bio-faster 0.2.2 → 0.4.2

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Files changed (63) hide show
  1. data/.travis.yml +2 -3
  2. data/Gemfile +2 -0
  3. data/Gemfile.lock +2 -0
  4. data/LICENSE.txt +1 -1
  5. data/README.md +2 -3
  6. data/Rakefile +9 -15
  7. data/VERSION +1 -1
  8. data/bio-faster.gemspec +56 -12
  9. data/ext/faster.c +115 -52
  10. data/ext/mkrf_conf.rb +40 -0
  11. data/lib/bio-faster.rb +5 -4
  12. data/lib/bio/faster.rb +57 -0
  13. data/lib/bio/faster/library.rb +26 -0
  14. data/spec/fastq_error_spec.rb +55 -0
  15. data/spec/parser_spec.rb +28 -116
  16. data/test/data/errors/error_header.fastq +20 -0
  17. data/test/data/errors/error_long_qual.fastq +20 -0
  18. data/test/data/errors/error_qual_del.fastq +20 -0
  19. data/test/data/errors/error_qual_escape.fastq +20 -0
  20. data/test/data/errors/error_qual_null.fastq +0 -0
  21. data/test/data/errors/error_qual_space.fastq +20 -0
  22. data/test/data/errors/error_qual_tab.fastq +20 -0
  23. data/test/data/errors/error_qual_unit_sep.fastq +20 -0
  24. data/test/data/errors/error_qual_vtab.fastq +20 -0
  25. data/test/data/errors/error_spaces.fastq +20 -0
  26. data/test/data/errors/error_tabs.fastq +21 -0
  27. data/test/data/errors/error_trunc_at_qual.fastq +19 -0
  28. data/test/data/errors/error_trunc_at_seq.fastq +18 -0
  29. data/test/data/errors/error_trunc_in_qual.fastq +20 -0
  30. data/test/data/errors/error_trunc_in_seq.fastq +18 -0
  31. data/test/data/formats/illumina_full_range_as_illumina.fastq +8 -0
  32. data/test/data/formats/illumina_full_range_as_sanger.fastq +8 -0
  33. data/test/data/formats/illumina_full_range_as_solexa.fastq +8 -0
  34. data/test/data/formats/illumina_full_range_original_illumina.fastq +8 -0
  35. data/test/data/formats/longreads_as_illumina.fastq +40 -0
  36. data/test/data/formats/longreads_as_sanger.fastq +40 -0
  37. data/test/data/formats/longreads_as_solexa.fastq +40 -0
  38. data/test/data/formats/misc_dna_as_illumina.fastq +16 -0
  39. data/test/data/formats/misc_dna_as_sanger.fastq +16 -0
  40. data/test/data/formats/misc_dna_as_solexa.fastq +16 -0
  41. data/test/data/formats/misc_dna_original_sanger.fastq +16 -0
  42. data/test/data/formats/misc_rna_as_illumina.fastq +16 -0
  43. data/test/data/formats/misc_rna_as_sanger.fastq +16 -0
  44. data/test/data/formats/misc_rna_as_solexa.fastq +16 -0
  45. data/test/data/formats/misc_rna_original_sanger.fastq +16 -0
  46. data/test/data/formats/sanger_full_range_as_illumina.fastq +8 -0
  47. data/test/data/formats/sanger_full_range_as_sanger.fastq +8 -0
  48. data/test/data/formats/sanger_full_range_as_solexa.fastq +8 -0
  49. data/test/data/formats/sanger_full_range_original_sanger.fastq +8 -0
  50. data/test/data/formats/solexa_full_range_as_illumina.fastq +8 -0
  51. data/test/data/formats/solexa_full_range_as_sanger.fastq +8 -0
  52. data/test/data/formats/solexa_full_range_as_solexa.fastq +8 -0
  53. data/test/data/formats/solexa_full_range_original_solexa.fastq +8 -0
  54. data/test/data/formats/wrapping_as_illumina.fastq +12 -0
  55. data/test/data/formats/wrapping_as_sanger.fastq +12 -0
  56. data/test/data/formats/wrapping_as_solexa.fastq +12 -0
  57. metadata +88 -24
  58. data/ext/extconf.rb +0 -7
  59. data/ext/kseq.h +0 -223
  60. data/test/data/sample.fasta +0 -10
  61. data/test/data/sample.fastq +0 -24
  62. data/test/data/sample.fastq.gz +0 -0
  63. data/test/data/sff_sample.fastq +0 -16
data/test/data/sample.fasta DELETED
@@ -1,10 +0,0 @@
1
- >seq1 comment1
2
- AGCAATTTCCCTTTTCCTGTCCTTTTTATAACATTGTGGAGGAAGACGGCAGCATAAAAAGGACAGTATTTGATTAAAAAATGATAAAAATTTTCAAAC
3
- >seq2 comment 2
4
- GTGGGGCCAAAGGGGTTTGGAGGTGCCTTGTTCTTAGTCCCCAGAAGACTAGAGAGACTGCGTTTCAGGGAGGAGGAGATAAGACGAGCAGGAGACTTC
5
-
6
- >seq3 comment3
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- CTCATAGACACGGTCCGAGGAGCCAAACACCAAGCTGTTGGGGAAGACTCGGCTGAGGAACTGCAGGGGCCCAAGCCACGACTGGATGAGGAGCAGTGA
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-
