bio-faster 0.2.2 → 0.4.2

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 (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/errors/error_qual_unit_sep.fastq ADDED
@@ -0,0 +1,20 @@
1
+ @SLXA-B3_649_FC8437_R1_1_1_610_79
2
+ GATGTGCAATACCTTTGTAGAGGAA
3
+ +SLXA-B3_649_FC8437_R1_1_1_610_79
4
+ YYYYYYYYYYYYYYYYYYWYWYYSU
5
+ @SLXA-B3_649_FC8437_R1_1_1_397_389
6
+ GGTTTGAGAAAGAGAAATGAGATAA
7
+ +SLXA-B3_649_FC8437_R1_1_1_397_389
8
+ YYYYYYYYYWYYYYWWYYYWYWYWW
9
+ @SLXA-B3_649_FC8437_R1_1_1_850_123
10
+ GAGGGTGTTGATCATGATGATGGCG
11
+ +SLXA-B3_649_FC8437_R1_1_1_850_123
12
+ YYYYYYYYYYYYWYYWYYSYYYSY
13
+ @SLXA-B3_649_FC8437_R1_1_1_362_549
14
+ GGAAACAAAGTTTTTCTCAACATAG
15
+ +SLXA-B3_649_FC8437_R1_1_1_362_549
16
+ YYYYYYYYYYYYYYYYYYWWWWYWY
17
+ @SLXA-B3_649_FC8437_R1_1_1_183_714
18
+ GTATTATTTAATGGCATACACTCAA
19
+ +SLXA-B3_649_FC8437_R1_1_1_183_714
20
+ YYYYYYYYYYWYYYYWYWWUWWWQQ
data/test/data/errors/error_qual_vtab.fastq ADDED
@@ -0,0 +1,20 @@
1
+ @SLXA-B3_649_FC8437_R1_1_1_610_79
2
+ GATGTGCAATACCTTTGTAGAGGAA
3
+ +SLXA-B3_649_FC8437_R1_1_1_610_79
4
+ YYYYYYYYYY YYYYYYYWYWYYSU
5
+ @SLXA-B3_649_FC8437_R1_1_1_397_389
6
+ GGTTTGAGAAAGAGAAATGAGATAA
7
+ +SLXA-B3_649_FC8437_R1_1_1_397_389
8
+ YYYYYYYYYWYYYYWWYYYWYWYWW
9
+ @SLXA-B3_649_FC8437_R1_1_1_850_123
10
+ GAGGGTGTTGATCATGATGATGGCG
11
+ +SLXA-B3_649_FC8437_R1_1_1_850_123
12
+ YYYYYYYYYYYYYWYYWYYSYYYSY
13
+ @SLXA-B3_649_FC8437_R1_1_1_362_549
14
+ GGAAACAAAGTTTTTCTCAACATAG
15
+ +SLXA-B3_649_FC8437_R1_1_1_362_549
16
+ YYYYYYYYYYYYYYYYYYWWWWYWY
17
+ @SLXA-B3_649_FC8437_R1_1_1_183_714
18
+ GTATTATTTAATGGCATACACTCAA
19
+ +SLXA-B3_649_FC8437_R1_1_1_183_714
20
+ YYYYYYYYYYWYYYYWYWWUWWWQQ
data/test/data/errors/error_spaces.fastq ADDED
@@ -0,0 +1,20 @@
1
+ @SLXA-B3_649_FC8437_R1_1_1_610_79
2
+ GATGTGCAA TACCTTTGTA GAGGAA
3
+ +SLXA-B3_649_FC8437_R1_1_1_610_79
4
+ YYYYYYYYY YYYYYYYYYW YWYYSU
5
+ @SLXA-B3_649_FC8437_R1_1_1_397_389
6
+ GGTTTGAGA AAGAGAAATG AGATAA
7
+ +SLXA-B3_649_FC8437_R1_1_1_397_389
8
+ YYYYYYYYY WYYYYWWYYY WYWYWW
9
+ @SLXA-B3_649_FC8437_R1_1_1_850_123
10
+ GAGGGTGTT GATCATGATG ATGGCG
11
+ +SLXA-B3_649_FC8437_R1_1_1_850_123
12
+ YYYYYYYYY YYYYWYYWYY SYYYSY
13
+ @SLXA-B3_649_FC8437_R1_1_1_362_549
14
+ GGAAACAAA GTTTTTCTCA ACATAG
15
+ +SLXA-B3_649_FC8437_R1_1_1_362_549
16
+ YYYYYYYYY YYYYYYYYYW WWWYWY
17
+ @SLXA-B3_649_FC8437_R1_1_1_183_714
18
+ GTATTATTT AATGGCATAC ACTCAA
19
+ +SLXA-B3_649_FC8437_R1_1_1_183_714
20
+ YYYYYYYYY YWYYYYWYWW UWWWQQ
data/test/data/errors/error_tabs.fastq ADDED
@@ -0,0 +1,21 @@
1
+ @SLXA-B3_649_FC8437_R1_1_1_610_79
2
+ GATGTGCAA TACCTTTGTA GAGGAA
3
+ +SLXA-B3_649_FC8437_R1_1_1_610_79
4
+ YYYYYYYYY YYYYYYYYYW YWYYSU
5
+ @SLXA-B3_649_FC8437_R1_1_1_397_389
6
+ GGTTTGAGA AAGAGAAATG AGATAA
7
+ +SLXA-B3_649_FC8437_R1_1_1_397_389
8
+ YYYYYYYYY WYYYYWWYYY WYWYWW
9
+ @SLXA-B3_649_FC8437_R1_1_1_850_123
10
+ GAGGGTGTT GATCATGATG ATGGCG
11
+ +SLXA-B3_649_FC8437_R1_1_1_850_123
12
+ YYYYYYYYY YYYYWYYWYY SYYYSY
13
+ @SLXA-B3_649_FC8437_R1_1_1_362_549
14
+ GGAAACAAA GTTTTTCTCA ACATAG
15
+ +SLXA-B3_649_FC8437_R1_1_1_362_549
16
+ YYYYYYYYY YYYYYYYYYW WWWYWY
17
+ @SLXA-B3_649_FC8437_R1_1_1_183_714
18
+ GTATTATTT AATGGCATAC ACTCAA
19
+ +SLXA-B3_649_FC8437_R1_1_1_183_714
20
+ YYYYYYYYY YWYYYYWYWW UWWWQQ
21
+
data/test/data/errors/error_trunc_at_qual.fastq ADDED
@@ -0,0 +1,19 @@
1
+ @SLXA-B3_649_FC8437_R1_1_1_610_79
2
+ GATGTGCAATACCTTTGTAGAGGAA
3
+ +SLXA-B3_649_FC8437_R1_1_1_610_79
4
+ YYYYYYYYYYYYYYYYYYWYWYYSU
5
+ @SLXA-B3_649_FC8437_R1_1_1_397_389
6
+ GGTTTGAGAAAGAGAAATGAGATAA
7
+ +SLXA-B3_649_FC8437_R1_1_1_397_389
8
+ YYYYYYYYYWYYYYWWYYYWYWYWW
9
+ @SLXA-B3_649_FC8437_R1_1_1_850_123
10
+ GAGGGTGTTGATCATGATGATGGCG
11
+ +SLXA-B3_649_FC8437_R1_1_1_850_123
12
+ YYYYYYYYYYYYYWYYWYYSYYYSY
13
+ @SLXA-B3_649_FC8437_R1_1_1_362_549
14
+ GGAAACAAAGTTTTTCTCAACATAG
15
+ +SLXA-B3_649_FC8437_R1_1_1_362_549
16
+ YYYYYYYYYYYYYYYYYYWWWWYWY
17
+ @SLXA-B3_649_FC8437_R1_1_1_183_714
18
+ GTATTATTTAATGGCATACACTCAA
19
+ +SLXA-B3_649_FC8437_R1_1_1_183_714
data/test/data/errors/error_trunc_at_seq.fastq ADDED
@@ -0,0 +1,18 @@
1
+ @SLXA-B3_649_FC8437_R1_1_1_610_79
2
+ GATGTGCAATACCTTTGTAGAGGAA
3
+ +SLXA-B3_649_FC8437_R1_1_1_610_79
4
+ YYYYYYYYYYYYYYYYYYWYWYYSU
5
+ @SLXA-B3_649_FC8437_R1_1_1_397_389
6
+ GGTTTGAGAAAGAGAAATGAGATAA
7
+ +SLXA-B3_649_FC8437_R1_1_1_397_389
8
+ YYYYYYYYYWYYYYWWYYYWYWYWW
9
+ @SLXA-B3_649_FC8437_R1_1_1_850_123
10
+ GAGGGTGTTGATCATGATGATGGCG
11
+ +SLXA-B3_649_FC8437_R1_1_1_850_123
12
+ YYYYYYYYYYYYYWYYWYYSYYYSY
13
+ @SLXA-B3_649_FC8437_R1_1_1_362_549
14
+ GGAAACAAAGTTTTTCTCAACATAG
15
+ +SLXA-B3_649_FC8437_R1_1_1_362_549
16
+ YYYYYYYYYYYYYYYYYYWWWWYWY
17
+ @SLXA-B3_649_FC8437_R1_1_1_183_714
18
+
data/test/data/errors/error_trunc_in_qual.fastq ADDED
@@ -0,0 +1,20 @@
1
+ @SLXA-B3_649_FC8437_R1_1_1_610_79
2
+ GATGTGCAATACCTTTGTAGAGGAA
