTGGGTACATAGGCATAGTCTGAGCCATAGTCTCAAT
105
- TGGCTTCCTGGGCTTTATCGTATGGGCCCACCACATATTCACAGTAGGAATAGACGTGGA
106
- CACACGAGCCTACTTCACCTCCGCTACCATAATCATTGCCATCCCCACCGGCGTCAAAGT
107
- ATTTAGCTGACTCGCTACACTCCACGGAAGCAACACTAAATGATCTGCCGCAATCCTCTG
108
- AGCCTTAGGATTCATTTTCCTCTTCACCGTAGGCGGCCTAACAGGCATCGTACTAGCAAA
109
- CTCATCACTAGACATTGTATTACACGATACATACTACGTTGTAGCCCACTTTCATTACGT
110
- CCTATCAATAGGAGCTGTATTCGCCATCATGGGAGGCTTCATCCACTGGTTCCCACTATT
111
- CTCAGGCTACACCTTAGACCAGACCTATGCTAAAATTCACTTCATCACCATATTTATCGG
112
- CGTAAATTTAACTTTCTTCCCACAACATTTCCTCGGCCTGTCAGGCATACCCCGACGCTA
113
- CTCCGACTACCCCGACGCGTACACCACCTGAAATATTTTATCATCCGCAGGCTCATTTAT
114
- CTCCCTAACAGCAGTCATACTAATAATTTTCATAATTTGAGAAGCCTTCGCCTCAAAACG
115
- AAAAGTCCCAATAGTTGAACAACCCTCCACAAGCCTAGAGTGATTGTACGGATGCCCCCC
116
- ACCCTACCACACATTTGAAGAACCCGTCTATATAAAACCAGAACAAAAAAGGAAGGAATC
117
- GAACCTCCTAAAGCTGGTTTCAAGCCAACCCCACAACCTCCATGACTTTTTCAAGAGATA
118
- CTAGAAAAACCATTTCATGACTTTGTCAAAGTTAAGTTACAGGCCAAACCCTGTGTATCT
119
- TAATGGCGCACGCAGCACAGGTAGGTTTACAAGACGCTACCTCTCCTATCATAGAAGAAT
120
- TGGTCATCTTTCACGACCACGCCCTCATAATCATTTTCCTAATCTGCTTCCTAGTCCTGT
121
- ACGCCCTATTCCTAACACTCACAACAAAACTCACCAACACCAGCATCTCAGACGCCCAAG
122
- AGATAGAGACTATTTGAACTATCCTACCGGCCATCATCCTAATTCTAATCGCCCTCCCAT
123
- CCCTACGCATCCTCTACTTAACAGACGAGATCAACGACCCTTCCTTCACCATCAAATCAA
124
- TCGGTCATCAATGATACTGAACCTACGAGTACACTGACTACGGTGGATTGATCTTCAACT
125
- CTTACATGCTCCCACCACTATTCCTAGAACCAGGCGACCTTCGACTCCTCGACGTCGACA
126
- ACCGAGTAGTCCTCCCAGTCGAAGCTCCCGTTCGCATAATAATCACATCCCAAGACGTCT
127
- TACACTCATGAACTGTACCCTCACTAGGCCTGAAAACGGACGCAATCCCCGGACGCCTAA
128
- ACCAAACCACATTCACTGCCACGCGACCAGGAGTGTACTATGGCCAATGCTCAGAAATCT
129
- GTGGAGCTAACCACAGCTTTATGCCTATCGTCCTAGAACTAATCCCCCTAAAAATCTTCG
130
- AAATAGGGCCCGTATTCACTTTATAACTTCCCCCACCCCCACAACCCATCCTACCCCCTT
131
- TCCTGAGGCCCACTGCAAAGCTAATCTAGCATTAACCTTTTAAGTTAAAGACTAAGAGAA
132
- TCAACCCCTCTTTGCAGTGAAATGCCCCAACTAAATACCACCACATGGCCCACCATCATC
133
- ACCCCAATACTCCTTGCACTATTCCTCATCACTCAACTAAAACTACTAAACTCACACCTC
134
- CACCCACCCACCCCACCAAAATTCACTAAACCAAAACTCCACGCCAAACCCTGAGGACCA
135
- AAATGAACGAAAGTCTATTTACCCCATTCATTACCCCCACAGTACTAGGCCTCCCCGCCG
136
- CAGTACTAGTCATCTTATTTCCCCCCTTACTGATCCCCACCTCCAAACATCTCATCAACA
137
- ACCGACTAATTATTATCCAACAATGACTAATCCGACTCATCCTAAAACAAATAATAACCA
138
- CCCATAACGCTAAAGGACGAACTTGATCCCTCATACTAACGTCCCTAATCATTTTCATCG
139
- CCTCAACCAACCTCCTAGGACTCCTCCCCTACTCATTTACACCAACCACCCAACTATCCA
140
- TAAATTTAGCTATAGCAATTCCCTTATGAGCAAGCACGGTAGCTATGGGCCTTCGCTTCA
141
- AAGCCAAAATTACCCTAACCCACCTCTTACCACAAGGTACCCCCACACCTCTCATCCCTA
142
- TACTAATTATTATTGAAACCGTCAGCCTTTTCATTCAACCACTAGCCTTAGCCGTACGCC
143
- TAACTGCTAACATCACTGCAGGCCACCTACTCATGCACCTAATCGGAAGCTCTGCACTAG
144
- CTATACTAGCCATCAACCTCCCCCTAACCCTCATCACCCTTACAATCTTAACCCTGCTAA
145
- CAATCCTGGAGACTGCCATCGCCCTAATTCAAGCCTACGTCTTCACACTTCTAGTAAGCC
146
- TCTACCTGCACGACAACTCATAATGGCCCATCAATCACACGCCTACCACATAGTAAAACC
147
- TAGCCCATGACCCCTAACAGGAGCTCTCTCAGCCCTCCTAACAACATCTGGCCTAACCAT
148
- GTGATTCCACTTCCACTCCACAACCCTACTATTAACAGGCCTACTAACCAATGCACTAAC
149
- CATATACCAATGGTGACGAGATGTAGTGCGAGAAAGCACATACCAAGGCCACCACACACT
150
- ACCCGTCCAAAAAGGCCTCCGATATGGAATAATCCTATTCATCACTTCAGAAGTCTTTTT
151
- CTTCGCCGGATTCTTCTGAGCATTCTACCACTCCAGCCTAGCCCCCACCCCTCAACTTGG
152
- AGGACACTGACCCCCAACAGGCATTATCCCCCTCAACCCCCTAGAAGTCCCACTCCTAAA
153
- CACATCCGTACTACTCGCATCAGGAGTCTCAATTACCTGAGCCCATCACAGCCTGATGGA
154
- AAATAATCGAACCCAAATAATTCAAGCACTACTCATCACAATCTTACTAGGCATCTACTT
155
- CACTCTCCTTCAGGCTTCAGAATACATTGAAGCTCCTTTCACCATCTCTGACGGCATCTA
156
- CGGCTCAACATTCTTCATAGCCACGGGATTCCACGGCCTCCACGTCATTATCGGATCAAC
157
- TTTCCTCACTGTATGCCTAGCCCGCCAGCTATTATTCCACTTCACATCCAAACATCACTT
158
- TGGCTTTGAGGCCGCCGCCTGATACTGGCACTTTGTAGACGTAGTCTGACTGTTTCTGTA
159
- CGTCTCCATCTACTGATGAGGTTCCTACTCTTTTAGTATAAACAGTACCGTTAACTTCCA
160
- ATTAACTAGTTTTGACAACGCCCAAAAAAGAGTAATTAACTTCGTCCTAGCTCTAACAGT
161
- CAACACCCTCCTAGCCCTGCTACTAATAACCATCACATTCTGACTACCACAACTCTACCC
162
- CTACATAGAAAAATCCGACCCATACGAATGTGGATTTGACCCCGCATACCCCGCTCGCAT
163
- TCCTTTCTCCATAAAATTTTTCTTAGTAGCCATCACCTTCCTACTATTCGACCTAGAAAT
164
- CGCCCTGCTACTACCCCTGCCATGGGCCCTACAAACAACCAACTTACCACTAATAACTAC
165
- ATCATCACTTATATTAATTATCATCCTAGCCCTAGGCCTAACTTACGAATGATCACAAAA
166
- AGGATTAGACTGAGCCGAATTGGTAAATAGTTTAAACAAAACAAATGATTTCGACTCATT
167
- AAATTATGACAGCCATATTTACCAAATGCCCCTTATCTACATAAATATCACACTAGCATT
168
