minimap2 0.2.22.0 → 0.2.24.1

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 (101) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +60 -76
  3. data/ext/Rakefile +55 -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 +821 -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 +369 -0
  41. data/ext/minimap2/main.c +459 -0
  42. data/ext/minimap2/map.c +714 -0
  43. data/ext/minimap2/minimap.h +410 -0
  44. data/ext/minimap2/minimap2.1 +725 -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 +132 -0
  50. data/ext/minimap2/options.c +234 -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/lib/minimap2/aligner.rb +4 -4
  93. data/lib/minimap2/alignment.rb +11 -11
  94. data/lib/minimap2/ffi/constants.rb +20 -16
  95. data/lib/minimap2/ffi/functions.rb +5 -0
  96. data/lib/minimap2/ffi.rb +4 -5
  97. data/lib/minimap2/version.rb +2 -2
  98. data/lib/minimap2.rb +51 -15
  99. metadata +97 -79
  100. data/lib/minimap2/ffi_helper.rb +0 -53
  101. data/vendor/libminimap2.so +0 -0
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
@@ -0,0 +1,2 @@
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:
10
+ pdftops -eps $< $@
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+
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+ all:minimap2.pdf
13
+
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+ roc-color.eps:roc.gp
15
+ 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