3
+ +SLXA-B3_649_FC8437_R1_1_1_610_79
4
+ YYYYYYYYYYYYYYYYYYWYWYYSU
5
+ @SLXA-B3_649_FC8437_R1_1_1_397_389
6
+ GGTTTGAGAAAGAGAAATGAGATAA
7
+ +SLXA-B3_649_FC8437_R1_1_1_397_389
8
+ YYYYYYYYYWYYYYWWYYYWYWYWW
9
+ @SLXA-B3_649_FC8437_R1_1_1_850_123
10
+ GAGGGTGTTGATCATGATGATGGCG
11
+ +SLXA-B3_649_FC8437_R1_1_1_850_123
12
+ YYYYYYYYYYYYYWYYWYYSYYYSY
13
+ @SLXA-B3_649_FC8437_R1_1_1_362_549
14
+ GGAAACAAAGTTTTTCTCAACATAG
15
+ +SLXA-B3_649_FC8437_R1_1_1_362_549
16
+ YYYYYYYYYYYYYYYYYYWWWWYWY
17
+ @SLXA-B3_649_FC8437_R1_1_1_183_714
18
+ GTATTATTTAATGGCATACACTCAA
19
+ +SLXA-B3_649_FC8437_R1_1_1_183_714
20
+ YYYYYYYYYYWYYYYWYWWUWWWQ
data/test/data/errors/error_trunc_in_seq.fastq ADDED
@@ -0,0 +1,18 @@
1
+ @SLXA-B3_649_FC8437_R1_1_1_610_79
2
+ GATGTGCAATACCTTTGTAGAGGAA
3
+ +SLXA-B3_649_FC8437_R1_1_1_610_79
4
+ YYYYYYYYYYYYYYYYYYWYWYYSU
5
+ @SLXA-B3_649_FC8437_R1_1_1_397_389
6
+ GGTTTGAGAAAGAGAAATGAGATAA
7
+ +SLXA-B3_649_FC8437_R1_1_1_397_389
8
+ YYYYYYYYYWYYYYWWYYYWYWYWW
9
+ @SLXA-B3_649_FC8437_R1_1_1_850_123
10
+ GAGGGTGTTGATCATGATGATGGCG
11
+ +SLXA-B3_649_FC8437_R1_1_1_850_123
12
+ YYYYYYYYYYYYYWYYWYYSYYYSY
13
+ @SLXA-B3_649_FC8437_R1_1_1_362_549
14
+ GGAAACAAAGTTTTTCTCAACATAG
15
+ +SLXA-B3_649_FC8437_R1_1_1_362_549
16
+ YYYYYYYYYYYYYYYYYYWWWWYWY
17
+ @SLXA-B3_649_FC8437_R1_1_1_183_714
18
+ GTATTATTTAATGG
data/test/data/formats/illumina_full_range_as_illumina.fastq ADDED
@@ -0,0 +1,8 @@
1
+ @FAKE0005 Original version has PHRED scores from 0 to 62 inclusive (in that order)
2
+ ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG
3
+ +
4
+ @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
5
+ @FAKE0006 Original version has PHRED scores from 62 to 0 inclusive (in that order)
6
+ GCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
7
+ +
8
+ ~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@
data/test/data/formats/illumina_full_range_as_sanger.fastq ADDED
@@ -0,0 +1,8 @@
1
+ @FAKE0005 Original version has PHRED scores from 0 to 62 inclusive (in that order)
2
+ ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG
3
+ +
4
+ !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_
5
+ @FAKE0006 Original version has PHRED scores from 62 to 0 inclusive (in that order)
6
+ GCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
7
+ +
8
+ _^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"!
data/test/data/formats/illumina_full_range_as_solexa.fastq ADDED
@@ -0,0 +1,8 @@
1
+ @FAKE0005 Original version has PHRED scores from 0 to 62 inclusive (in that order)
2
+ ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG
3
+ +
4
+ ;;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
5
+ @FAKE0006 Original version has PHRED scores from 62 to 0 inclusive (in that order)
6
+ GCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
7
+ +
8
+ ~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJHGFECB@>;;
data/test/data/formats/illumina_full_range_original_illumina.fastq ADDED
@@ -0,0 +1,8 @@
1
+ @FAKE0005 Original version has PHRED scores from 0 to 62 inclusive (in that order)
2
+ ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG
3
+ +
4
+ @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
5
+ @FAKE0006 Original version has PHRED scores from 62 to 0 inclusive (in that order)
6
+ GCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
7
+ +
8
+ ~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@
data/test/data/formats/longreads_as_illumina.fastq ADDED
@@ -0,0 +1,40 @@
1
+ @FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95]
2
+ tcagTTAAGATGGGATAATATCCTCAGATTGCGTGATGAACTTTGTTCTGGTGGAGGAGAAGGAAGTGCATTCGACGTATGCCCGTTTGTCGATATTTGtatttaaagtaatccgtcacaaatcagtgacataaatattatttagatttcgggagcaactttatttattccacaagcaggtttaaattttaaatttaaattattgcagaagactttaaattaacctcgttgtcggagtcatttgttcggttattggtcgaaagtaaccncgggaagtgccgaaaactaacaaacaaaagaagatagtgaaattttaattaaaanaaatagccaaacgtaactaactaaaacggacccgtcgaggaactgccaacggacgacacagggagtagnnn
3
+ +
4
+ eeeccccccc`UUU^UWWeegffhhhhhhhhhhhhhhhhhhggghhhhhhhhhfgfeeeee\\\\ceeeeeeeeeeeeeec^^^YRPOSNVU\YTMMMSMRKKKRUUNNNNS[`aa```\bbeccccccccYUUUbceeee\[`a`\ZYRRRPPP[\\\XXZaWWXeeeeeeccacaccc\WWSSQRPMMKKKLKKKKKKKKPPRRMMLLLPVPPPKKKKKQQTTTPRPPQPMLLMKRRRPPKMKKRLLKKMKKLLKRTPPPQRMMLL@KKKKLLKLLLLXKKKKW\KKLKKKLKKKKLLLQUYXYTLMMPKKKKPPNNKKKK@KKPXPVLLKKKKLRMKLLKKPVKKKKLLLJPPPPRMOROOOOKKKOSSSOOORUZXUUUQMNNZV][Z@@@
5
+ @FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74]
6
+ tcagCCAGCAATTCCGACTTAATTGTTCTTCTTCCATCATTCATCTCGACTAACAGTTCTACGATTAATGAGTTTGGCtttaatttgttgttcattattgtcacaattacactactgagactgccaaggcacncagggataggnn
7
+ +
8
+ eeeeeeeeecccceeeefecccca`````\[SSSS__a\TTTYaaaaa__^WYW[^[WXWXW[WSSSQZ\\RKKKTPSKKKPPKKKMKKQPVVVTTTTPRKMMLLPPPTVTWMNNRSSWW][[ZZZZXXSSN@NSKKKTVWTT@@
9
+ @FSRRS4401B64ST [length=382] [gc=40.58] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=346]
