minimap2 0.2.31.0 → 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 (66) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +47 -64
  3. data/ext/ruby_minimap2/extconf.rb +47 -0
  4. data/ext/ruby_minimap2/native_main.c +15 -0
  5. data/ext/ruby_minimap2/ruby_minimap2.c +1134 -0
  6. data/lib/minimap2/aligner.rb +66 -383
  7. data/lib/minimap2/alignment.rb +15 -8
  8. data/lib/minimap2/version.rb +2 -1
  9. data/lib/minimap2.rb +39 -110
  10. metadata +8 -89
  11. data/ext/Rakefile +0 -63
  12. data/ext/cmappy/cmappy.c +0 -134
  13. data/ext/cmappy/cmappy.h +0 -46
  14. data/ext/minimap2/FAQ.md +0 -46
  15. data/ext/minimap2/MANIFEST.in +0 -10
  16. data/ext/minimap2/Makefile.simde +0 -97
  17. data/ext/minimap2/NEWS.md +0 -1022
  18. data/ext/minimap2/README.md +0 -429
  19. data/ext/minimap2/code_of_conduct.md +0 -30
  20. data/ext/minimap2/cookbook.md +0 -243
  21. data/ext/minimap2/minimap2.1 +0 -844
  22. data/ext/minimap2/misc/README.md +0 -180
  23. data/ext/minimap2/misc/pafcluster.js +0 -241
  24. data/ext/minimap2/misc/paftools.js +0 -3830
  25. data/ext/minimap2/pyproject.toml +0 -2
  26. data/ext/minimap2/python/README.rst +0 -198
  27. data/ext/minimap2/python/cmappy.h +0 -152
  28. data/ext/minimap2/python/cmappy.pxd +0 -157
  29. data/ext/minimap2/python/mappy.pyx +0 -297
  30. data/ext/minimap2/python/minimap2.py +0 -43
  31. data/ext/minimap2/setup.py +0 -55
  32. data/ext/minimap2/test/MT-human.fa +0 -278
  33. data/ext/minimap2/test/MT-orang.fa +0 -276
  34. data/ext/minimap2/test/q-inv.fa +0 -4
  35. data/ext/minimap2/test/q2.fa +0 -2
  36. data/ext/minimap2/test/t-inv.fa +0 -127
  37. data/ext/minimap2/test/t2.fa +0 -2
  38. data/ext/minimap2/test/x3s-aln.txt +0 -5
  39. data/ext/minimap2/test/x3s-qry.fa +0 -5
  40. data/ext/minimap2/test/x3s-ref.fa +0 -10
  41. data/ext/minimap2/tex/Makefile +0 -21
  42. data/ext/minimap2/tex/bioinfo.cls +0 -930
  43. data/ext/minimap2/tex/blasr-mc.eval +0 -17
  44. data/ext/minimap2/tex/bowtie2-s3.sam.eval +0 -28
  45. data/ext/minimap2/tex/bwa-s3.sam.eval +0 -52
  46. data/ext/minimap2/tex/bwa.eval +0 -55
  47. data/ext/minimap2/tex/eval2roc.pl +0 -33
  48. data/ext/minimap2/tex/graphmap.eval +0 -4
  49. data/ext/minimap2/tex/hs38-simu.sh +0 -10
  50. data/ext/minimap2/tex/minialign.eval +0 -49
  51. data/ext/minimap2/tex/minimap2.bib +0 -460
  52. data/ext/minimap2/tex/minimap2.tex +0 -724
  53. data/ext/minimap2/tex/mm2-s3.sam.eval +0 -62
  54. data/ext/minimap2/tex/mm2-update.tex +0 -240
  55. data/ext/minimap2/tex/mm2.approx.eval +0 -12
  56. data/ext/minimap2/tex/mm2.eval +0 -13
  57. data/ext/minimap2/tex/natbib.bst +0 -1288
  58. data/ext/minimap2/tex/natbib.sty +0 -803
  59. data/ext/minimap2/tex/ngmlr.eval +0 -38
  60. data/ext/minimap2/tex/roc.gp +0 -60
  61. data/ext/minimap2/tex/snap-s3.sam.eval +0 -62
  62. data/ext/minimap2.patch +0 -19
  63. data/lib/minimap2/ffi/constants.rb +0 -267
  64. data/lib/minimap2/ffi/functions.rb +0 -245
  65. data/lib/minimap2/ffi/mappy.rb +0 -104
  66. data/lib/minimap2/ffi.rb +0 -27
data/ext/minimap2/Makefile.simde DELETED
@@ -1,97 +0,0 @@
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- CFLAGS= -g -Wall -O2 -Wc++-compat #-Wextra
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- CPPFLAGS= -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES
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- INCLUDES= -Ilib/simde
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- OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o lchain.o align.o hit.o map.o format.o pe.o seed.o esterr.o splitidx.o \
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- ksw2_extz2_simde.o ksw2_extd2_simde.o ksw2_exts2_simde.o ksw2_ll_simde.o
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- PROG= minimap2
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- PROG_EXTRA= sdust minimap2-lite
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- LIBS= -lm -lz -lpthread
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-
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-
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- ifneq ($(arm_neon),) # if arm_neon is defined
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- ifeq ($(aarch64),) #if aarch64 is not defined
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- CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char
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- else #if aarch64 is defined
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- CFLAGS+=-D_FILE_OFFSET_BITS=64 -fsigned-char
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- endif
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- endif
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-
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- ifneq ($(asan),)
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- CFLAGS+=-fsanitize=address
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- LIBS+=-fsanitize=address
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- endif
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-
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- ifneq ($(tsan),)
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- CFLAGS+=-fsanitize=thread
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- LIBS+=-fsanitize=thread
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- endif
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-
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- .PHONY:all extra clean depend
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- .SUFFIXES:.c .o
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-
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- .c.o:
