qu-cmdwrapper 1.0.0

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Files changed (67) hide show
  1. checksums.yaml +7 -0
  2. data/.gitignore +17 -0
  3. data/Gemfile +5 -0
  4. data/LICENSE.txt +22 -0
  5. data/README.md +32 -0
  6. data/Rakefile +1 -0
  7. data/lib/qu/cmdwrapper.rb +10 -0
  8. data/lib/qu/cmdwrapper/cmd.rb +109 -0
  9. data/lib/qu/cmdwrapper/ext_bin/linux/32/faToTwoBit +0 -0
  10. data/lib/qu/cmdwrapper/ext_bin/linux/32/ntdpal +0 -0
  11. data/lib/qu/cmdwrapper/ext_bin/linux/32/ntthal +0 -0
  12. data/lib/qu/cmdwrapper/ext_bin/linux/32/oligotm +0 -0
  13. data/lib/qu/cmdwrapper/ext_bin/linux/32/primer3_core +0 -0
  14. data/lib/qu/cmdwrapper/ext_bin/linux/32/twoBitToFa +0 -0
  15. data/lib/qu/cmdwrapper/ext_bin/linux/64/faToTwoBit +0 -0
  16. data/lib/qu/cmdwrapper/ext_bin/linux/64/ntdpal +0 -0
  17. data/lib/qu/cmdwrapper/ext_bin/linux/64/ntthal +0 -0
  18. data/lib/qu/cmdwrapper/ext_bin/linux/64/oligotm +0 -0
  19. data/lib/qu/cmdwrapper/ext_bin/linux/64/primer3_core +0 -0
  20. data/lib/qu/cmdwrapper/ext_bin/linux/64/twoBitToFa +0 -0
  21. data/lib/qu/cmdwrapper/ext_bin/mac/32/faToTwoBit +0 -0
  22. data/lib/qu/cmdwrapper/ext_bin/mac/32/ntthal +0 -0
  23. data/lib/qu/cmdwrapper/ext_bin/mac/32/oligotm +0 -0
  24. data/lib/qu/cmdwrapper/ext_bin/mac/32/primer3_core +0 -0
  25. data/lib/qu/cmdwrapper/ext_bin/mac/32/twoBitToFa +0 -0
  26. data/lib/qu/cmdwrapper/ext_bin/mac/64/faToTwoBit +0 -0
  27. data/lib/qu/cmdwrapper/ext_bin/mac/64/ntthal +0 -0
  28. data/lib/qu/cmdwrapper/ext_bin/mac/64/oligotm +0 -0
  29. data/lib/qu/cmdwrapper/ext_bin/mac/64/primer3_core +0 -0
  30. data/lib/qu/cmdwrapper/ext_bin/mac/64/twoBitToFa +0 -0
  31. data/lib/qu/cmdwrapper/primer3_config/dangle.dh +128 -0
  32. data/lib/qu/cmdwrapper/primer3_config/dangle.ds +128 -0
  33. data/lib/qu/cmdwrapper/primer3_config/interpretations/dangle_i.dh +131 -0
  34. data/lib/qu/cmdwrapper/primer3_config/interpretations/dangle_i.ds +131 -0
  35. data/lib/qu/cmdwrapper/primer3_config/interpretations/loops_i.dh +34 -0
  36. data/lib/qu/cmdwrapper/primer3_config/interpretations/loops_i.ds +31 -0
  37. data/lib/qu/cmdwrapper/primer3_config/interpretations/stack_i.dh +257 -0
  38. data/lib/qu/cmdwrapper/primer3_config/interpretations/stack_i.ds +256 -0
  39. data/lib/qu/cmdwrapper/primer3_config/interpretations/stackmm_i_mm.dh +257 -0
  40. data/lib/qu/cmdwrapper/primer3_config/interpretations/stackmm_i_mm.ds +256 -0
  41. data/lib/qu/cmdwrapper/primer3_config/interpretations/tetraloop_i.dh +79 -0
  42. data/lib/qu/cmdwrapper/primer3_config/interpretations/tetraloop_i.ds +81 -0
  43. data/lib/qu/cmdwrapper/primer3_config/interpretations/triloop_i.dh +21 -0
  44. data/lib/qu/cmdwrapper/primer3_config/interpretations/triloop_i.ds +18 -0
  45. data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack2_i.dh +256 -0
  46. data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack2_i.ds +256 -0
  47. data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack_i.dh +256 -0
  48. data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack_i.ds +256 -0
  49. data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack_tm_inf_i.dh +256 -0
  50. data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack_tm_inf_i.ds +256 -0
  51. data/lib/qu/cmdwrapper/primer3_config/loops.dh +30 -0
  52. data/lib/qu/cmdwrapper/primer3_config/loops.ds +30 -0
  53. data/lib/qu/cmdwrapper/primer3_config/stack.dh +256 -0
  54. data/lib/qu/cmdwrapper/primer3_config/stack.ds +256 -0
  55. data/lib/qu/cmdwrapper/primer3_config/stackmm.dh +256 -0
  56. data/lib/qu/cmdwrapper/primer3_config/stackmm.ds +256 -0
  57. data/lib/qu/cmdwrapper/primer3_config/tetraloop.dh +77 -0
  58. data/lib/qu/cmdwrapper/primer3_config/tetraloop.ds +77 -0
  59. data/lib/qu/cmdwrapper/primer3_config/triloop.dh +16 -0
  60. data/lib/qu/cmdwrapper/primer3_config/triloop.ds +16 -0
  61. data/lib/qu/cmdwrapper/primer3_config/tstack.dh +256 -0
  62. data/lib/qu/cmdwrapper/primer3_config/tstack2.dh +256 -0
  63. data/lib/qu/cmdwrapper/primer3_config/tstack2.ds +256 -0
  64. data/lib/qu/cmdwrapper/primer3_config/tstack_tm_inf.ds +256 -0
  65. data/lib/qu/cmdwrapper/version.rb +5 -0
  66. data/qu-cmdwrapper.gemspec +24 -0
  67. metadata +137 -0
data/lib/qu/cmdwrapper/primer3_config/stackmm.dh ADDED
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data/lib/qu/cmdwrapper/primer3_config/stackmm.ds ADDED
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