10
+ tcagTTTTCTTAAATTACTTGAATCTGTTGAAGTGGATGTCCACTTTTGTATGCCAAATATGCCCAGCGTATACGATCTTGGCCACATCTCCACATAATCATCAGTCGGATGCAAAAAGCGATTAAACTAAAAATGAATGCGTTTTTAGATGAGTAAATAGGTAATACTTTGTTTAAATAATAAATGTCACAAACAGAACGCGGATTACAGTACCTGAAAATAGTTGTACTGTATCTGTGCCGGCACTTCCTCGGCCCTGAGAAGTTGTCCCGTTGTTTCCATTCGCACCATCCAATGGCCAAAGTTTGCGAAGAATCTGTTCCGTTCCATTACCAATTGTTTTTCCATGctgagactgccaaggcacacaggggataggnn
11
+ +
12
+ hhhhbbbbh^^UUUhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhUUUUh`hhhhh^^^hhhhbbbhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhUURRRdhbdYYRRW\NLLLLKW\]]^^YQLNNNNV]bddhdhggghhhhhhhhhdZZXXPPPXXa^^^habghhhhhhggghhggghhhhhhhhhhhhhhhhhhaabbhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhfffhhhhhhhhhc^\\\chhhggghhhhhhhhhggghhhhhhhhhhggghggghhhhhhhhhhhhhhhhhhhhhh^]ZXXWW\\TLLLLM__`dfhhhhhhhhhgg^^^^dhhheeXXXZdhhaa@@
13
+ @FSRRS4401EJ0YH [length=381] [gc=48.29] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=343]
14
+ tcagTTTTTGGAGAATTCCGTCAGGGACGGCATGGCATATTTGTGGGTTCGGCACGGCGTCCTGGCCAAGAAGAAGAAGACGAATTAGCCCGTTAATTTAATGACACCTTCCCCAATTTTGCAGCAATGATTGGTTCATTCTTGGCGGTGCGTTTTTGTGCTTCGTCGAATTGTTGGCCATTTTGGTCCACCGGCCATCATCTTTACGCTATCCGACTGATTGGAAATCACCGCCTAGCATTTTGCCGAAGATTGTTGCGTTGTACGGCCATGTGCTGATTGTTTACATTGGCATTCTTGGCAATTTGTCCTTGGTCGGCTTTGACGGCAAATTTGCGGTGTTAAGTctgagactgccaaggcacacagggggatagggnn
15
+ +
16
+ hhhh^^^^^hhhhhhhhhhhhhhggghhhhhhhhhhhhhggghhggghhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhggghhhhhggghhhhhhhhhhh````hh]]]]hhhhhhhhhhhhhhhhhhhhhhhhhhddhddZRRRRRcVhhhhhhhhhhhhhhhhhhhhhbb__gghhhhhhhhhhhhhhhhggghhhhhhhhhhhhhhhhhhhggghhhhhhhhhhhhhaaaahgbcbghhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhggghhhggbbchhhhhhggghhbbbg\bbhhhhhhhhhfffhhhhhhgggggghhhhhhhhhhhhhhhggghhggd^^]]^dedd^NNNNNZYWOLL@@
17
+ @FSRRS4401BK0IB [length=507] [gc=49.31] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=208]
18
+ tcagTTGACCGGCGTTGTGTAACAATAATTCATTATTCTGAGACGATGCCAATGTAATCGACGGTTTATGCCCAATTATTCCCATCTATGCTTAACTGATCAAATACTATTTGCATTACGTCACGAAATTGCGCGAACACCGCCGGCCGACAATAATTTATACCGGACATACCGGAGTTGATGGTAATCGGTAAAGAGTTTTATTTAATTATntattatcnctattaattattgttancaacaatgtgcacgctntgccgcccgccgccgccgtgtcggtaggaccccggacggacccggacccggttcgggtacccgttttcgggttcccggaaccgtttttcgggtacccggttttttcggggggccccccggtaaaaaaccggggaaccccctaaaacgggtaaacgtaccgtaagggaccccctaaacgggggccccgaaaaaccgggacccaaaccggggggaaacggttaaaggggggggaagtaggngnnnnnnnnnnnn
19
+ +
20
+ eee`__eeeeeeeeeeggaYYY_aeeeeffghghhhhhhhhhhhhhhhhhhhhhhheeeeeeeee^\a`_PPPWWOPP[[WWZ^``accb^^^cc````c`UUUc^ccc\\\\\``]^]][[[\[PPPWW[[^^^``^XTTT\`aaa__^\]]^__PPPSQYYcc`^^^ceeeeeeeeeeeeea````[[OOOOMQQ\NNNNWKLLPPPPPP@QRLLNQS@RVYUUUU[ZWQQNMMS@SUTQPPVVTTRMLMQR@QRPPQPPPQKKLKKQPP\\TLLLLLLKPQKKKKKKLKKKLPKKKKLKKPTTLLKKKKPRPPPMKKKKKKKKJJPPPMMPPMMPKKKKKKKKKJRKKKKKLLQQLLLLLNNLLLLTTNNIINLLQQLLIIKKKKIIKKKKKKMPMKIKKKKIIIKKKKKKKKKKKKKKKKKKKKKKKHKKLKKKKKKHKKKKKIINNMHKKKNNNKKKKKKKKKKKMHHRRLLLKKKKKKKKKKGOKKK@M@@@@@@@@@@@@
21
+ @FSRRS4401ARCCB [length=258] [gc=46.90] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=193]
22
+ tcagTTATTGCAGTCGTTCCGCGCCATCGCCGGTAACCGTCCGCGTGTTATTCTGTGTATCGGCCAACCTTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGATCTATACCGGCGAAACTCAGCCGAAAGGTCTCGCGGTAGAGCCTATGAGCTGCCCGACCGATGCATTTAAATTTCCGGGGATCGtcgctgatctgagactgccaaaggcacactagggggataggnnnnnnnnnnnnnnnnnnnn
23
+ +
24
+ eee[WYY_ceeeeeeeffecb`````a__OOOOSU[ZUURQQRUUVUQQSRRSW[[\^^SSSTYY]`a```_[[\\a\YTTTYaac^^\acccceeebbbbbbbeebccceeeeeca``\\WWWWOOOS][[[XXUWWZWWX[WWX^aaaa`\^^^ccaaa__^^WWWWXLLLQRVVVPKKKKKKKKLLPPTQ[[OOPTW`_][[[[[SRQVVVPPKKKLLRV\\\VTKLLLLRSUUU@@@@@@@@@@@@@@@@@@@@
25
+ @FSRRS4401CM938 [length=453] [gc=44.15] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=418]
26
+ tcagGTTTTAAATCGCTTTCCAAGGAATTTGAGTCTAAATCCGGTGGATCCCATCAGTACAAATGCGGCGACAAGGCCGTGAAAACACTGCTTAATTCTTTGCACTTTTTGGCCACCTTTTTGGAAATGTTGTTTTGTGTTCTCAAAATTTTCCATCTCAGAACAAACATTCCATCGGGCTGATGTTGTGGCTTTTGGCGCGCGAAGTGCTGCTACTGCGCGGCAAAATCAGTCGCCAGACCGGTTTTGTTGTGGACGACAAAGTGATCATGCCTGACTTGTACTTCTACCGCGATCCGCAAGCGCGAATTGGTCACATAGTTATAGAATTTTTGAGCCTTTTTCTTGACATAAAAAGTGTGGTTTTAAAAATTTCCTGGCAGGACCCACGCCAACGTTCAGGAATAATATCTTTTAAAAAGctgagactgccaaggcacacaggggataggn
27
+ +
28
+ hhhhhbb]]UUUhhhhbbbhhhhhhhhggghhhhhfUUUhhhhhhhhhhggghhhhhhhhbbbhhhhhhhhhhhhhhhhhh____hhhhhhhhhhhhhggghhhh^^^\ZhhddhYYNNNNNVTSSY^haaVQQSSdWddbdab\_______gghhhhhhhhhhaaahhhhhhhhhggghhhhhhhhhhhhhbbbbhhhhhhhhhhhhhhhhhhhhhhhhhhhhUUUUcdhhgda^^c_VVVVVQQQQcWXddhhhhhhhggghhhhhhhhggghhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhggghhhhhhhhhhhhhhh\\^\\hhhhh^^^\ZhURcccWQLLKKKRW\\YYLLLLKKLLLJJJRROUUZ_URWOOOWNYWWX[Yafhhhhhhhhhed[^eTTOOLLLLLTYZZZY]^_b[[VXXXdddddd____ddddd@
29
+ @FSRRS4401EQLIK [length=411] [gc=34.31] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=374]
30