- CACCATATCACTCCTAGGCATACTAGTCTACCGCTCACACCTAATATCTTCTCTACTATG
169
- TCTAGAAGGAATAATATTATCATTGTTCATTATAATTACTCTCATAACCCTCAACACCCA
170
- CTCTCTCCTAGCTAACATCATACCCATCACCATGCTAGTCTTCGCTGCCTGCGAAGCAGC
171
- AGTAGGCCTCGCCCTACTAGCCTCAATCTCCAATACATACGGCCTAGACTACGTCAACAA
172
- CCTAAACCTACTTCAATGCTAAAACTAATTATCCCAACAATCATACTGCTGCCCCTAACA
173
- TGACTCTCCAAAACGCACATAATCTGAATCAACACCACCACCCACAGCCTAATCATCAGC
174
- TCCATCCCCCTACTATTCCTCAATCAAACCAACAGCAACCTGTACAGCTACTCCCTTCTT
175
- TTCTCCTCCGACCCCTTATCAACCCCCCTTCTAATACTAACAACCTGACTCCTACCCCTC
176
- ATAATTATAGCAAGCCAACACCATCTATCCAACGAACCCCCATCACGAAAAAAATTATAC
177
- CTCACCATACTAATCTCTCTTCAAATCTCCCTAATCATAACATTCACAGCCACAGAGCTA
178
- ATTATATTTTATATCCTCTTCGAAACCACTCTCATCCCCACCCTAGTCATTATCACCCGC
179
- TGAGGCAACCAGCCAGAGCGCTTAAATGCAGGCACATACTTTCTATTCTACACACTAGTA
180
- GGCTCCCTCCCCCTACTCATTGCCCTAATCCACACCTACAACACCCTAGGCTCGCTTAAC
181
- ATTGTATTACTAACTCTCACCGCCCGGGAGCTAACAGACTCCTGATCCAACAGCCTAATA
182
- TGACTAGCGTACACAATAGCTTTCATAGTAAAAATACCCCTCTACGGACTACACCTATGA
183
- CTCCCTAAAGCCCATGTAGAAGCCCCCATTGCCGGCTCAATAGTACTCGCCGCAGTGCTC
184
- TTAAAACTAGGTGGTTACGGTATAATACGCCTTATCCCCATTCTCAATCCCCTAACTAAA
185
- CACATAGCCTACCCCTTTATCATACTATCCCTATGAGGCATAATCATAACAAGCTCCATC
186
- TGCTTACGACAAACCGACCTAAAATCACTCATCGCATACTCCTCAGTCAGCCACATAGCG
187
- CTTGTTGTAGCAGCTATCCTCATTCAAACCCCCTGAAGCTTCACCGGCGCAACCACCCTC
188
- ATAATTGCCCATGGACTCACATCCTCCCTACTGTTCTGCCTAGCAAACTCAAACTACGAA
189
- CGAACCCACAGCCGCATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATA
190
- GCCCTCTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCAACCTA
191
- CTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAACATCACCATCCTACTA
192
- ACAGGACTCAACATACTAATCACAACCCTATACTCTCTCTATATATTCACCACAACACAA
193
- CGAGGTACACCCACACATCACACCAACAACATAAAACCTTCTTTCACACGTGAAAACACC
194
- CTCATGCTCATACACCTATCCCCCATTCTCCTCTTGTCCCTCAACCCCAGCATCATCGCT
195
- GGATTCGCCTACTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTAATAATAGG
196
- GCCCACAACCCCTTATTTACCGAGAAAGCTCACAAGAACTGCTAACTCTCACCCCATGTG
197
- TAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCCTTGGTCTTAGGACCCA
198
- AAAATTTTGGTGCAACTCCAAATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTC
199
- ACCTTGACTTCCCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAAC
200
- TCATACCCCCACTATGTAAAAACTGCCATCGCATCCGCCTTTACTATCAGCCTTATCCCA
201
- ACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCACAAACTGATGCTGAACAACC
202
- ACCCAGACACTACAACTCTCACTAAGCTTCAAACTTGACTACTTCTCCATAACATTCCTC
203
- CCCGTAGCACTACTCATCACTTGATCCATTATAGAATTTTCACTATGGTATATAGCCTCA
204
- GACCCAAACATCAACCAATTTCTCAAATTCCTCCTTATTTTCCTAATCACCATAATTATC
205
- CTAGTCACTGCCAATAACCTACTCCAACTCTTCATCGGCTGAGAGGGCGTAGGGATCATA
206
- TCCTTCCTGCTCATTAGTTGATGATACGCCCGAACAGACGCCAACACGGCAGCTATTCAA
207
- GCAATCCTATACAATCGTATCGGCGATATTGGCTTCATCCTGGCTCTAGCATGATTCCTC
208
- CTACACTCCAACTCATGGGAACTACAACAAGTATTCCTCCTAAACAATAACCCTAACCTC
209
- CTCCCACTACTAGGACTCCTCCTAGCCGCAGCTGGCAAATCAGCCCAACTAGGCCTTCAC
210
- CCCTGACTACCCTCAGCCATAGAAGGCCCAACCCCCGTCTCAGCCCTACTTCACTCAAGC
211
- ACCATGGTCGTGGCTGGGGTCTTCCTACTCATCCGCTTTCACCCATTAACAGAAAACAGC
212
- CCACATATCCAAACCCTTACACTATGCTTAGGGGCCATCACCACCCTGTTCGCAGCAATC
213
- TGCGCCCTCACACAAAACGACATTAAGAAAATCGTAGCTTTCTCCACCTCAAGTCAACTA
214
- GGACTTATAATGGTCACAATTGGCATTAACCAGCCACACCTGGCACTCCTCCACATCTGC
215
- ACCCACGCCTTCTTCAAAGCCCTTTTATTCATATGTTCTGGGTCCATCATCCACAACCTC
216
- AACAATGAGCAAGACATCCGAAAAATAGGAGGACTACTCAAAACCATACCCCTAACCTCA
217
- ACCTCCCTCACTATCAGCAGCCTAGCCCTCGCAGGAATACCCTTCCTCTCAGGCTTCTAC
218
- TCCAAAGACCTCATTATCGAGACCGCAAACATATCCTATACCAACACCTGAGCCCTGTCT
219
- ATCACTCTCATCGCCACCTCCTTAACAGGCGCCTACAGCACTCGAATAATCCTCCACACC
220
- CTTACAAGCAAACCCCACTTCCCAACCCCAATCTCTATCAATGAAAACAACCCCACTCTA
221
- CTTAAACCCATCAAGCGCCTTATGCTAGGAAGCCTATTCGCAGGATTCCTAATCACCAAC
222
- AACATCCCCCCTATATCCCTGCCCCAAGTAACAACCCCCCCTTACCTAAAACTCGCAGCT
223
- CTAGCTGCCACCCTCCTAGGTCTCCTAGTAGCCCTAGACTTAAACTACCTAGCCAACAAA
224
- CTCAAGACAAAAACCCCTCCACCCACATTCTATTTCTCCATCATACTCGGATTCTACCCT
225
- AGCATCATCCACCGCATAATCCCCCACCTAAGCCTTCTCATAAGCCAAAACTTATCCCTA
226
- CTCCTACTAGACCTAACCTGACTAAAAAAACTAATACCCAAAACAATCTCACAACACCAA
227
- ACCTCAGCCTCCATCACTATTTCAACCCAAAAAGGTTTAATCAAACTCTACTTCCTCTCT
228
- TTCCTCATCCCACTCCTCCTAATCCTCCTTATAATCTCATAACCTATTACCCCGAGCAAT
229
- CTCAATTACAACATAAACACCAACAAATAACGTTCAACCAGTAACCACCACCAACCAACG
230
- CCCATAATCATATAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCCGACCCTTC
231
- CCCTTCATAAATTATCCAGCTCCCCACGCTATTAAAATTCACCACTACCACCACTCCATC
232
- ATACTCTTTTACCCACAACACCAGCCCCACTTCCATCACTAATCCCACCAGAACACTCAC
233
- CAATACCTCAACCCCTGACCCCCATGCCTCAGGATATTCCTCAATAGCTATTGCCGTAGT
234
- ATACCCAAAAACAACCATCATACCCCCTAAATAAATTAAAAAAACCATTAAACCCATATA
235
- ACCTCCCCCACAATTTAAAATAACTGCACACCCAACCGCACCACTAATAATCAACACTAA
236
- ACCCCCATAAATAGGAGAGGGCTTAGAAGAAAACCCCACGAACCCTATCACTAAAATTAC
237
- ACTCAACAGAAACAAAGCATATGTCATTGTTCTCGCATAGACTGTGACTATGACCAATGG
238
- TATGAAAAAACATCGTTGTACCTCAACTACAAGAACACTAATGACCTCAACACGTAAAAC
239
- CAACCCACTAATAAAATTAATCAACCACTCACTTATCGACCTCCCCACCCCATCAAACAT
240
- CTCCGCATGATGGAACTTCGGCTCACTCCTAGGCGCCTGCTTAATCATCCAAATCACCAC
241
- TGGACTATTCCTAGCTATACATTATTCACCAGACGCCTCCACTGCCTTTTCATCAATCGC
242
- CCACATCACTCGAGATGTAAACTACGGCTGAATAATTCGCCACCTCCACGCTAACGGCGC
243
- CTCAATATTCTTTATCTGCCTCTTCTTACATATCGGCCGAGGCCTATACTATGGCTCATT
244
- CACCCACCTAGAAACCTGAAACATCGGCATCATCCTACTATTTACAACTATAATAACAGC
245
- CTTCATAGGTTACGTCCTCCCATGAGGCCAAATATCCTTCTGAGGAGCCACAGTAATCAC
246
- AAATCTACTGTCCGCCATCCCATACATTGGAACAGACCTGGTCCAATGAGTCTGAGGTGG
247
- CTACTCAGTAAATAGCCCCACTCTAACACGATTCTTCACCCTACACTTCATACTACCCTT
248
- CATTATTACAGCCCTAACAACTCTACACCTCTTATTCCTACACGAAACAGGATCAAATAA
249
- CCCCCTGGGAATCCCCTCCCATTCCGACAAAATCACCTTCCACCCCTACTACACAATCAA
250
- AGACATCCTAGGCCTACTCCTTTTTCTCCTCGCCCTAATAACACTAACACTACTCTCACC
251
- AGACCTCCTAAGCGACCCAGACAACTACACCTTAGCTAACCCCCTAAGCACCCCACCCCA
252
- CATTAAACCCGAATGATATTTCCTATTCGCCTACGCAATCCTACGATCCGTCCCCAACAA
253
- ACTAGGAGGTGTAATAGCCCTCATACTATCCATCCTAATCCTAACAACAATCCCTGCCCT
254
- TCACATGTCCAAGCAACAGAGCATAACATTTCGCCCATTGAGCCAATTCCTATATTGACT
255
- TTTAATCGCCGACCTTCTAATTCTCACCTGAATTGGAGGGCAACCAGTAAGCTACCCCTT
256
- CATCACCATTAGCCAAGTAGCATCCACATTGTACTTCACTACTATCCTTCTACTTATACC
257
- AGCCTCTTCCCTGATCGAAAACCACATACTCAAATGAACCTGCCCCTGTAGTACAAATAA
258
- GTACACCAGCCTTGTAACCTGAAAATGAAGACCCTCTTCCATGGGCAAAAAAAATCAGAG
259
- AAAAAGCACTTAACTTCACCGTCAGCCCCCAAAGCCAACATTCTAATTTTAAACTACTCT
260
- CTGTTCTTTCATGGGGGACCAGATTTGGGTGCCACCCCAGTACTGACCCATTTCTAACGG
261
- CCTATGTATTTCGTACATTCCTGCTAGCCAACATGAATATCACCCAACACAACAATCGCT
262
- TAACCAACTATAATGCATACAAAACTCCAACCACACTCGACCTCCACACCCCGCTTACAA
263
- GCAAGTACCCCCCCATGCCCCCCCACCCAAACACATACACCGATCTCTCCACATAACCCC
264
- TCAACCCCCAGCATATCAACAGACCAAACAAACCTTAAAGTACATAGCACATACTATCCT
265
- AACCGCACATAGCACATCCCGTTAAAACCCTGCTCATCCCCACGGATGCCCCCCCTCAGT
266
- TAGTAATCCCTTACTCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCC
267
- CCTCGCTCCGGGCCCATAAAACCTGGGGGTAGCTAAAGTGAGCTGTATCCGGCATCTGGT
268
- TCTTACTTCAGGGCCATAAAACCCAAGATCGCCCACACGTTCCCCTTAAATAAGACATCA
269
- CGATGGATCACAGGCCTATCACCCTATTAATCACTCACGGGAGCTCTCCATGCATCTGGT
270
- ATTTTTTCGGGGGGGGATGCACGCGATAGCATCGCGGGCCGCTGGAACCGGAGCACCCTA
271
- TGTCGCAGGATCTGTCTTTGATTCCTACCTCATGCCATTATTAATCGCGCCTAATATCCA
272
- ATATCCTAGCCCCACCCTCAGTGTTTGAAGCTGCTATTTAATTTATGCTAGAGGACATAA
273
- AATTACCAAAAAAAAATAAACGAACTCTCAACAACCCTACCCCATCAACCCAACAAAATC
274
- CAATTTTTATCTTTAGGCTATGTGCACTTTCAACAGGCACCCCTCAACTAACACAATCTC
275
- CTTCTTATCCCACCCACCAACCCCCCCCCCCCCTTCCTCCCTCTTTCTCCATTTTCCCCA
276
- CAAACACCGCTACTACCCCCACACCCCAGACCAACCCAACCCAAAAGACACCCCGCACG
data/ext/minimap2/test/q-inv.fa DELETED
@@ -1,4 +0,0 @@
1
- >read1
2
- CCCAGAGCCTCCAAAAGTATAGTGGTCTGCGATACCTTTGATTTACGGACCTAGAAGATTCCATTTGGGGACCTCGCACTCGTCATAAGATCATTAAATCTGTGATGTTTCGAGCCACTAAGTTGGTGGGAATTGATTAAGCAGTATAGGGTTTGTGCTGTGTCCTCACGCCAAACTCATCTTGAGATTTTAGCTCCCATAATTTCCTATGTGTTGTGGGGTAGCGAAATCCAGTGGGAGACAATTGAATCATGAGCATACGTTTTCCCCTTGCTGTCTCTCAATGGTGGTGAAAAGTCTCATGTGATCTGATGGTTTTTATTAAGGGGAAACCCCTTTCACTTGGTCCTCAAGTGTCTCTCTTTGTCTGCTTCCATGTAAGATGCTGCCTTTCACCTTCATGCCATCGAATTGTGAGGCCTCCCACAGCCACCATGCAACGTATGAGTACATTATAGGCTGCTTTATTCTTTATAAATATCCAGTCTTCAGGTATGCATTTATGGGCAGTGTGAAAACAGACTAATATAAGCAGCAATGGAAGGCTAACACAACGTGCCCTAAAGGCCATGTGCAAACAATCCCGTTCATTTAGGACAGCCACTCTGGCCTTCCTGTCAGTGACTCCCAATTCTCTCCCCCACAGGTGCCCACTGTCACCACACGAGCGAAGACTTACTTTACCATTGCTGTAGAACTGTTCCCCCTCTTTATGCTCATGTTATCCAAGCTCCAGCGAACATACTGTAATCTTTTGTTCTTGGACGGAATCTTGTTTATTCTACCTCCTCTGTGTAGTTGGGTGCTTGGCCTGCTGAATCAAACTGAGGTGGGAATCTTACCTTGGGGGCATGCCCTAGATCCCCAGTGGGGTAGCTTGGCTTCTCGAGTCCCCATAGTATCCTGGACCACGGGAGTGGACATTCTAAGTGCCCTCATGGTTTAGTTTGATTCTGGGTAAAGACGGGCTCGCACAAGGTATTGATAGCAGATAACTAGAAATATCACCCAATTTTTAGATCACAACTTATTTCTAAGTGTCTGGGTAAACCAAAAGCATTATTTTATATTTTCATAGTCAACCATACTGCATCGCACACTACAGACAACTGTACCTTCCAACATGAAGGTAAGAGGATAAATCATCACATATTTAAATTAGGGCATGCTAGAAAACCCCCAACAGCCAATCAGAGGACAAGCAAGAGCATGGGTCATTCCACAGGGGAATACGGGTCCATAAGGTGCTGGGCACTGGCCAGCAGAGTATCACCTAACTCCTCAATGCAAGCCAAGGGAAAAGAAGGGCTGGAGGCTTGCCGACAAACGTTTCCCAGAGCAACAGTTCTACAACTGATGTTGCCCAAACAGTTGCAGTCTTAATTACCCAATAGTAGTCAAAGAACAAAACTTTGAGAATAGCTTACAGAAATGAAAAACCCATAAGGGCAGAATCAAGAGCAATATCTTTTTCAAACAGATTTAGCATAGTTAGTAATTAGTTTCCAAGATATTCTGCACTGCTAAGCAGGCTTTCCTGAATAAATGGATATACGTTTATTTCCTAGGGCTCTTATAACATAACTTACACCAAACTCGATGGTCTTAACCAACAGAAATTTATTCTCTCATAGTTCGCTGGAGACTAGAAGTTCAAAAATCAAGGTTGTCAGTAGCACCATACTCTCCTGAAACCTCTAAGAAGGAATGCTTCTCTGCATTCTTCCAGCTGCTGGTAGACTCCTGCAATTCTTGGCTTGTGGGTGCCTCACTTTGATCTCTGCCTCCATCTTGGTCCCATGGCCATTCGTCCCTGTGTGTCTTGGCTTGGTCCTCCCGTTGTGTCACGTCTGCTCCATGCATCGTCTTCTCTTGGAATTAGGACCCACCATAATGACCTCATCTTTAACAACTTAGTGAGCCATCCTGCGAAAGACCCGTTCGGTTAGATTCTCAGGTTAGTCATAACCCAGATACCAGACTTCGTGTTTTAAAACAACAGAAATGATTTCCAATTTATCATCCGTGTCCCTTAGCAAAGGACATGAACCTCATCATATTTTTATGGCTGACAGTAGTTCCGTGGTGTATATGTGCCACAATTTTCTTAATCCAGTCTATATGTTGGACATTTGGGTTCGGTTCCAAGTCTTTTGCTAATTGTGAATAGTGCCGCAATAAACAATACGTGTGCATGGTCTTTATGAGCAGCATATTATAGTCCTTTGGGGTATATACCGCAGTAATGTGGATGGCTGGGGTCAAATGGTATATTCTAGTTGTCTAGATCCCGTGAGGAATCAGCACACTGACGTCCACAAATTGGTTGAACTAAGTTTACCAGTTCCCACCAACAGTGTAAAAAGTGTTCCTGGTTTCTCCACATCCTCATCCAGCACCTGTTGCTTTCCCATGACTTTTTAATTGATTGCCATTTTTAACTGGTGTGAGATGGTAATCTCATTGTGGTTTTGGTTTGCAATTTCTCTGATGTGCCAGTGATGATGAGCATTTTTGTCTATGTGTCTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTCTCTGTTCATATCCTTTCCCAACCTTTTTGATGGGGTTGTTTTGTTTTTTTACTTGTAAACTTTGATTTGAGTTCATTGTAGATTCTGGATATTTAGCCCTTTGTCAGATGAGCAGGTTGTGAAAATTTTATCTCCATTTTGCTGAGGTTGCCTGTTCACTCTGATAGGTAGTTTCTTTGGCTGTGCAGAAGCTTTAGGGACATGATGGACAATTAGAAATCATCATTCTCAGTAAACTATTGCGAAGGACAAAAAACCAAACAATCGCATGTTCTCACTCAATAGATGGGGATTGAACAATGAGAACACATGGACACAGGAAGGGGAACACTCTGGGGACTGTGTTGGGTGTGGGGAGAGGGGGAAGGGAATAGCATTAGGAGGAATGAACCTAAATGCTAAATGATGAGTCTAATGGGTGCAGCACACCAGCATGGCACAATGTATACATACTGTAACTAACCTGGCACCGATGTGTGCACATGGACCCGTAAAATCTTAAAGTTATAATAATAATTAAAAAAAAGAAAAGTAACGTCAAATGATATCGATATGTTAACATCAATAACTGAATTGTTGATGAAAGCAAAAGAAATCTCTCAATTGATTGGAATGCTATTAGAAGTCAAGCCTTGGTAGCACCAAAGCTAGAAAAACAAGATAAGTCACAAGAAAAACGGGTAGAGAAGATGATGTTCATGCATTACAGCCCTGGCGTTTCAGCTTCCCTTCTTTTTGGCGTTATATATGTTCTTGTACCTTCCATGGAGAGACCAGTTGTGCATTTAAATGGGATGTTTGTTATATTTTTTATCCAAAATTTCTAGATGTTTTAAAGTCGTCTTTTAGGTTTATCTATTCTACCAGCGTGCCCAAAACAGCGGATGGAAAAGGGATGCGAATGAGATGTCAGAGCTATAGCTGCACTGGTCCCCCGACGTGCAACTCCAACCATAATTATCCTGAAGCCTGCAAACAGAGAATATAATGAGCACTAAAAGAAACTGATCTTGATTAAAGGAGAAAATAAAGATAAAAGTTATGATAAGCAATAATGATTGTGGTGATGACAGTAGAGAAAATAGCACAACAGCATACGAAACTGTGGAGGAAGCAGGACCCACAGCTATTGTAACAACTGGGTCGAATATAGATAACCTTACTGGAGATTGACAGAAAAAAAACTAGATGGATTTAAACTCATGAATAAAATTCCCTAGTACCCTGTATTGGTTACGGTTAGCAACGTGGGCACCCTCTTGGAATAAAAAAAAAAAAAATTTATTCTGTTGGCACTCTCTTCTCTGGATCACATTGTATTCTGTCATTGGTCCGTAAAATTTAGATACCCACAATTGAACATACTCCTCTAGATACTGGATCTAGCTAATGCAAAAGAACTGCGCCTTCCAACTTGTTCAGATCATCATATGTTTGTTGTCAAACGCTAAGTTGAGTTGTATCGTTTTAAGTTTAGTTTTTTTTGGACCTGGAAAAACATCATGTGAGGAATAGAGGTTATGAGAATGTTTAAAACTGGGAGGAAAAATGGCAGCAAGAGAGAATATGATCATGTCTTCAAATAATTCAGAATACCATTGTTGCTGATCAAAAAGAAGAAATCGCCCTCTATTAAACTAGGGACTTCAAGTCTTGGTCTCTTACTCATTCTCTCTTTCCTTCACTTCATATCAAAGGAAGCATCCTTCTGTTTCATTAACACTAAATTCGTCCACTGTGTGCTCTTTATTCTATGCATTGCTGCCTTCTTCTTGATATTTTCGATCATCTCCTTCCTTCTTGCTCTTCAAGGCCAATCTTTCTCCTATTAAAGCATTACATCTTCCGACTTCATTTTAAAAACAGAAACAAATGACCAATAGAACTCGTGTGAACCTGCTTTCACTTCAAGCTTTCTATCCGCTAATCTTATTTCTTTTATTCCACACTTTAAGAAAAGTCATCTTCCCTCTTTTAGGGCACAATTTTTGACCTAGTTTTGTTACTGCTGTATCCTCTGGCACATAGTAGCACTCAATAAATATAGCTGATAAATGAATTGATTACATGAAAAAAAAATAAACAACAGCAAATGTATTTCTAAGTTCTGGAGGCTGAAGTTCGAGATCAATGTACACAATTCAGTTCTCAGTGACGGTCTCTCTTCGTGGCTTGTAGATATCTGCCTTCTTGATCCTGTGTCCTTTTATACTAGAAAGAGAGGTAAATGCTTTTTTTCCTGCCTTTTCTAGTAAGGCCACATCCTCCTGTTGGTTTAGGGCCCACTAACCCACTTGACCTTGCATTGAACCTTAAATTCACCTCTCTTAAAGATACTCTGTCTCTAGGTATAGTCACACTGGGGGGCTAGGGCTTAGAAATATGAATTTGGTGAGGGACACGAATTTAGCTCCCATAGAACCTCAATTTCAAATAAAATCACAGTTTATAGACACCAAAGTGGTTTTGAACTTCAATGTATCTTTGTATGGGAATAATTCACCCCTCAAACAAAAGGTCATCAGTGGTGAGGGGTTCCCGTAAAATGTGTCTAGGATTGGCATTGTCCCCTGGAGGTGACTCCCAGAGATGCCCATCCTCCATGTATGCCCCTGGTGACATACCCATACCGAGAAGAGAGACTCTCCGTGCACCCCTCGGGGGGTCCTGAAATCCCAAGAGCCAACAGGTTAGCGTCGCATGGATGAGCCTTGGGAAAGCTAGCACTTCCCTTGCCTACACTTCCGACACAGGCCCAGGAAGGATCCCACAAGCCTCAGGCTAGCAGCAGCCCATCAGCGTTGGCAAGGGAAAAGCACAACCCTCCCACAGGGCCCAAGCTGTGCCCGTTGGCCTGTGGCACTGGGGGCTTTTGCCCTCTTCTTCTGCTGACAGATACACTTCGACATTGTGAACACTTACAGGGGTGCCCGAGTCATTTTCCTTCTTGTTTTATGACACTGATTGGTTGCCATAATGCCGATTCTGTAGCGTGGATCTGTACCTGTGCTGGAGGGCATTTGACACACCCAAAGACCATCCTAAGTGAGCTTGGAAAGTGGGGCGAGAGACCTGGAAGTCTAGACACAAGCAGAACCACCGTTAGCTCGGGAAGCTAGAGAGCCTCCTTGCTCCCT