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- $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
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-
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- all:$(PROG)
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-
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- extra:all $(PROG_EXTRA)
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-
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- minimap2:main.o libminimap2.a
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- $(CC) $(CFLAGS) main.o -o $@ -L. -lminimap2 $(LIBS)
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-
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- minimap2-lite:example.o libminimap2.a
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- $(CC) $(CFLAGS) $< -o $@ -L. -lminimap2 $(LIBS)
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-
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- libminimap2.a:$(OBJS)
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- $(AR) -csru $@ $(OBJS)
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-
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- sdust:sdust.c kalloc.o kalloc.h kdq.h kvec.h kseq.h ketopt.h sdust.h
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- $(CC) -D_SDUST_MAIN $(CFLAGS) $< kalloc.o -o $@ -lz
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-
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- ksw2_ll_simde.o:ksw2_ll_sse.c ksw2.h kalloc.h
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- $(CC) -c $(CFLAGS) -msse2 $(CPPFLAGS) $(INCLUDES) $< -o $@
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-
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- ksw2_extz2_simde.o:ksw2_extz2_sse.c ksw2.h kalloc.h
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- $(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@
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-
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- ksw2_extd2_simde.o:ksw2_extd2_sse.c ksw2.h kalloc.h
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- $(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@
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-
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- ksw2_exts2_simde.o:ksw2_exts2_sse.c ksw2.h kalloc.h
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- $(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@
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-
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- # other non-file targets
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-
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- clean:
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- rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy*.so mappy.c python/mappy.c mappy.egg*
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-
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- depend:
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- (LC_ALL=C; export LC_ALL; makedepend -Y -- $(CFLAGS) $(CPPFLAGS) -- *.c)
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-
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- # DO NOT DELETE
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-
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- align.o: minimap.h mmpriv.h bseq.h kseq.h ksw2.h kalloc.h
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- bseq.o: bseq.h kvec.h kalloc.h kseq.h
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- chain.o: minimap.h mmpriv.h bseq.h kseq.h kalloc.h
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- esterr.o: mmpriv.h minimap.h bseq.h kseq.h
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- example.o: minimap.h kseq.h
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- format.o: kalloc.h mmpriv.h minimap.h bseq.h kseq.h
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- hit.o: mmpriv.h minimap.h bseq.h kseq.h kalloc.h khash.h
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- index.o: kthread.h bseq.h minimap.h mmpriv.h kseq.h kvec.h kalloc.h khash.h
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- index.o: ksort.h
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- kalloc.o: kalloc.h
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- ksw2_extd2_sse.o: ksw2.h kalloc.h
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- ksw2_exts2_sse.o: ksw2.h kalloc.h
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- ksw2_extz2_sse.o: ksw2.h kalloc.h
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- ksw2_ll_sse.o: ksw2.h kalloc.h
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- kthread.o: kthread.h
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- main.o: bseq.h minimap.h mmpriv.h kseq.h ketopt.h
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- map.o: kthread.h kvec.h kalloc.h sdust.h mmpriv.h minimap.h bseq.h kseq.h
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- map.o: khash.h ksort.h
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- misc.o: mmpriv.h minimap.h bseq.h kseq.h ksort.h
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- options.o: mmpriv.h minimap.h bseq.h kseq.h
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- pe.o: mmpriv.h minimap.h bseq.h kseq.h kvec.h kalloc.h ksort.h
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- sdust.o: kalloc.h kdq.h kvec.h sdust.h
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- self-chain.o: minimap.h kseq.h
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- sketch.o: kvec.h kalloc.h mmpriv.h minimap.h bseq.h kseq.h
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- splitidx.o: mmpriv.h minimap.h bseq.h kseq.h