+ tcagTTTAATTTGGTGCTTCCTTTCAATTCCTTAGTTTAAACTTGGCACTGAAGTCTCGCATTTATAACTAGAGCCCGGATTTTAGAGGCTAAAAAGTTTTCCAGATTTCAAAATTTATTTCGAAACTATTTTTCTGATTGTGATGTGACGGATTTCTAAATTAAATCGAAATGATGTGTATTGAACTTAACAAGTGATTTTTATCAGATTTTGTCAATGAATAAATTTTAATTTAAATCTCTTTCTAACACTTTCATGATTAAAATCTAACAAAGCGCGACCAGTATGTGAGAAGAGCAAAAACAACAAAAAGTGCTAGCACTAAAGAAGGTTCGAACCCAACACATAACGTAAGAGTTACCGGGAAGAAAACCACTctgagactgccaaggcacacagggggataggnn
31
+ +
32
+ hhh^UUU^^ggghhhhhhhhhfffhhhhhhhhhhhfffggghhhhhhhhhhhhhhhhhhhhfffhhhhhhhhhhggghhh____hhhhdhdPPPPOOLLLLQQ^\WLLLYLLLLLLLKKKKRRLLLTYRKLLLLYPaadddghhhhhhhhhhha^^`PQQOOOMMMY^\OQSfhhhhhhhhhhhhhhhhhhdbbgga\NNLKKQP^^[TLOOQ\Ueaa^YX[\PPNSSSSNNLNNVV^^fdhddgh`bbhhhggghhhhhhhbbb`hhhgggggghhhhhhhhhhhhhhhhhhhhhhddPNNLLWQQZLLLLMVVV_dhhhhhh^^^hhhhhhhhhhhggghhhhhhhhhhhhhhhhhhhhXXSQQVVVTTTT`dZhdddddhhhhh^^XVTT]_\\YRKKKKKRRRRU@@
33
+ @FSRRS4401AOV6A [length=309] [gc=22.98] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=273]
34
+ tcagTTTTCAAATTTTCCGAAATTTGCTGTTTGGTAGAAGGCAAATTATTTGATTGAATTTTGTATTTATTTAAAACAATTTATTTTAAAATAATAATTTTCCATTGACTTTTTACATTTAATTGATTTTATTATGCATTTTATATTTGTTTTCTAAATATTCGTTTGCAAACTCACGTTGAAATTGTATTAAACTCGAAATTAGAGTTTTTGAAATTAATTTTTATGTAGCATAATATTTTAAACATATTGGAATTTTATAAAACATTATATTTTTctgagactgccaaggcacacagggggataggn
35
+ +
36
+ hhhhbbbbhZZZbbbbhhh^^^ggghhhhggghhhhhhhhhhggghhhggghhhhhhh____hehbbbhb``ZZZZdc^a__cUUSSTTTT[[[fhh]]``hhhhhhhhZZZYYhhh^^^bbbhhhZZZZheehhhhhbbbahahddcbSSSS^Saaad^dhhhbgghhZZZghhhhhhggZZZgghhhhhZZZhhhhggghhhhhh]]^^]hddaffYYPPPPNSUeaeaa^\Z\`^XVVVPPPXYd```ccacVVVV\NPPPPQQc`__aUWZZZhWgghhhhhZZZZ^]hdbbbaNNNNNZVST\@
37
+ @FSRRS4401EG0ZW [length=424] [gc=23.82] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=389]
38
+ tcagTTTTGATCTTTTAATAATGAATTTTAATGTGTTAAAATGATTGCATTGATGGCATAACCGCATTTAAATTAATTACATGAAGTGTAAGTATGAAATTTTCCTTTCCAAATTGCAAAAACTAAAATTTAAAATTTATCGTAAAAATTAACATATATTTTAAACGATTTTAAGAAACATTTGTAAATTATATTTTTGTGAAGCGTTCAAACAAAAATAAACAATAAAATATTTTTCTATTTAATAGCAAAACATTTGACGATGAAAAGGAAAATGCGGGTTTGAAAATGGGCTTTGCCATGCTATTTTCATAATAACATATTTTTATTATGAATAATAAATTTACATACAATATATACAGTCTTAAATTTATTCATAATATTTTTGAGAATctgagactgccaaggcacacaggggataggn
39
+ +
40
+ hh`XSSSTddhh\\\]hhhhhhhhhbbbbhhghhhbbZZZZhhhhhhhhhhhhhhhhhhhhhhhhheZZUUUcchhhhhhhhhhhhhhhhhhhddXSSSQQSS__UUUbb[[acc`\LLLLLQ[KKKKUTXNNOO\\\WbhhhZ]]\\ggZZhhhhhhbb__^^^hhh____hb^UUUghccbh^a^^bb[ddPPPPPaSaccbaZ\_aVVV]NNNNL\RQR^SQRKKKN\PKKKKLYSdZ^^dhhhhhbbbbh]ZZZhhhhhhh[[__^\NNNNV\`XXXWW[[SSTThdddhhhhhhhhhhhhh[XXXghhhhhhhhhhh^^^^^hhhhhhhhhhhb`bZTTTRXdhhhhhhhhhhhhhhhhggXXXgggh`\`ddee_\MMMMM`c___ccddddehhhZZZXVVeebbb_QSSSX^ecc@
data/test/data/formats/longreads_as_sanger.fastq ADDED
@@ -0,0 +1,40 @@
1
+ @FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95]
2
+ tcagTTAAGATGGGATAATATCCTCAGATTGCGTGATGAACTTTGTTCTGGTGGAGGAGAAGGAAGTGCATTCGACGTATGCCCGTTTGTCGATATTTGtatttaaagtaatccgtcacaaatcagtgacataaatattatttagatttcgggagcaactttatttattccacaagcaggtttaaattttaaatttaaattattgcagaagactttaaattaacctcgttgtcggagtcatttgttcggttattggtcgaaagtaaccncgggaagtgccgaaaactaacaaacaaaagaagatagtgaaattttaattaaaanaaatagccaaacgtaactaactaaaacggacccgtcgaggaactgccaacggacgacacagggagtagnnn
3
+ +
4
+ FFFDDDDDDDA666?688FFHGGIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIGHGFFFFF====DFFFFFFFFFFFFFFD???:3104/76=:5...4.3,,,366////4<ABBAAA=CCFDDDDDDDD:666CDFFFF=<ABA=;:333111<===99;B889FFFFFFDDBDBDDD=8844231..,,,-,,,,,,,,1133..---17111,,,,,22555131121.--.,33311,.,,3--,,.,,--,3511123..--!,,,,--,----9,,,,8=,,-,,,-,,,,---26:9:5-..1,,,,11//,,,,!,,1917--,,,,-3.,--,,17,,,,---+11113.030000,,,044400036;96662.//;7><;!!!
5
+ @FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74]
6
+ tcagCCAGCAATTCCGACTTAATTGTTCTTCTTCCATCATTCATCTCGACTAACAGTTCTACGATTAATGAGTTTGGCtttaatttgttgttcattattgtcacaattacactactgagactgccaaggcacncagggataggnn
7
+ +
8
+ FFFFFFFFFDDDDFFFFGFDDDDBAAAAA=<4444@@B=555:BBBBB@@?8:8<?<89898<84442;==3,,,514,,,11,,,.,,21777555513,..--1115758.//34488><<;;;;9944/!/4,,,57855!!
9
+ @FSRRS4401B64ST [length=382] [gc=40.58] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=346]
10
+ tcagTTTTCTTAAATTACTTGAATCTGTTGAAGTGGATGTCCACTTTTGTATGCCAAATATGCCCAGCGTATACGATCTTGGCCACATCTCCACATAATCATCAGTCGGATGCAAAAAGCGATTAAACTAAAAATGAATGCGTTTTTAGATGAGTAAATAGGTAATACTTTGTTTAAATAATAAATGTCACAAACAGAACGCGGATTACAGTACCTGAAAATAGTTGTACTGTATCTGTGCCGGCACTTCCTCGGCCCTGAGAAGTTGTCCCGTTGTTTCCATTCGCACCATCCAATGGCCAAAGTTTGCGAAGAATCTGTTCCGTTCCATTACCAATTGTTTTTCCATGctgagactgccaaggcacacaggggataggnn
11
+ +
12
+ IIIICCCCI??666IIIIIIIIIIIIIIIIIIIIIIIIIIIIII6666IAIIIII???IIIICCCIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII66333EICE::338=/----,8=>>??:2-////7>CEEIEIHHHIIIIIIIIIE;;9911199B???IBCHIIIIIIHHHIIHHHIIIIIIIIIIIIIIIIIIBBCCIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGIIIIIIIIID?===DIIIHHHIIIIIIIIIHHHIIIIIIIIIIHHHIHHHIIIIIIIIIIIIIIIIIIIIII?>;9988==5----.@@AEGIIIIIIIIIHH????EIIIFF999;EIIBB!!
