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
@@ -0,0 +1,460 @@
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+ @article{Chaisson:2012aa,
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+ Journal = {BMC Bioinformatics},
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+ Title = {Aligning sequence reads, clone sequences and assembly contigs with {BWA-MEM}},
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+ Author = {Iwata, Hiroaki and Gotoh, Osamu},
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+ Author = {Jain, Chirag and others},
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+ Pages = {i111-i118},
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+ Title = {Weighted minimizer sampling improves long read mapping},
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+ Volume = {36},
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+ Year = {2020}}
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+ author = {Jain, Chirag and others},
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+ title = {A long read mapping method for highly repetitive reference sequences},
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+ elocation-id = {2020.11.01.363887},
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+ year = {2020},
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+ doi = {10.1101/2020.11.01.363887},
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+ publisher = {Cold Spring Harbor Laboratory},
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+ URL = {https://www.biorxiv.org/content/early/2020/11/02/2020.11.01.363887},
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+ eprint = {https://www.biorxiv.org/content/early/2020/11/02/2020.11.01.363887.full.pdf},
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+ journal = {bioRxiv}
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+ }
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+ Journal = {Genome Biol},
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+ Pages = {265},
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+ Title = {The design and construction of reference pangenome graphs with minigraph},
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+ Volume = {21},
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+ Year = {2020}}
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+ Author = {Ren, Jingwen and Chaisson, Mark J P},
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+ Journal = {PLoS Comput Biol},
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+ Pages = {e1009078},
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+ Title = {lra: A long read aligner for sequences and contigs},
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+ Volume = {17},
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+ Year = {2021}}
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+ @inproceedings{DBLP:conf/wabi/AbouelhodaO03,
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+ Author = {Mohamed Ibrahim Abouelhoda and Enno Ohlebusch},
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+ Booktitle = {Algorithms in Bioinformatics, Third International Workshop, {WABI} 2003, Budapest, Hungary, September 15-20, 2003, Proceedings},
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+ Crossref = {DBLP:conf/wabi/2003},
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+ Pages = {1--16},
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+ Title = {A Local Chaining Algorithm and Its Applications in Comparative Genomics},
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+ Year = {2003}}
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+ @article{Ono:2021aa,
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+ Author = {Ono, Yukiteru and others},
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+ Journal = {Bioinformatics},
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