3
- >read2
4
- AAACTAGGCAAAAACTTGTGCCTAAAAGAGGGAAGATGACTTTTCTTAAAGTGTGGAATAAAGAAAAGTAAGATAGCGGATAGAAGCGTTGAAGTGAAAGCAGGTTCACAGGAAGTTTCTTTGGTCATTATGTTTTGTTTTTAGAATAGTGGAAAGATGTATATGTTTATGGAGAAAGATTGCCTTGAAGATGCAAGAGGAAGAGATGATCAAAATTCAAGAGAAGGCATGAAAGTGATAGAATAAAGAGCACAAGTGGAGAATTAGTGTTAATGAAAAGAAGGATGCTTCCTTTGATATGAAGTGAAGGAAGAGAGAATGAGTAAAGACCAAGACTTGAAGTCCCTAGTTTAATAGAGGGAGATTTCTTCTTTGTGATAGCAACAATGGTATTCGTGAATTATTTGAAGACATGTCATATTTCTCTTGATAGCCATTTTCCTCCCAGTTTTAAACATTCTCATAACCTCTATTCCTCACATGATGTTTTTCCAGAGTCCAAAACAAAAACAAAACTTAAAAGATAACAACTCAACTTAGCGTTTGACAACAAACATATGATGTCTGAACAAGTTGGAAGGCAGCAGTTCTTTTGCATTAGCTAGACCATATCTAGAGGAGTATGTTCAATTGTGGGTATCTAAATTTTAGGACCAATGACAGAATACAATGTGTCCAGAGAAGAGAGTGCCAAAGAATAAATTTTTTTTTTCTTTTAATTCCAACGAGGTGCCCACGTTGGCTAAGTACCAAACAGGGTACTAGGGAATTTTACTTCTGAGTTAAATGGCCATTCTAGTTGTTTTTTCTTCATCTCCAGTAAGGTTATTCTTTATTCACCAGTTGTTACAATAGCTGTGGGTCTTGCTTCTCACAGTTTTATGCTGTCTGTGCTATTTTCTCTACTGATCATCAACCACAATCATTATTGCTTATCATAATTGTTATCTTTATTTTCTCCTTTAATCTAAGAATCAGTCTTCCTTTATCTCATTATTCTCTTTTGCAGGCTTCAGGATAATTATGGTTGGAGTGCACTGGGGGAACCAGTGCAGCTAAGCTCTGACATCTTTGCATCCCCTTTATCCATCTGCTGTTTTGGCACTCTGGTAGAATAGATAACCTAAAAACGACTTTTAAAACATCTAGAAATTTTGGATAAAATATAACAAACATCCCGCTTTAAATGCACAACTGATCTTCCATGGAGAGTCACAGAAATAGTATAACGCCAACAAAGAAGGGAAGCTGAAACCCAGGGCTGTAACATGAACATCATCTTCTCTCCCTTTTTCTTGTGATTTCTTGTTTTTCTCAGCTTTGGTGCTACCAAGGCTTGAACTTTAATAGCATTTCCAATCAATGAGAGAATTTCCTTTTTGCTTTCATCAACAATTCAGTTATTGATGTCTAACATATATATCATTTGAGTACTTTTCTTTTTTTATTATTATTATACTTATAAGTTTTAGGGTCCATGGTGCACAATGTGCAGGTTAGTTACTGTATGTATACATGTGCCATGCTGTGTGCTGCACCCATTAACTCATCATTTAGCATTAGGTATAGTCTCCTAATGCTATCCCTTCCCCCTCTCCCCACCCCACAACAGTCCCCAGAGTGTTCCCCTTCCTGTGTCCATGTGTTCTCATTGTTCAATCCCCATCTATGAGTGAGAACATGCGTGTGTTTGGTTTTTGTCCTTGCAATAGTTTACTGAGAATGATGATTTCTAATTTCATCCATGTCCCTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGCGCAACCTACAAAATGGGAGAAAATTTTCACAACCCTGCTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTACAAACAAATTTACAAGAAACAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGACAGACACTGTCTCAAAAGAAGACATTTTATGCAGCCAAAAGACACATGAAAAAATGCTTCATCATCACTGGCCATCAGAGAAATGCAAACCAAAACCACAATGAGATAACCATTCACACCAGTTAAAATGGCAATCATTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAACAGGAACACTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGTCAGTGTGCTGATTCCTCAGGGATCTAGAACTTAGAAATACCATTTGGACCCAGCCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTGTATTGCGGCACTATTCACAATAGCAAAGACTTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATTAAGGAAAAATTGTGGCACATATACACCACGGAATACTGTGCAGCCATAAAAAATGAGTGAGTTCATGTCCTTTGTAGGGACACGGATGAAATTGGAAATCATTTCTGTTGTTTAAACCACGAAGTCTATGGTATCTGGTTATGACAACCTGAGAATACTAACTCAAGGGTCTTTCGCAGATGTCATTAAGTCTGTTAAAGTGAGGTCAATTATGGTGGGTCCTTAATCCAAGAGAAGAAGATGCATGGACACAGACGTGCACAATCGGGAGGACCAAGCCAAGACACACAGGGAGAATGGCCATGGGAAGATGGAGGCAGAGATCAAAGTGAGGCACCCACAAGCCAAGAAATGGCAGGAGCTACCCAGCAGCTGGAAGATGCAGAGAAGCATTCCTTCTTAGAGGTTTCAGAGAGAGTATGGTGCTACTGACACGCTTGATTTTGAACTTCTAGTCTCCAGAACTATGAGAGAATAAATTTCTGTTGGTTAAGCCATCGAGTTGTGTAGAGTTTGTTATAAGAGCCCTAGGAAATAAACATATCCATTTATTCAGGAAAGGCCTGGCTAGAGTGCAAATATTTGGACAAAGATCACTACTATGCAAATGTTTGAAAAAGATATTGCTGCTTGATTCTGCCTTATGGGTTTTTTCATTTCTGTAAGCTATTCTCAAAGTTTTGTTCTTGGACTACTATTGGTAATTAAGACTGCAACATGTTTGGCAACATCAGTTGAGAACTGCTTGCTCTGGGAACGTTTTCGGGCAAGCCTCGAGCCCTTCTTTTCCCTTGGCTTGCATTGAGGAGTAGGTGATACTCTGCTGCTGCAGGCCCAGCACCTTTATGGACCGTATTCCCCTGGTGGAATGACCATCTCTGCTTGCTCTAGATTGGCCTTGTTGGGGTTTTCTAGCATGCCCTATTTAATATGTATGATTTATCTCTTACATTCAGTTGGAAGGTACAGTTGCTCTGCTAGTTGGGCATGCAGTCATGGTGACTATGAAAATATAAAATAACTGTTTTGGTTGTCAGACACTTAGAAATAAGTTGTGTCTCAAAATTGGGTGACTATTCTAGTTATCTGCTACTCAATATCCTTGTGCGAGCCCTCTTTACCCAGAATCAAACTAAACCATGAGTGGGCACTATAGAATGTCACCCCTGGGTCTCAGGGATACTATGGGGACTCAGCAAGCCAAGCTCCCACTGGGGGATCTGAGGGCATGCCCCCAAGGTAAGATTCCCACCTCTTTGTTCAGCAGGAAGCACCCATCACACAAGGAGGTAGGAATAAACAAGCATTCGTCAAGAACAAAAGATACAGATGTTCTGCTGGAGCTTGGATACATAGCATAAGAGGGAACAGTTCTCACATGGTAAGAGTAAGTTTTCCTCTGGTGGTGACAGTGGGACCTGTGGGGGGAGAGAATTGGGAGTACTGACAGGAAGGCAGAGTGGCTGTCCAAATGAACGGAATTGTTTGCACATGGCCTTTAGGGCACGTTGTGTTAGCCTTCCATTGCTGCTTGATATTAGTCTGTTTTCACACTGCCCATAACAATGCATACCTTGAGACTGGATAATTTATAAAGAAAAAGAGCCTTAATGTACTCATAGTTGCATGTGGCTGGGGAGGCCTCACAATCATGGCAGAAGGTGAAAGGCACATCTTACATGGAAGCAGACAAGAGAGAATTGAGGACCAAGTGAAAGGGGTTTCCCCTTATAAAACCATCAGATCACATGAGACTTTTTCACCACCATGAGAACAGTAAGGGGAAAACTATGCTCATGATTCAATTGTCTCCCACTGGATTCCTCCCAACAACACATAGGAATTATGGGAGCTAAAATTCAAGATGAGATTTGGGTGCAGGACACAGCCAAACCCTATCACTGCTGTAATCAATTCCCACCAACTTAGTGGCTCGAAACATCACAGATTTATGATCTTATGACGGTGGAGGTCCCCAAATGGATCTTCTAGGTCTAGAATCAAGGTATCAGCAGACCACTTTCTTTTGGAGGCTCTGGTGGATGAAACCATTTCCTCGCCTTTTCCAGCTTCTAGAGGCTGCCCTTCTCATTCCTTGGTTCACGGCCACACTCATTTCCATCTCTGCTTCCACTGTGACAACTTCTCTGCCTCAGACCCCTCCTGCTTTGCCTTTGTAAGGACCCTTGTTGATGAGATCAGGCCCATCCAGGATTATCCCTCATCTCAAGACCTTTACCTTAATCACATTTGCAAGGTCTCTTCCACTGTGTCAGGCTAACATTTTCACAGGTTCCAGGGATTAGGGTGTGGACATCTTGGGGAGCTGGAGGATATTATTTCATCTACCACCACATCTCTACCTTGTACAGGCAAGCACTTGCAAAGTGCAATGTGATCCTCTGGAGCCACTGTCCTCTCCAAGAGCTTATATACTACTCTGAAAGTCAACTCTCGAGACCACAGCCTCCTGTCCATGCACCACTCTCATCAACACCCCCACCCGAAACACTTTCACTCCACCCTCTTTGTCCCCTAACTCATGGAGAAGAAAATCTAATTAGTAGGAGTGGAAATTTGGCTTTCATTCTTTACCAGTACTAGAAATATGGTGTGTGTCTTTTTGTAAAAATTCTCTCAACTAAATTGTTTTTATTAATTTCTGCAAAATGTGAACATCAACTCCCTTCATGTGAATGTCACATAAGATTAAATGAGCTGTCTCAGCTCCTAGCCTGTGCAAGTCTAACAGCTCAGGAGATGTTTATTTCTTTCCCTCTTCTTTCCTTAATGAAGCCCTCTCCTTTGACCATCCTTCAATTCTAGGAGCGCTTCTTTTCTGAGGCCTTGGCTCCCCCACATTGCCCACCCTTTCTCCTGCTCGTCCACATTTCTGGCTTCTATTCTCTTGTCTTTACCATCTCCCTGAACAATGTTATCGCGTTCCAATGACTTCAACAGTCTCTCCAGCTTACATATGATGCCTCTCAAACTCTGATCTCCAAACTCTTCCAAAGAGCTCTGGACCTTTGTTCCAATTACCTGAAAAACCATCTTCTTGGATGTCCCATTAGCACTGTTAAATCAAACAAGAATTTCCCTCCCTCCTGCCTTGCTGTAGTTCCCCTAGGGATTCGGTTGTGTGGGAAGATGTGTGGAGAGCTCTTAGTTAGACTCCCTTCTCTGCAGTTCTA
data/ext/minimap2/test/q2.fa DELETED
@@ -1,2 +0,0 @@
1
- >q2
2
- GGACATCCCGATGGTGCAGTCCTACCTGTACGAAAGGAC
data/ext/minimap2/test/t-inv.fa DELETED
@@ -1,127 +0,0 @@
1
- >ref
2
- TGCGGAGGCTGAAGCAACTCCATCTTGGAAGCTAATCTACCATGTTGGCTTCTGATTAAC
3
- ATCAGTTCTGGGAAGGCTTGTAAGATTTCCTGTTTGTCTATTATTTCCTAGGTAAGAGCA
4
- GATACTTACTGTAAATCCTGCCCCTAGATTAAACAACCTTGGTGTTATCGTACTTCCATT
5
- GTCCTATACATCCCTTCGGAATCCCCCTTTCCCTATGGTCCTCAAGCCCTTGGTCTGGGG
6
- AGTAACAGCATAGGGATCAACCATCTCGTCTTGCCACTGCCCGAAATACAGACATGGCTT
7
- CTGTTCCTAAGTCCCTATTCAACTTTTCTTTCTAAGAAACTGGATTTGTCAGCCTCTTTC
8
- TTCACCTCTCAGCTTCCTTGGACTTTGGGGGTAGGTTTGCGTAGACATGCTCACCACAGA
9
- CACAATATCAGCTTCATTCTACAGATGAGGAAGGCAAGCCTTGGGGAGCTTAACCAACTT
10
- GTCGAGACTCATGTATATACCAACACTGAAAAGCAGATATTCCAGACTCCCAGTCATGCC
11
- ACAGGCACACCCCTCAGTGAGAGGTGGGGTTTGTAGTTGAGGCTATTTCCTGCCCAGGGA
12
- GCAGGGAGGCACTCTAGCTTCCCTGAGCTAACGTGGTTCTGCTTGTGTCTGACTTCCAGG
13
- TCTCTGCCCTTTCCAAGCTCACTAGGATGGGCTTCGGGTGTGTCAAATGCCTCAGACAGT
14
- ACAGATCCACACAGAATGGGCATATGCAACCAATCAGTGTCATAAAAAAGAAGGAAATGA
15
- CTCGGGCCCCCTGTGTGTTCAACATGTCGAAGGTATCTGTGCAGCAGAAGAAAGAGGGGC
16
- AAAAGCCCCCAGTGCCACAGGCCAGAGGCAGCAGCTTGGGCCCATGTGGGAGGGTTTGCT
17
- TTCCCCTGCCAAAGTGATGGGCTGCTGCAGCCTGGGGCTTGTGGGAATCCTTCCTGGGCC
18
- TGTGTGGGAAGTGTAGGCAGGGAGAGTGCTGCTTTCCCAAGCTCATCCCAGCTACAGCTA
19
- CCTTTGTGCTCTGGGATTCAGGACCCCCGAGGGGGCTGGCAGGAGAGTCTCTGTTCTCGG
20
- ATGGGTTGTCACCAGGGCATACATGGGAAGTGGGCTCTCTGGAGTCACCCTCCAGGGGAC
21
- AATGCCAATTCCAGACACATTTACTGGAACCCCTACACTGATGACCTTTTGTTGAGGGTT
22
- GAATTATGTCCCCAAAAAAGATACATTGAAGTCCAAACCTCTGGTGTCTATAAATGTGAT
23
- TTTATTTGAAAATGAGGTTTCTATGGACTAAATTGTGTCCCTCCCAAATTCATATTTTGA
24
- AGCCCTAGCCCCCAGTGTGACTATACCTAGAGACAGAGATCTTTAGGAGGTAATTAAGGT
25
- TCAATGAGGTCAGGTGGGTGGGGCCCTAAACCAACAGGAAGGACTGTGGCCTTACTAGAA
26
- AAGGAAGAAAAAGCATTTCCTCTCTTCTAGTATAAAAGGACACAGAAAGAAGGCAGATAT
27
- CTACAAGCCACGAAGAGAGACGTCACTGAGAACTGAATTTGTGTACATTGATCTGGAACT
28
- TCCAGCCTCCAGAACTTGAGAAATACATTTCTGTTGTTTATTTTTTTTTCATGTAATCAA
29
- TTCATTTATCATATATTTATTGAGTGCCTACTATGTGCCAGAGGATACAGCAGTAACAAA
30
- ACTAGGCAAAAATTGTGCCTAAAAGAGGGAAGATGACTTTTCTTAAAGTGTGGAATAAAG
31
- AAAAGTAAGATAGCGGATAGAAGCTTGAAGTGAAAGCAGGTTCACAGGAAGTTTCTTTGG
32
- TCATTTGTTTTGTTTTTAAATAGTGGAAAGATGTATATGTTTATGGAGAAAGATTGCCTT
33
- GAAGATGCAAGAGGAAGAGATGATCAAAATTCAAGAAGAAGCAGAAAGTGATAGAATAAA
34
- GAGCACAAGTGGAGAATTAGTGTTAATGAAAAGAAGGATGCTTCCTTTGATATGAAGTGA
35
- AGGAAGAGAGAATGAGTAAAGACCAAGACTTGAAGTCCCTAGTTTAATAGAGGGAGATTT
36
- CTTCTTTTGATAGCAACAATGGTATTCTGAATTATTTGAAGACATGTCATATTTCTCTTG