13
+ @FSRRS4401EJ0YH [length=381] [gc=48.29] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=343]
14
+ tcagTTTTTGGAGAATTCCGTCAGGGACGGCATGGCATATTTGTGGGTTCGGCACGGCGTCCTGGCCAAGAAGAAGAAGACGAATTAGCCCGTTAATTTAATGACACCTTCCCCAATTTTGCAGCAATGATTGGTTCATTCTTGGCGGTGCGTTTTTGTGCTTCGTCGAATTGTTGGCCATTTTGGTCCACCGGCCATCATCTTTACGCTATCCGACTGATTGGAAATCACCGCCTAGCATTTTGCCGAAGATTGTTGCGTTGTACGGCCATGTGCTGATTGTTTACATTGGCATTCTTGGCAATTTGTCCTTGGTCGGCTTTGACGGCAAATTTGCGGTGTTAAGTctgagactgccaaggcacacagggggatagggnn
15
+ +
16
+ IIII?????IIIIIIIIIIIIIIHHHIIIIIIIIIIIIIHHHIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIHHHIIIIIIIIIIIAAAAII>>>>IIIIIIIIIIIIIIIIIIIIIIIIIIEEIEE;33333D7IIIIIIIIIIIIIIIIIIIIICC@@HHIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIBBBBIHCDCHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIHHCCDIIIIIIHHHIICCCH=CCIIIIIIIIIGGGIIIIIIHHHHHHIIIIIIIIIIIIIIIHHHIIHHE??>>?EFEE?/////;:80--!!
17
+ @FSRRS4401BK0IB [length=507] [gc=49.31] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=208]
18
+ tcagTTGACCGGCGTTGTGTAACAATAATTCATTATTCTGAGACGATGCCAATGTAATCGACGGTTTATGCCCAATTATTCCCATCTATGCTTAACTGATCAAATACTATTTGCATTACGTCACGAAATTGCGCGAACACCGCCGGCCGACAATAATTTATACCGGACATACCGGAGTTGATGGTAATCGGTAAAGAGTTTTATTTAATTATntattatcnctattaattattgttancaacaatgtgcacgctntgccgcccgccgccgccgtgtcggtaggaccccggacggacccggacccggttcgggtacccgttttcgggttcccggaaccgtttttcgggtacccggttttttcggggggccccccggtaaaaaaccggggaaccccctaaaacgggtaaacgtaccgtaagggaccccctaaacgggggccccgaaaaaccgggacccaaaccggggggaaacggttaaaggggggggaagtaggngnnnnnnnnnnnn
19
+ +
20
+ FFFA@@FFFFFFFFFFHHB:::@BFFFFGGHIHIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFF?=BA@11188011<<88;?AABDDC???DDAAAADA666D?DDD=====AA>?>><<<=<11188<<???AA?9555=ABBB@@?=>>?@@11142::DDA???DFFFFFFFFFFFFFBAAAA<<0000.22=////8,--111111!23--/24!37:6666<;822/..4!46521177553.-.23!231121112,,-,,211==5------,12,,,,,,-,,,-1,,,,-,,155--,,,,13111.,,,,,,,,++111..11..1,,,,,,,,,+3,,,,,--22-----//----55//**/--22--**,,,,**,,,,,,.1.,*,,,,***,,,,,,,,,,,,,,,,,,,,,,,),,-,,,,,,),,,,,**//.),,,///,,,,,,,,,,,.))33---,,,,,,,,,,(0,,,!.!!!!!!!!!!!!
21
+ @FSRRS4401ARCCB [length=258] [gc=46.90] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=193]
22
+ tcagTTATTGCAGTCGTTCCGCGCCATCGCCGGTAACCGTCCGCGTGTTATTCTGTGTATCGGCCAACCTTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGATCTATACCGGCGAAACTCAGCCGAAAGGTCTCGCGGTAGAGCCTATGAGCTGCCCGACCGATGCATTTAAATTTCCGGGGATCGtcgctgatctgagactgccaaaggcacactagggggataggnnnnnnnnnnnnnnnnnnnn
23
+ +
24
+ FFF<8::@DFFFFFFFGGFDCAAAAAB@@000046<;66322366762243348<<=??4445::>ABAAA@<<==B=:555:BBD??=BDDDDFFFCCCCCCCFFCDDDFFFFFDBAA==88880004><<<99688;889<889?BBBBA=???DDBBB@@??88889---237771,,,,,,,,--1152<<00158A@><<<<<43277711,,,--37===75,----34666!!!!!!!!!!!!!!!!!!!!
25
+ @FSRRS4401CM938 [length=453] [gc=44.15] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=418]
26
+ tcagGTTTTAAATCGCTTTCCAAGGAATTTGAGTCTAAATCCGGTGGATCCCATCAGTACAAATGCGGCGACAAGGCCGTGAAAACACTGCTTAATTCTTTGCACTTTTTGGCCACCTTTTTGGAAATGTTGTTTTGTGTTCTCAAAATTTTCCATCTCAGAACAAACATTCCATCGGGCTGATGTTGTGGCTTTTGGCGCGCGAAGTGCTGCTACTGCGCGGCAAAATCAGTCGCCAGACCGGTTTTGTTGTGGACGACAAAGTGATCATGCCTGACTTGTACTTCTACCGCGATCCGCAAGCGCGAATTGGTCACATAGTTATAGAATTTTTGAGCCTTTTTCTTGACATAAAAAGTGTGGTTTTAAAAATTTCCTGGCAGGACCCACGCCAACGTTCAGGAATAATATCTTTTAAAAAGctgagactgccaaggcacacaggggataggn
27
+ +
28
+ IIIIICC>>666IIIICCCIIIIIIIIHHHIIIIIG666IIIIIIIIIIHHHIIIIIIIICCCIIIIIIIIIIIIIIIIII@@@@IIIIIIIIIIIIIHHHIIII???=;IIEEI:://///7544:?IBB72244E8EECEBC=@@@@@@@HHIIIIIIIIIIBBBIIIIIIIIIHHHIIIIIIIIIIIIICCCCIIIIIIIIIIIIIIIIIIIIIIIIIIII6666DEIIHEB??D@777772222D89EEIIIIIIIHHHIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIII==?==IIIII???=;I63DDD82--,,,38==::----,,---+++33066;@6380008/:889<:BGIIIIIIIIIFE<?F5500-----5:;;;:>?@C<<7999EEEEEE@@@@EEEEE!
29
+ @FSRRS4401EQLIK [length=411] [gc=34.31] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=374]
30
+ tcagTTTAATTTGGTGCTTCCTTTCAATTCCTTAGTTTAAACTTGGCACTGAAGTCTCGCATTTATAACTAGAGCCCGGATTTTAGAGGCTAAAAAGTTTTCCAGATTTCAAAATTTATTTCGAAACTATTTTTCTGATTGTGATGTGACGGATTTCTAAATTAAATCGAAATGATGTGTATTGAACTTAACAAGTGATTTTTATCAGATTTTGTCAATGAATAAATTTTAATTTAAATCTCTTTCTAACACTTTCATGATTAAAATCTAACAAAGCGCGACCAGTATGTGAGAAGAGCAAAAACAACAAAAAGTGCTAGCACTAAAGAAGGTTCGAACCCAACACATAACGTAAGAGTTACCGGGAAGAAAACCACTctgagactgccaaggcacacagggggataggnn
31
+ +
32
+ III?666??HHHIIIIIIIIIGGGIIIIIIIIIIIGGGHHHIIIIIIIIIIIIIIIIIIIIGGGIIIIIIIIIIHHHIII@@@@IIIIEIE111100----22?=8---:-------,,,,33---5:3,----:1BBEEEHIIIIIIIIIIIB??A122000...:?=024GIIIIIIIIIIIIIIIIIIECCHHB=//-,,21??<5-002=6FBB?:9<=11/4444//-//77??GEIEEHIACCIIIHHHIIIIIIICCCAIIIHHHHHHIIIIIIIIIIIIIIIIIIIIIIEE1//--822;----.777@EIIIIII???IIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIII994227775555AE;IEEEEEIIIII??9755>@==:3,,,,,33336!!
33
+ @FSRRS4401AOV6A [length=309] [gc=22.98] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=273]
34
+ tcagTTTTCAAATTTTCCGAAATTTGCTGTTTGGTAGAAGGCAAATTATTTGATTGAATTTTGTATTTATTTAAAACAATTTATTTTAAAATAATAATTTTCCATTGACTTTTTACATTTAATTGATTTTATTATGCATTTTATATTTGTTTTCTAAATATTCGTTTGCAAACTCACGTTGAAATTGTATTAAACTCGAAATTAGAGTTTTTGAAATTAATTTTTATGTAGCATAATATTTTAAACATATTGGAATTTTATAAAACATTATATTTTTctgagactgccaaggcacacagggggataggn
35
+ +
36
+ IIIICCCCI;;;CCCCIII???HHHIIIIHHHIIIIIIIIIIHHHIIIHHHIIIIIII@@@@IFICCCICAA;;;;ED?B@@D66445555<<<GII>>AAIIIIIIII;;;::III???CCCIII;;;;IFFIIIIICCCBIBIEEDC4444?4BBBE?EIIICHHII;;;HIIIIIIHH;;;HHIIIII;;;IIIIHHHIIIIII>>??>IEEBGG::1111/46FBFBB?=;=A?97771119:EAAADDBD7777=/111122DA@@B68;;;I8HHIIIII;;;;?>IECCCB/////;745=!