9
- >seq4
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- mgltrrealssiaavggekalkdalavlggps
data/test/data/sample.fastq DELETED
@@ -1,24 +0,0 @@
1
- @HISEQ1:86:D0306ACXX:2:1101:20970:17588 1:N:0:CTTGTA
2
- CGGTGCTGTTGTTATGCTGATGCTTATTAGTGCAAGTGTAGCTCCTCCGATTAGATGAATTAACAGGTGTCCTGCAGTAATGTTGGCTGTTAGTCGTAC
3
- +
4
- @C@:DDFFHGHHHIJJJJIGIJIJJCHIGGHGIIJJGGHGIJIGJJIJJGGIIBGGCFIAFGF4CGI;AHIFGIEHEEH>EDFFEFFD@AECCDCBDD<
5
- @HISEQ1:86:D0306ACXX:2:1101:20839:17705 1:N:0:CTTGTA
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- AGCAATTTCCCTTTTCCTGTCCTTTTTATAACATTGTGGAGGAAGACGGCAGCATAAAAAGGACAGTATTTGATTAAAAAATGATAAAAATTTTCAAAC
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- +
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- @@<DFFFFHBDHHJEAFHIJJEHIIIJGHGIGEHGEEGGCGGDG>@GB:@DBGGIIGBGEHHIGFE:@A?B>?>;>>>@;>BCA@>ACCC?:A>;>>@3
9
- @HISEQ1:86:D0306ACXX:2:1101:21047:17715 1:Y:0:CTTGTA
10
- GTTAAGAATCTGCCTGCCAATGCAGGAGATGCAAGAGATGCAAGAGACGTGGGTTCCATAGCTGGGTCAGGAAAATTACCTGAAGGAGGACATATCAAA
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- +
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- =7+2?@++?4?7A7+++<+++3+3<AA<;3A@A9AA###############################################################
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- @HISEQ1:86:D0306ACXX:2:1101:21299:17513 1:N:0:CTTGTA
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- GTAGCACACTTTCACTATGTCCTATCAATAGGAGCTGTGTTCGCCATTATAGGAGGATTTGTAAATTGATTTCCACTGTTCTCATACTATAACCTAAAA
15
- +
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- 8:?;=;B?;B>+A,<AEACEDE@AFF,A:99CEF@E*1??:CDII:?@*9?@*9D:BCB@.88>AAAA)==4==7=C;==);@################
17
- @HISEQ1:86:D0306ACXX:2:1101:1352:17782 1:N:0:CTTGTA
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- AATAATTGTTTGCATTGCCTTTTATATATATTTATATATATATATAAAACATGGGTCTTGGTTTTTTGATTTATTAGTGTGAAGAAATAACTACATTCT
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- +
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- @<?DABADHGFA<,CECFIHGIIDEGG@DHGDGI<<CHEBCEGIIIGCD<CFGC=09?<F@GEHIDHI=A:C;EH>3?EE;?C@@DDFA>@>@>C3;AC
21
- @HISEQ1:86:D0306ACXX:2:1101:1411:17830 1:Y:0:CTTGTA
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- CGGCGGGCGTGGGGAGAGAGCTATGAAGGCCTCAGGGAAGCTTCGAGAGTATAAGGTGTTGGGGTGCTGCCTGCCAACCCCCAAATTCCACACACCACC
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- +
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- ###################################################################################################
data/test/data/sample.fastq.gz DELETED
Binary file
data/test/data/sff_sample.fastq DELETED
@@ -1,16 +0,0 @@
1
- @SRR014849.1 EIXKN4201CFU84/1
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- GGGGGGGGGGGGGGGGCTTTTTTTGTTTGGAACCGAAAGGGTTTTGAATTTCAAACCCTTTTCGGTTTCCAACCTTCCAAAGCAATGCCAATACTGAGCGGGCTGGCAAGGCNNNNNNNNNNNN
3
- +
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- 3+&$#"""""""""""7F@71,'";C?,B;?6B;:EA1EA1EA5'9B:?:#9EA0D@2EA5':>5?:%A;A8A;?9B;D@/=<?7=9<2A8==<=5<6:?:$::9.;:0:/3!!!!!!!!!!!!
5
- @SRR014849.2 EIXKN4201AKDUH/1
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- TCAAGTGGTGAACGGCAGAAA
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- +
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- <=B:==B:=<?6=B;<;=B=)
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- @SRR014849.3 EIXKN4201D4ZBL/1
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- GGGGGGGGGCTGTTGGCCGAGGTTGGAGTAGCCAGGGGGAAGGCATGGCCAGCCGTTGAGAAATGCTTGTTGAAGTTTTCGATAATAATGGATTTATCGGTGGTGACCGTGTTACCTAGCC
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- +
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- ;3.*(&$"";<=A9@8A9;<B;B;B;8=<==B;<FB8/'@8B:==<B;A9<<A8=B;==;A=)=<<B;=A9<@7<FB5(<<=<B;<B;:A9=EA0;<;B:<A8=<<@8<<<B;<A99=<B:
13
- @SRR014849.4 EIXKN4201AHFLR/1
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- GGGGTTCAAGAATATGCCCC
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- +
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- B8/&?9<B;=B;=<9<FB5(