37
- TGCCATTTTCCTCCCAGTTTAAACATTCTCATAACCTCTATTCCTCACATGATGTTTTTC
38
- CAGGTCCTTTATTCTTTGGCACTCTCTTCTCTGGACACATTGTATTCTGTCATTGGTCCT
39
- AAAATTTAGATACCCACAATTGAACATACTCCTCTAGATATGGTCTAGCTAATGCAAAAG
40
- AACTGCTGCCTTCCAACTTGTTCAGACATCATATGTTTGTTGTCAAACGCTAAGTTGAGT
41
- TGTTATCTTTTAAGTTTTGTTTTTGTTTTTTTTTTTTTTTTTTAATTCCAAGAGGTGCCC
42
- ACGTTGGCTAAGTACCAAACAGGGTACTAGGGAATTTTACTTCTGAGTTAAATGCCATTC
43
- TAGTTGTTTTTTCTTCATCTCCAGTAAGGTTATCTTTATTCACCAGTTGTTACAATAGCT
44
- GTGGGTCTTGCTTCTCACAGTTTTATGCTGTCTGTGCTATTTTCTCTACTGATCATCACC
45
- ACAATCATTATTGCTTATCATAATTGTTATCTTTATTTTCTCCTTTAATCAAGAATCAGT
46
- CTTCCTTTATCTCATTATTCTCTTTTGCAGGCTTCAGGATAATTATGGTTGGAGTGCACT
47
- GGGGGAACCAGTGCAGCTAAGCTCTGACATCTTTGCATCCCTTTTCCATCTGCTGTTTTG
48
- GCACTCTGGTAGAATAGATAACCTAAAAACGACTTTAAAACATCTAGAAATTTTGGATAA
49
- AATATAACAAACATCCCTTTAAATGCACAACTGATCTTCCATGGAAGTCACAGAAATATA
50
- TAACGCCAAAAAGAAGGGAAGCTGAAACCCAGGGCTGTAAACATGAACATCATCTTCTCT
51
- CCCTTTTTCTTGTGACTTATCTTGTTTTTCTCAGCTTTGGTGCTACCAAGGCTTGACTTT
52
- AATAGGCATTTCCAATCAATGAGAGAATTTCTTTTGCTTTCATCAACAATTCAGTTATTG
53
- ATGTTAACATATATATCATTTGAGTACTTTTCTTTTTTTTATTATTATTATACTTTAAGT
54
- TTTAGGGTCCATGTGCACAATGTGCAGGTTAGTTACGTATGTATACATGTGCCATGCTGG
55
- TGTGCTGCACCCATTAACTCATCATTTAGCATTAGGTATATCTCCTAATGCTATCCCTTC
56
- CCCCTCTCCCCACCCCACAACAGTCCCCAGAGTGTTCCCCTTCCTGTGTCCATGTGTTCT
57
- CATTGTTCAATCCCCATCTATGAGTGAGAACATGCGGTGTTTGGTTTTTTGTCCTTGCAA
58
- TAGTTTACTGAGAATGATGATTTCTAATTTCATCCATGTCCCTAAAGAGCTTCTGCACAG
59
- CAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAAAATGGGAGAAAATTTTCACAA
60
- CCTGCTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACA
61
- AGAAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTCAA
62
- AAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATCATCACTGGCCATCA
63
- GAGAAATGCAAACCAAAACCACAATGAGATACCATCTCACACCAGTTAAAATGGCAATCA
64
- TTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAACAGGAACACTTTTAC
65
- ACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGTCAGTGTGCTGATTCCTCA
66
- GGGATCTAGAACTAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCCAA
67
- AGGACTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTATTGCGGCACTAT
68
- TCACAATAGCAAAGACTTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATTAAGA
69
- AAATGTGGCACATATACACCACGGAATACTGTGCAGCCATAAAAAATGATGAGTTCATGT
70
- CCTTTGTAGGGACACGGATGAAATTGGAAATCATTTCTGTTGTTTAAACCACGAAGTCTA
71
- TGGTATCTGGTTATGACAACCTGAGAATACTAACTCAAGGGTCTTTCGCAGATGTCATTA
72
- AGTTGTTAAAGTGAGGTCATTATGGTGGGTCCTAATCCAAGAGAAGAGATGCATGGACAG
73
- ACGTGCACAACGGGAGGACCAAGCCAAGACACACAGGGAGAATGGCCATGGGAAGATGGA
74
- GGCAGAGATCAAAGTGAGGCACCCACAAGCCAAGAAATGGCAGGAGCTACCAGCAGCTGG
75
- AAGATGCAGAGAAGCATTCCTTCTTAGAGGTTTCAGAGAGAGTATGGTGCTACTGACACC
76
- TTGATTTTGAACTTCTAGTCTCCAGAACTATGAGAGAATAAATTTCTGTTGGTTAAGCCA
77
- TCGAGTTTGTGTAAGTTTGTTATAAGAGCCCTAGGAAATAAACATATCCATTTATTCAGG
78
- AAAGCCTGCTAGAGTGCAAATATTTGGAAAAGATACTACTATGCAAATGTTTGAAAAAGA
79
- TATTGCTCTTGATTCTGCCTTATGGGTTTTTCATTTCTGTAAGCTATTCTCAAAGTTTTG
80
- TTCTTGGACTACTATTGGTAATTAAGACTGCAACATGTTTGGCAACATCAGTTGAGAACT
81
- GTTGCTCTGGGAACGTTTTCGGCAAGCCTCAGCCCTTCTTTTCCCTTGGCTTGCATTGAG
82
- GAGTTAGGTGATACTCTGCTGCTCAGGCCCAGCACCTTTATGGACCGTATTCCCCTGGTG
83
- GAATGACCATCTCTGCTTGCTCTGATTGGCTGTTGGGGTTTTCTAGCATGCCCTATTTAA
84
- TATGTATGATTTATCTCTTACTTCAGTTGGAAGGTACAGTTGCTCTGTAGTTGGCATGCA
85
- GTCATGGTGACTATGAAAATATAAAATAATGTTTTGGTTTACAGACACTTAGAAATAAGT
86
- TGTGTCTCAAAATTGGGTGACTATTCTAGTTATCTGCTACTCAATATCCTTGTGCGAGCC
87
- CTCTTTACCCAGAATCAAACTAAACCATGAGGGGCACTATAGAATGTCACCCCTGGGTCC
88
- AGGATACTATGGGGACTCAGAAGCCAAGCTCCCACTGGGGGATCTAGGGCATGCCCCCAA
89
- GGTAAGATTCCCACCTCTTTGTTCAGCAGGAAGCACCCATCACACAAGGAGGTAGGAATA
90
- AACAAGCATTCGTCAAGAACAAAAGATACAGATGTTCTGCTGGAGCTTGGATACATAGCA
91
- TAAGAGGGAACAGTTCTCACAGGTAAGAGTAAGTTTTCCTCTGGTGGTGACAGTGGGACC
92
- TGTGGGGGAGAGAATTGGGAGTACTGACAGGAAGGCAGAGTGGCTGTCCAAATGAACGGA
93
- TTGTTTGCACATGGCCTTTAGGGCACGTTGTGTTAGCCTTCCATTGCTGCTTATATTAGT
94
- CTGTTTTCACACTGCCCATAAATGCATACCTGAGACTGGATAATTTATAAAGAAAAAGAG
95
- CCTTAATGTACTCATAGTTGCATGTGGCTGGGGAGGCCTCACAATCATGGCAGAAGGTGA
96
- AAGGCACATCTTACATGGAAGCAGACAAGAGAGAATTGAGGACCAAGTGAAAGGGGTTTC
97
- CCCTTATAAAACCATCAGATCACATGAGACTTTTTCACCACCATGAGAACAGTAAGGGGA
98
- AAACTATGCTCATGATTCAATTGTCTCCCACTGGATTCCTCCCACAACACATAGGAATTA
99
- TGGGAGCTAAAATTCAAGATGAGATTTGGGTGAGGACACAGCCAAACCCTATCACTGCTG