37
+ @FSRRS4401EG0ZW [length=424] [gc=23.82] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=389]
38
+ tcagTTTTGATCTTTTAATAATGAATTTTAATGTGTTAAAATGATTGCATTGATGGCATAACCGCATTTAAATTAATTACATGAAGTGTAAGTATGAAATTTTCCTTTCCAAATTGCAAAAACTAAAATTTAAAATTTATCGTAAAAATTAACATATATTTTAAACGATTTTAAGAAACATTTGTAAATTATATTTTTGTGAAGCGTTCAAACAAAAATAAACAATAAAATATTTTTCTATTTAATAGCAAAACATTTGACGATGAAAAGGAAAATGCGGGTTTGAAAATGGGCTTTGCCATGCTATTTTCATAATAACATATTTTTATTATGAATAATAAATTTACATACAATATATACAGTCTTAAATTTATTCATAATATTTTTGAGAATctgagactgccaaggcacacaggggataggn
39
+ +
40
+ IIA94445EEII===>IIIIIIIIICCCCIIHIIICC;;;;IIIIIIIIIIIIIIIIIIIIIIIIIF;;666DDIIIIIIIIIIIIIIIIIIIEE94442244@@666CC<<BDDA=-----2<,,,,659//00===8CIII;>>==HH;;IIIIIICC@@???III@@@@IC?666HIDDCI?B??CC<EE11111B4BDDCB;=@B777>////-=323?423,,,/=1,,,,-:4E;??EIIIIICCCCI>;;;IIIIIII<<@@?=////7=A99988<<4455IEEEIIIIIIIIIIIII<999HIIIIIIIIIII?????IIIIIIIIIIICAC;55539EIIIIIIIIIIIIIIIIHH999HHHIA=AEEFF@=.....AD@@@DDEEEEFIII;;;977FFCCC@24449?FDD!
data/test/data/formats/longreads_as_solexa.fastq ADDED
@@ -0,0 +1,40 @@
1
+ @FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95]
2
+ tcagTTAAGATGGGATAATATCCTCAGATTGCGTGATGAACTTTGTTCTGGTGGAGGAGAAGGAAGTGCATTCGACGTATGCCCGTTTGTCGATATTTGtatttaaagtaatccgtcacaaatcagtgacataaatattatttagatttcgggagcaactttatttattccacaagcaggtttaaattttaaatttaaattattgcagaagactttaaattaacctcgttgtcggagtcatttgttcggttattggtcgaaagtaaccncgggaagtgccgaaaactaacaaacaaaagaagatagtgaaattttaattaaaanaaatagccaaacgtaactaactaaaacggacccgtcgaggaactgccaacggacgacacagggagtagnnn
3
+ +
4
+ eeeccccccc`UUU^UWWeegffhhhhhhhhhhhhhhhhhhggghhhhhhhhhfgfeeeee\\\\ceeeeeeeeeeeeeec^^^YRPOSNVU\YTMMMSMRKKKRUUNNNNS[`aa```\bbeccccccccYUUUbceeee\[`a`\ZYRRRPPP[\\\XXZaWWXeeeeeeccacaccc\WWSSQRPMMKKKLKKKKKKKKPPRRMMLLLPVPPPKKKKKQQTTTPRPPQPMLLMKRRRPPKMKKRLLKKMKKLLKRTPPPQRMMLL;KKKKLLKLLLLXKKKKW\KKLKKKLKKKKLLLQUYXYTLMMPKKKKPPNNKKKK;KKPXPVLLKKKKLRMKLLKKPVKKKKLLLJPPPPRMOROOOOKKKOSSSOOORUZXUUUQMNNZV][Z;;;
5
+ @FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74]
6
+ tcagCCAGCAATTCCGACTTAATTGTTCTTCTTCCATCATTCATCTCGACTAACAGTTCTACGATTAATGAGTTTGGCtttaatttgttgttcattattgtcacaattacactactgagactgccaaggcacncagggataggnn
7
+ +
8
+ eeeeeeeeecccceeeefecccca`````\[SSSS__a\TTTYaaaaa__^WYW[^[WXWXW[WSSSQZ\\RKKKTPSKKKPPKKKMKKQPVVVTTTTPRKMMLLPPPTVTWMNNRSSWW][[ZZZZXXSSN;NSKKKTVWTT;;
9
+ @FSRRS4401B64ST [length=382] [gc=40.58] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=346]
10
+ tcagTTTTCTTAAATTACTTGAATCTGTTGAAGTGGATGTCCACTTTTGTATGCCAAATATGCCCAGCGTATACGATCTTGGCCACATCTCCACATAATCATCAGTCGGATGCAAAAAGCGATTAAACTAAAAATGAATGCGTTTTTAGATGAGTAAATAGGTAATACTTTGTTTAAATAATAAATGTCACAAACAGAACGCGGATTACAGTACCTGAAAATAGTTGTACTGTATCTGTGCCGGCACTTCCTCGGCCCTGAGAAGTTGTCCCGTTGTTTCCATTCGCACCATCCAATGGCCAAAGTTTGCGAAGAATCTGTTCCGTTCCATTACCAATTGTTTTTCCATGctgagactgccaaggcacacaggggataggnn
11
+ +
12
+ hhhhbbbbh^^UUUhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhUUUUh`hhhhh^^^hhhhbbbhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhUURRRdhbdYYRRW\NLLLLKW\]]^^YQLNNNNV]bddhdhggghhhhhhhhhdZZXXPPPXXa^^^habghhhhhhggghhggghhhhhhhhhhhhhhhhhhaabbhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhfffhhhhhhhhhc^\\\chhhggghhhhhhhhhggghhhhhhhhhhggghggghhhhhhhhhhhhhhhhhhhhhh^]ZXXWW\\TLLLLM__`dfhhhhhhhhhgg^^^^dhhheeXXXZdhhaa;;
13
+ @FSRRS4401EJ0YH [length=381] [gc=48.29] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=343]
14
+ tcagTTTTTGGAGAATTCCGTCAGGGACGGCATGGCATATTTGTGGGTTCGGCACGGCGTCCTGGCCAAGAAGAAGAAGACGAATTAGCCCGTTAATTTAATGACACCTTCCCCAATTTTGCAGCAATGATTGGTTCATTCTTGGCGGTGCGTTTTTGTGCTTCGTCGAATTGTTGGCCATTTTGGTCCACCGGCCATCATCTTTACGCTATCCGACTGATTGGAAATCACCGCCTAGCATTTTGCCGAAGATTGTTGCGTTGTACGGCCATGTGCTGATTGTTTACATTGGCATTCTTGGCAATTTGTCCTTGGTCGGCTTTGACGGCAAATTTGCGGTGTTAAGTctgagactgccaaggcacacagggggatagggnn
15
+ +
16
+ hhhh^^^^^hhhhhhhhhhhhhhggghhhhhhhhhhhhhggghhggghhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhggghhhhhggghhhhhhhhhhh````hh]]]]hhhhhhhhhhhhhhhhhhhhhhhhhhddhddZRRRRRcVhhhhhhhhhhhhhhhhhhhhhbb__gghhhhhhhhhhhhhhhhggghhhhhhhhhhhhhhhhhhhggghhhhhhhhhhhhhaaaahgbcbghhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhggghhhggbbchhhhhhggghhbbbg\bbhhhhhhhhhfffhhhhhhgggggghhhhhhhhhhhhhhhggghhggd^^]]^dedd^NNNNNZYWOLL;;
17
+ @FSRRS4401BK0IB [length=507] [gc=49.31] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=208]
18
+ tcagTTGACCGGCGTTGTGTAACAATAATTCATTATTCTGAGACGATGCCAATGTAATCGACGGTTTATGCCCAATTATTCCCATCTATGCTTAACTGATCAAATACTATTTGCATTACGTCACGAAATTGCGCGAACACCGCCGGCCGACAATAATTTATACCGGACATACCGGAGTTGATGGTAATCGGTAAAGAGTTTTATTTAATTATntattatcnctattaattattgttancaacaatgtgcacgctntgccgcccgccgccgccgtgtcggtaggaccccggacggacccggacccggttcgggtacccgttttcgggttcccggaaccgtttttcgggtacccggttttttcggggggccccccggtaaaaaaccggggaaccccctaaaacgggtaaacgtaccgtaagggaccccctaaacgggggccccgaaaaaccgggacccaaaccggggggaaacggttaaaggggggggaagtaggngnnnnnnnnnnnn
19
+ +
20
+ eee`__eeeeeeeeeeggaYYY_aeeeeffghghhhhhhhhhhhhhhhhhhhhhhheeeeeeeee^\a`_PPPWWOPP[[WWZ^``accb^^^cc````c`UUUc^ccc\\\\\``]^]][[[\[PPPWW[[^^^``^XTTT\`aaa__^\]]^__PPPSQYYcc`^^^ceeeeeeeeeeeeea````[[OOOOMQQ\NNNNWKLLPPPPPP;QRLLNQS;RVYUUUU[ZWQQNMMS;SUTQPPVVTTRMLMQR;QRPPQPPPQKKLKKQPP\\TLLLLLLKPQKKKKKKLKKKLPKKKKLKKPTTLLKKKKPRPPPMKKKKKKKKJJPPPMMPPMMPKKKKKKKKKJRKKKKKLLQQLLLLLNNLLLLTTNNHHNLLQQLLHHKKKKHHKKKKKKMPMKHKKKKHHHKKKKKKKKKKKKKKKKKKKKKKKGKKLKKKKKKGKKKKKHHNNMGKKKNNNKKKKKKKKKKKMGGRRLLLKKKKKKKKKKFOKKK;M;;;;;;;;;;;;
21
+ @FSRRS4401ARCCB [length=258] [gc=46.90] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=193]
22
