minimap2 0.2.23.0 → 0.2.23.1

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Files changed (96) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +60 -76
  3. data/ext/Rakefile +41 -0
  4. data/ext/cmappy/cmappy.c +129 -0
  5. data/ext/cmappy/cmappy.h +44 -0
  6. data/ext/minimap2/FAQ.md +46 -0
  7. data/ext/minimap2/LICENSE.txt +24 -0
  8. data/ext/minimap2/MANIFEST.in +10 -0
  9. data/ext/minimap2/Makefile +132 -0
  10. data/ext/minimap2/Makefile.simde +97 -0
  11. data/ext/minimap2/NEWS.md +807 -0
  12. data/ext/minimap2/README.md +403 -0
  13. data/ext/minimap2/align.c +1020 -0
  14. data/ext/minimap2/bseq.c +169 -0
  15. data/ext/minimap2/bseq.h +64 -0
  16. data/ext/minimap2/code_of_conduct.md +30 -0
  17. data/ext/minimap2/cookbook.md +243 -0
  18. data/ext/minimap2/esterr.c +64 -0
  19. data/ext/minimap2/example.c +63 -0
  20. data/ext/minimap2/format.c +559 -0
  21. data/ext/minimap2/hit.c +466 -0
  22. data/ext/minimap2/index.c +775 -0
  23. data/ext/minimap2/kalloc.c +205 -0
  24. data/ext/minimap2/kalloc.h +76 -0
  25. data/ext/minimap2/kdq.h +132 -0
  26. data/ext/minimap2/ketopt.h +120 -0
  27. data/ext/minimap2/khash.h +615 -0
  28. data/ext/minimap2/krmq.h +474 -0
  29. data/ext/minimap2/kseq.h +256 -0
  30. data/ext/minimap2/ksort.h +153 -0
  31. data/ext/minimap2/ksw2.h +184 -0
  32. data/ext/minimap2/ksw2_dispatch.c +96 -0
  33. data/ext/minimap2/ksw2_extd2_sse.c +402 -0
  34. data/ext/minimap2/ksw2_exts2_sse.c +416 -0
  35. data/ext/minimap2/ksw2_extz2_sse.c +313 -0
  36. data/ext/minimap2/ksw2_ll_sse.c +152 -0
  37. data/ext/minimap2/kthread.c +159 -0
  38. data/ext/minimap2/kthread.h +15 -0
  39. data/ext/minimap2/kvec.h +105 -0
  40. data/ext/minimap2/lchain.c +344 -0
  41. data/ext/minimap2/main.c +455 -0
  42. data/ext/minimap2/map.c +714 -0
  43. data/ext/minimap2/minimap.h +409 -0
  44. data/ext/minimap2/minimap2.1 +722 -0
  45. data/ext/minimap2/misc/README.md +179 -0
  46. data/ext/minimap2/misc/mmphase.js +335 -0
  47. data/ext/minimap2/misc/paftools.js +3149 -0
  48. data/ext/minimap2/misc.c +162 -0
  49. data/ext/minimap2/mmpriv.h +131 -0
  50. data/ext/minimap2/options.c +233 -0
  51. data/ext/minimap2/pe.c +177 -0
  52. data/ext/minimap2/python/README.rst +196 -0
  53. data/ext/minimap2/python/cmappy.h +152 -0
  54. data/ext/minimap2/python/cmappy.pxd +153 -0
  55. data/ext/minimap2/python/mappy.pyx +273 -0
  56. data/ext/minimap2/python/minimap2.py +39 -0
  57. data/ext/minimap2/sdust.c +213 -0
  58. data/ext/minimap2/sdust.h +25 -0
  59. data/ext/minimap2/seed.c +131 -0
  60. data/ext/minimap2/setup.py +55 -0
  61. data/ext/minimap2/sketch.c +143 -0
  62. data/ext/minimap2/splitidx.c +84 -0
  63. data/ext/minimap2/sse2neon/emmintrin.h +1689 -0
  64. data/ext/minimap2/test/MT-human.fa +278 -0
  65. data/ext/minimap2/test/MT-orang.fa +276 -0
  66. data/ext/minimap2/test/q-inv.fa +4 -0
  67. data/ext/minimap2/test/q2.fa +2 -0
  68. data/ext/minimap2/test/t-inv.fa +127 -0
  69. data/ext/minimap2/test/t2.fa +2 -0
  70. data/ext/minimap2/tex/Makefile +21 -0
  71. data/ext/minimap2/tex/bioinfo.cls +930 -0
  72. data/ext/minimap2/tex/blasr-mc.eval +17 -0
  73. data/ext/minimap2/tex/bowtie2-s3.sam.eval +28 -0
  74. data/ext/minimap2/tex/bwa-s3.sam.eval +52 -0
  75. data/ext/minimap2/tex/bwa.eval +55 -0
  76. data/ext/minimap2/tex/eval2roc.pl +33 -0
  77. data/ext/minimap2/tex/graphmap.eval +4 -0
  78. data/ext/minimap2/tex/hs38-simu.sh +10 -0
  79. data/ext/minimap2/tex/minialign.eval +49 -0
  80. data/ext/minimap2/tex/minimap2.bib +460 -0
  81. data/ext/minimap2/tex/minimap2.tex +724 -0
  82. data/ext/minimap2/tex/mm2-s3.sam.eval +62 -0
  83. data/ext/minimap2/tex/mm2-update.tex +240 -0
  84. data/ext/minimap2/tex/mm2.approx.eval +12 -0
  85. data/ext/minimap2/tex/mm2.eval +13 -0
  86. data/ext/minimap2/tex/natbib.bst +1288 -0
  87. data/ext/minimap2/tex/natbib.sty +803 -0
  88. data/ext/minimap2/tex/ngmlr.eval +38 -0
  89. data/ext/minimap2/tex/roc.gp +60 -0
  90. data/ext/minimap2/tex/snap-s3.sam.eval +62 -0
  91. data/ext/minimap2.patch +19 -0
  92. data/{vendor → ext/vendor}/libminimap2.so +0 -0
  93. data/lib/minimap2/ffi/functions.rb +5 -0
  94. data/lib/minimap2/version.rb +1 -1
  95. data/lib/minimap2.rb +32 -0
  96. metadata +94 -4
data/ext/minimap2/test/t-inv.fa ADDED
@@ -0,0 +1,127 @@
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 ADDED
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1
+ >t2
2
+ GGACATCCCGATGGTGCAGgtGCTATTAAAGGTTCGTTTGTTCAACGATTAAagTCCTACCTGTACGAAAGGAC
data/ext/minimap2/tex/Makefile ADDED
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+ .SUFFIXES: .gp .tex .eps .pdf .eps.gz
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+
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+ .eps.pdf:
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+ epstopdf --outfile $@ $<
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+
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+ .eps.gz.pdf:
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+ gzip -dc $< | epstopdf --filter > $@
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+
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+ .pdf.eps:
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+ pdftops -eps $< $@
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+
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+ all:minimap2.pdf
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+
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+ roc-color.eps:roc.gp
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+ gnuplot roc.gp
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+
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+ minimap2.pdf:minimap2.tex minimap2.bib roc-color.pdf
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+ pdflatex minimap2; bibtex minimap2; pdflatex minimap2; pdflatex minimap2;
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+
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+ clean:
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+ rm -fr *.toc *.aux *.bbl *.blg *.idx *.log *.out *~ minimap2.pdf