100
- TAATCAATTCCCACCAACTTAGTGGCTCGAAACATCACAGATTTATGATCTTATGACGGT
101
- GGAGGTCCCCAAATGGATCTTCTAGGTCTAGAATCAAGGTATCAGCAGACCACTTCTTTT
102
- GGAGGCTCTGGTGGAGAAACCATTTCCTCGCCTTTTCCAGCTTCTAGAGGCTGCCCTTCT
103
- CATTCCTTGGTTCACGGCCACACTCATTTCCATCTCTGCTTCCACTGTGACAACTTCTCT
104
- GCCTCAGACCCTCCTGCTTTGCCTTTGTAAGGACCCTTGTGATGAGATCAGGCCCATCCA
105
- GGATTATCCCTCATCTCAAGACCTTTACCTTAATCACATTTGCAAGGTCTCTTCCACTGT
106
- GTCAGGTAACATTTTCACAGGTTCCAGGGATTAGGGTGTGGACATCTTGGGGAGCTGGAG
107
- GATATTATTTCATCTACCACACACATCTCTACCTTGTACAGGCAAGCACTTGCAAAGTGC
108
- AATGTGATCCTCTGGAGCCACTGTCCTCCCAGAGCTTATATATACTCTGAAAGTCAACTC
109
- TCAGACCACAGCCTCCTGTCCATGCACCACTCTCATCAACACCCCCACCCGAAACACTTT
110
- CACTCCACCCTCTTTGTCCCCTAACTCATGGAGAAGAAAATCTAATTAGTAGGAGTGGAA
111
- TTTGGCTTTCATCTTTACCAGTACTAGAAATATGGTGTGTGTCTTTTTGTAAAAATTCTC
112
- TCAACTAAATTGTTTTTATTAATTTCTGCAAAATGTGAACATCAACTCCCTTCATGTGAA
113
- TGTCAATAAGATTAAATGAGCTGTCTCAGCTCCTAGCCTGTGCAAGCTAACAGCTCAGGA
114
- GATGTTTATTTCTTTCCCTCTTCTTTCCTTAATGAAGCCCTCTCCTTTGACATCTTCAAT
115
- TCTGGAGCGCTTCTTTTCTGAGGCCTTGGCTCCCCCACATTGCCCACCCTTTTCCTGCTC
116
- GTCCACATTTCTGGCTTCTATTCTCTTGTCTTTACCATCTCCCTGAACAATGTTATCCGT
117
- TCCAATGACTTCAACAGTCTCTCCGCTTACATATGATGCCTCTCAAACTCTGATCTCCAA
118
- CTCTTCCAAAGAGCTCTGGACCTTTGTTCCAATTACCTGAAAAACATCTTCTTGGATGTC
119
- CCATTAGCACTGTTAAATCAAACAAGAATTTCCCTCCCTCCTGCCTTGCTGTAGTTCCCC
120
- TAGGGATTCGGTTGTGTGGGAAGATGTGTGGAGAGCTCTTAGTTGACTCCCTTCTCTGCA
121
- GTTCTACCTCTCTAGAGACTTGGAGGACCCACTGTTTCCGCCTCGCTTTTTCAGGCCTAG
122
- AGATTGCTCGCTCCTGGGCTGGCTGCTTCATAATTCCTTATTAGTAGTTTCCCAAGCTTA
123
- CATATCTGTAAATATTTACTTTAGTTAAATTCTCCCCAATTTCCACAATATGTTGGCTGC
124
- ACATGCTTTCTACTAGGAGTCACACAACTATGATAAGAACCAAGAAATATTAGTAAACGT
125
- TTTTTACCATTATTGGCCTATACCCTGGAATAGCCAACAATAACCTAGAACCTATGCAAC
126
- AAGAATATCCAACAAGAACCTAGAGACCTGTCAGTCTATAGGTGGGAACTACAGGATGAG
127
- A
data/ext/minimap2/test/t2.fa DELETED
@@ -1,2 +0,0 @@
1
- >t2
2
- GGACATCCCGATGGTGCAGgtGCTATTAAAGGTTCGTTTGTTCAACGATTAAagTCCTACCTGTACGAAAGGAC
data/ext/minimap2/test/x3s-aln.txt DELETED
@@ -1,5 +0,0 @@
1
- mm2: TGTTATCCCTAGGGTAACTTGTTCCGTTGGTCAAGTTATTGGATCAATTGAGTATAGTAGTGCACTCAC......................................................................................................................................CACTTGGAGCCATTCATACAGGTCCCTATTTAAGGAACAAGTGATTATGCTACCTTTGCACGGTT
2
- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3
- ref: TGTTATCCCTAGGGTAACTTGTTCCGTTGGTCAAGTTATTGGATCAATTGAGTATAGTAGTGCACTCACctGCTTCGCTTTGACTGGTGAAGTCTTAGCATGTACTGCTCGGAGGTTGGGTTCTGCTCCGAGGTCGCCCCAACCGAAATTTTTAATGCAGGTTTGGTAGTTTAGGACCTGTGGGTTTGTTAGGCTAACCTCacCACTTGGAGCCATTCATACAGGTCCCTATTTAAGGAACAAGTGATTATGCTACCTTTGCACGGTT
4
- |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
5
- sta: TGTTATCCCTAGGGTAACTTGTTCCGTTGGTCAAGTTATTGGATCAATTGAGTATAGTAGTGCA......................................................................................................................................CTCACCACTTGGAGCCATTCATACAGGTCCCTATTTAAGGAACAAGTGATTATGCTACCTTTGCACGGTT
data/ext/minimap2/test/x3s-qry.fa DELETED
@@ -1,5 +0,0 @@
1
- >query
2
- AACCGTGCAAAGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCC
3
- AAGTG
4
- GTGAGTGCA
5
- CTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA
data/ext/minimap2/test/x3s-ref.fa DELETED
@@ -1,10 +0,0 @@
1
- >ref
2
- TGATCCAACATCGAGGTCGTAAACCCTATTGTTGATATGGACTCTAGAATAGGATTGCGC
3
- TGTTATCCCTAGGGTAACTTGTTCCGTTGGTCAAGTTATTGGATCAATTGAGTATAGTAG
4
- TGCACTCAC
5
- ctGCTTCGCTTTGACTGGTGAAGTCTTAGCATGTACTGCTCGGAGGTTGGGTTCTGCTCC
6
- GAGGTCGCCCCAACCGAAATTTTTAATGCAGGTTTGGTAGTTTAGGACCTGTGGGTTTGT
7
- TAGGCTAACCTCac
8
- CACTTGGAGCCATTCATACAGGTCCCTATTTAAGGAACAAGTGATTATGCTACCTTTGCA
9
- CGGTTAGGGTACCGCGGCCGTTAAACATGTGTCACTGGGCAGGCGGTGCCTCTAATACTG
10
- GTGAT
data/ext/minimap2/tex/Makefile DELETED
@@ -1,21 +0,0 @@
1
- .SUFFIXES: .gp .tex .eps .pdf .eps.gz
2
-
3
- .eps.pdf:
4
- epstopdf --outfile $@ $<
5
-
6
- .eps.gz.pdf:
7
- gzip -dc $< | epstopdf --filter > $@
8
-
9
- .pdf.eps:
10
- pdftops -eps $< $@
11
-
12
- all:minimap2.pdf
13
-
14
- roc-color.eps:roc.gp
15
- gnuplot roc.gp
16
-
17
- minimap2.pdf:minimap2.tex minimap2.bib roc-color.pdf
18
- pdflatex minimap2; bibtex minimap2; pdflatex minimap2; pdflatex minimap2;
19
-
20
- clean:
21
- rm -fr *.toc *.aux *.bbl *.blg *.idx *.log *.out *~ minimap2.pdf