+ tcagTTATTGCAGTCGTTCCGCGCCATCGCCGGTAACCGTCCGCGTGTTATTCTGTGTATCGGCCAACCTTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGATCTATACCGGCGAAACTCAGCCGAAAGGTCTCGCGGTAGAGCCTATGAGCTGCCCGACCGATGCATTTAAATTTCCGGGGATCGtcgctgatctgagactgccaaaggcacactagggggataggnnnnnnnnnnnnnnnnnnnn
23
+ +
24
+ eee[WYY_ceeeeeeeffecb`````a__OOOOSU[ZUURQQRUUVUQQSRRSW[[\^^SSSTYY]`a```_[[\\a\YTTTYaac^^\acccceeebbbbbbbeebccceeeeeca``\\WWWWOOOS][[[XXUWWZWWX[WWX^aaaa`\^^^ccaaa__^^WWWWXLLLQRVVVPKKKKKKKKLLPPTQ[[OOPTW`_][[[[[SRQVVVPPKKKLLRV\\\VTKLLLLRSUUU;;;;;;;;;;;;;;;;;;;;
25
+ @FSRRS4401CM938 [length=453] [gc=44.15] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=418]
26
+ tcagGTTTTAAATCGCTTTCCAAGGAATTTGAGTCTAAATCCGGTGGATCCCATCAGTACAAATGCGGCGACAAGGCCGTGAAAACACTGCTTAATTCTTTGCACTTTTTGGCCACCTTTTTGGAAATGTTGTTTTGTGTTCTCAAAATTTTCCATCTCAGAACAAACATTCCATCGGGCTGATGTTGTGGCTTTTGGCGCGCGAAGTGCTGCTACTGCGCGGCAAAATCAGTCGCCAGACCGGTTTTGTTGTGGACGACAAAGTGATCATGCCTGACTTGTACTTCTACCGCGATCCGCAAGCGCGAATTGGTCACATAGTTATAGAATTTTTGAGCCTTTTTCTTGACATAAAAAGTGTGGTTTTAAAAATTTCCTGGCAGGACCCACGCCAACGTTCAGGAATAATATCTTTTAAAAAGctgagactgccaaggcacacaggggataggn
27
+ +
28
+ hhhhhbb]]UUUhhhhbbbhhhhhhhhggghhhhhfUUUhhhhhhhhhhggghhhhhhhhbbbhhhhhhhhhhhhhhhhhh____hhhhhhhhhhhhhggghhhh^^^\ZhhddhYYNNNNNVTSSY^haaVQQSSdWddbdab\_______gghhhhhhhhhhaaahhhhhhhhhggghhhhhhhhhhhhhbbbbhhhhhhhhhhhhhhhhhhhhhhhhhhhhUUUUcdhhgda^^c_VVVVVQQQQcWXddhhhhhhhggghhhhhhhhggghhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhggghhhhhhhhhhhhhhh\\^\\hhhhh^^^\ZhURcccWQLLKKKRW\\YYLLLLKKLLLJJJRROUUZ_URWOOOWNYWWX[Yafhhhhhhhhhed[^eTTOOLLLLLTYZZZY]^_b[[VXXXdddddd____ddddd;
29
+ @FSRRS4401EQLIK [length=411] [gc=34.31] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=374]
30
+ tcagTTTAATTTGGTGCTTCCTTTCAATTCCTTAGTTTAAACTTGGCACTGAAGTCTCGCATTTATAACTAGAGCCCGGATTTTAGAGGCTAAAAAGTTTTCCAGATTTCAAAATTTATTTCGAAACTATTTTTCTGATTGTGATGTGACGGATTTCTAAATTAAATCGAAATGATGTGTATTGAACTTAACAAGTGATTTTTATCAGATTTTGTCAATGAATAAATTTTAATTTAAATCTCTTTCTAACACTTTCATGATTAAAATCTAACAAAGCGCGACCAGTATGTGAGAAGAGCAAAAACAACAAAAAGTGCTAGCACTAAAGAAGGTTCGAACCCAACACATAACGTAAGAGTTACCGGGAAGAAAACCACTctgagactgccaaggcacacagggggataggnn
31
+ +
32
+ hhh^UUU^^ggghhhhhhhhhfffhhhhhhhhhhhfffggghhhhhhhhhhhhhhhhhhhhfffhhhhhhhhhhggghhh____hhhhdhdPPPPOOLLLLQQ^\WLLLYLLLLLLLKKKKRRLLLTYRKLLLLYPaadddghhhhhhhhhhha^^`PQQOOOMMMY^\OQSfhhhhhhhhhhhhhhhhhhdbbgga\NNLKKQP^^[TLOOQ\Ueaa^YX[\PPNSSSSNNLNNVV^^fdhddgh`bbhhhggghhhhhhhbbb`hhhgggggghhhhhhhhhhhhhhhhhhhhhhddPNNLLWQQZLLLLMVVV_dhhhhhh^^^hhhhhhhhhhhggghhhhhhhhhhhhhhhhhhhhXXSQQVVVTTTT`dZhdddddhhhhh^^XVTT]_\\YRKKKKKRRRRU;;
33
+ @FSRRS4401AOV6A [length=309] [gc=22.98] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=273]
34
+ tcagTTTTCAAATTTTCCGAAATTTGCTGTTTGGTAGAAGGCAAATTATTTGATTGAATTTTGTATTTATTTAAAACAATTTATTTTAAAATAATAATTTTCCATTGACTTTTTACATTTAATTGATTTTATTATGCATTTTATATTTGTTTTCTAAATATTCGTTTGCAAACTCACGTTGAAATTGTATTAAACTCGAAATTAGAGTTTTTGAAATTAATTTTTATGTAGCATAATATTTTAAACATATTGGAATTTTATAAAACATTATATTTTTctgagactgccaaggcacacagggggataggn
35
+ +
36
+ hhhhbbbbhZZZbbbbhhh^^^ggghhhhggghhhhhhhhhhggghhhggghhhhhhh____hehbbbhb``ZZZZdc^a__cUUSSTTTT[[[fhh]]``hhhhhhhhZZZYYhhh^^^bbbhhhZZZZheehhhhhbbbahahddcbSSSS^Saaad^dhhhbgghhZZZghhhhhhggZZZgghhhhhZZZhhhhggghhhhhh]]^^]hddaffYYPPPPNSUeaeaa^\Z\`^XVVVPPPXYd```ccacVVVV\NPPPPQQc`__aUWZZZhWgghhhhhZZZZ^]hdbbbaNNNNNZVST\;
37
+ @FSRRS4401EG0ZW [length=424] [gc=23.82] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=389]
38
+ tcagTTTTGATCTTTTAATAATGAATTTTAATGTGTTAAAATGATTGCATTGATGGCATAACCGCATTTAAATTAATTACATGAAGTGTAAGTATGAAATTTTCCTTTCCAAATTGCAAAAACTAAAATTTAAAATTTATCGTAAAAATTAACATATATTTTAAACGATTTTAAGAAACATTTGTAAATTATATTTTTGTGAAGCGTTCAAACAAAAATAAACAATAAAATATTTTTCTATTTAATAGCAAAACATTTGACGATGAAAAGGAAAATGCGGGTTTGAAAATGGGCTTTGCCATGCTATTTTCATAATAACATATTTTTATTATGAATAATAAATTTACATACAATATATACAGTCTTAAATTTATTCATAATATTTTTGAGAATctgagactgccaaggcacacaggggataggn
39
+ +
40
+ hh`XSSSTddhh\\\]hhhhhhhhhbbbbhhghhhbbZZZZhhhhhhhhhhhhhhhhhhhhhhhhheZZUUUcchhhhhhhhhhhhhhhhhhhddXSSSQQSS__UUUbb[[acc`\LLLLLQ[KKKKUTXNNOO\\\WbhhhZ]]\\ggZZhhhhhhbb__^^^hhh____hb^UUUghccbh^a^^bb[ddPPPPPaSaccbaZ\_aVVV]NNNNL\RQR^SQRKKKN\PKKKKLYSdZ^^dhhhhhbbbbh]ZZZhhhhhhh[[__^\NNNNV\`XXXWW[[SSTThdddhhhhhhhhhhhhh[XXXghhhhhhhhhhh^^^^^hhhhhhhhhhhb`bZTTTRXdhhhhhhhhhhhhhhhhggXXXgggh`\`ddee_\MMMMM`c___ccddddehhhZZZXVVeebbb_QSSSX^ecc;
data/test/data/formats/misc_dna_as_illumina.fastq ADDED
@@ -0,0 +1,16 @@
1
+ @FAKE0007 Original version has lower case unambiguous DNA with PHRED scores from 0 to 40 inclusive (in that order)
2
+ ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTA
3
+ +
4
+ @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
5
+ @FAKE0008 Original version has mixed case unambiguous DNA with PHRED scores from 0 to 40 inclusive (in that order)
6
+ gTcatAGcgTcatAGcgTcatAGcgTcatAGcgTcatAGcg
7
+ +
8
+ @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
9
+ @FAKE0009 Original version has lower case unambiguous DNA with PHRED scores from 0 to 40 inclusive (in that order)
10
+ tcagtcagtcagtcagtcagtcagtcagtcagtcagtcagt
11
+ +
12
+ @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
13
+ @FAKE0010 Original version has mixed case ambiguous DNA and PHRED scores of 40, 30, 20, 10 (cycled)
14
+ gatcrywsmkhbvdnGATCRYWSMKHBVDN
15
+ +
16
+ h^TJh^TJh^TJh^TJh^TJh^TJh^TJh^
data/test/data/formats/misc_dna_as_sanger.fastq ADDED
@@ -0,0 +1,16 @@
1
+ @FAKE0007 Original version has lower case unambiguous DNA with PHRED scores from 0 to 40 inclusive (in that order)
2
+ ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTA
3
+ +
4
+ !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
5
+ @FAKE0008 Original version has mixed case unambiguous DNA with PHRED scores from 0 to 40 inclusive (in that order)
6
+ gTcatAGcgTcatAGcgTcatAGcgTcatAGcgTcatAGcg
7
+ +
8
+ !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
9
+ @FAKE0009 Original version has lower case unambiguous DNA with PHRED scores from 0 to 40 inclusive (in that order)
10
+ tcagtcagtcagtcagtcagtcagtcagtcagtcagtcagt
11
+ +
12
+ !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
13
+ @FAKE0010 Original version has mixed case ambiguous DNA and PHRED scores of 40, 30, 20, 10 (cycled)
14
+ gatcrywsmkhbvdnGATCRYWSMKHBVDN
15
+ +
16
+ I?5+I?5+I?5+I?5+I?5+I?5+I?5+I?
data/test/data/formats/misc_dna_as_solexa.fastq ADDED
@@ -0,0 +1,16 @@
1
+ @FAKE0007 Original version has lower case unambiguous DNA with PHRED scores from 0 to 40 inclusive (in that order)
2
+ ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTA
3
+ +
4
+ ;;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
5
+ @FAKE0008 Original version has mixed case unambiguous DNA with PHRED scores from 0 to 40 inclusive (in that order)
6
+ gTcatAGcgTcatAGcgTcatAGcgTcatAGcgTcatAGcg
7
+ +
8
+ ;;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
9
+ @FAKE0009 Original version has lower case unambiguous DNA with PHRED scores from 0 to 40 inclusive (in that order)
10
+ tcagtcagtcagtcagtcagtcagtcagtcagtcagtcagt
11
+ +
12
+ ;;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
13
+ @FAKE0010 Original version has mixed case ambiguous DNA and PHRED scores of 40, 30, 20, 10 (cycled)
14
+ gatcrywsmkhbvdnGATCRYWSMKHBVDN
15
+ +
16
+ h^TJh^TJh^TJh^TJh^TJh^TJh^TJh^
data/test/data/formats/misc_dna_original_sanger.fastq ADDED
@@ -0,0 +1,16 @@
1
+ @FAKE0007 Original version has lower case unambiguous DNA with PHRED scores from 0 to 40 inclusive (in that order)
2
+ ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTA
3
+ +
4
+ !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
5
+ @FAKE0008 Original version has mixed case unambiguous DNA with PHRED scores from 0 to 40 inclusive (in that order)
6
+ gTcatAGcgTcatAGcgTcatAGcgTcatAGcgTcatAGcg
7
+ +
8
+ !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
9
+ @FAKE0009 Original version has lower case unambiguous DNA with PHRED scores from 0 to 40 inclusive (in that order)
10
+ tcagtcagtcagtcagtcagtcagtcagtcagtcagtcagt
11
+ +
12
+ !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
13
+ @FAKE0010 Original version has mixed case ambiguous DNA and PHRED scores of 40, 30, 20, 10 (cycled)
14
+ gatcrywsmkhbvdnGATCRYWSMKHBVDN
15
+ +
16
+ I?5+I?5+I?5+I?5+I?5+I?5+I?5+I?
data/test/data/formats/misc_rna_as_illumina.fastq ADDED
@@ -0,0 +1,16 @@
1
+ @FAKE0011 Original version has lower case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
2
+ ACGUACGUACGUACGUACGUACGUACGUACGUACGUACGUA
3
+ +
4
+ @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
5
+ @FAKE0012 Original version has mixed case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
6
+ gUcauAGcgUcauAGcgUcauAGcgUcauAGcgUcauAGcg
7
+ +
8
+ @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
9
+ @FAKE0013 Original version has lower case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
10
+ ucagucagucagucagucagucagucagucagucagucagu
11
+ +
12
+ @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
13
+ @FAKE0014 Original version has mixed case ambiguous RNA with PHRED scores from 35 to 40 inclusive (cycled)
14
+ gaucrywsmkhbvdnGAUCRYWSMKHBVDN
15
+ +
16
+ cdefghcdefghcdefghcdefghcdefgh
data/test/data/formats/misc_rna_as_sanger.fastq ADDED
@@ -0,0 +1,16 @@
1
+ @FAKE0011 Original version has lower case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
2
+ ACGUACGUACGUACGUACGUACGUACGUACGUACGUACGUA
3
+ +
4
+ !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
5
+ @FAKE0012 Original version has mixed case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
6
+ gUcauAGcgUcauAGcgUcauAGcgUcauAGcgUcauAGcg
7
+ +
8
+ !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
9
+ @FAKE0013 Original version has lower case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
10
+ ucagucagucagucagucagucagucagucagucagucagu
11
+ +
12
+ !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
13
+ @FAKE0014 Original version has mixed case ambiguous RNA with PHRED scores from 35 to 40 inclusive (cycled)
14
+ gaucrywsmkhbvdnGAUCRYWSMKHBVDN
15
+ +
16
+ DEFGHIDEFGHIDEFGHIDEFGHIDEFGHI
data/test/data/formats/misc_rna_as_solexa.fastq ADDED
@@ -0,0 +1,16 @@
1
+ @FAKE0011 Original version has lower case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
2
+ ACGUACGUACGUACGUACGUACGUACGUACGUACGUACGUA
3
+ +
4
+ ;;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
5
+ @FAKE0012 Original version has mixed case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
6
+ gUcauAGcgUcauAGcgUcauAGcgUcauAGcgUcauAGcg
7
+ +
8
+ ;;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
9
+ @FAKE0013 Original version has lower case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
10
+ ucagucagucagucagucagucagucagucagucagucagu
11
+ +
12
+ ;;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
13
+ @FAKE0014 Original version has mixed case ambiguous RNA with PHRED scores from 35 to 40 inclusive (cycled)
14
+ gaucrywsmkhbvdnGAUCRYWSMKHBVDN
15
+ +
16
+ cdefghcdefghcdefghcdefghcdefgh