bio 1.3.1 → 1.4.0

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Files changed (303) hide show
  1. data/ChangeLog +2105 -3728
  2. data/KNOWN_ISSUES.rdoc +35 -3
  3. data/README.rdoc +8 -2
  4. data/RELEASE_NOTES.rdoc +166 -0
  5. data/bin/bioruby +4 -1
  6. data/bioruby.gemspec +146 -1
  7. data/bioruby.gemspec.erb +3 -1
  8. data/doc/ChangeLog-before-1.3.1 +3961 -0
  9. data/doc/Tutorial.rd +154 -22
  10. data/doc/Tutorial.rd.html +125 -68
  11. data/lib/bio.rb +21 -6
  12. data/lib/bio/appl/bl2seq/report.rb +11 -202
  13. data/lib/bio/appl/blast/format0.rb +0 -193
  14. data/lib/bio/appl/blast/report.rb +2 -147
  15. data/lib/bio/appl/blast/wublast.rb +0 -208
  16. data/lib/bio/appl/fasta.rb +4 -19
  17. data/lib/bio/appl/fasta/format10.rb +0 -14
  18. data/lib/bio/appl/genscan/report.rb +0 -176
  19. data/lib/bio/appl/hmmer.rb +1 -15
  20. data/lib/bio/appl/hmmer/report.rb +0 -100
  21. data/lib/bio/appl/meme/mast.rb +156 -0
  22. data/lib/bio/appl/meme/mast/report.rb +91 -0
  23. data/lib/bio/appl/meme/motif.rb +48 -0
  24. data/lib/bio/appl/psort.rb +0 -111
  25. data/lib/bio/appl/psort/report.rb +1 -45
  26. data/lib/bio/appl/pts1.rb +2 -4
  27. data/lib/bio/appl/sosui/report.rb +5 -54
  28. data/lib/bio/appl/targetp/report.rb +1 -104
  29. data/lib/bio/appl/tmhmm/report.rb +0 -36
  30. data/lib/bio/command.rb +94 -10
  31. data/lib/bio/data/aa.rb +1 -77
  32. data/lib/bio/data/codontable.rb +1 -95
  33. data/lib/bio/data/na.rb +1 -26
  34. data/lib/bio/db/aaindex.rb +1 -38
  35. data/lib/bio/db/fasta.rb +1 -134
  36. data/lib/bio/db/fasta/format_qual.rb +204 -0
  37. data/lib/bio/db/fasta/qual.rb +102 -0
  38. data/lib/bio/db/fastq.rb +645 -0
  39. data/lib/bio/db/fastq/fastq_to_biosequence.rb +40 -0
  40. data/lib/bio/db/fastq/format_fastq.rb +175 -0
  41. data/lib/bio/db/genbank/genbank.rb +1 -86
  42. data/lib/bio/db/gff.rb +0 -17
  43. data/lib/bio/db/go.rb +4 -72
  44. data/lib/bio/db/kegg/common.rb +112 -0
  45. data/lib/bio/db/kegg/compound.rb +29 -20
  46. data/lib/bio/db/kegg/drug.rb +74 -34
  47. data/lib/bio/db/kegg/enzyme.rb +26 -5
  48. data/lib/bio/db/kegg/genes.rb +128 -15
  49. data/lib/bio/db/kegg/genome.rb +3 -41
  50. data/lib/bio/db/kegg/glycan.rb +19 -24
  51. data/lib/bio/db/kegg/orthology.rb +16 -56
  52. data/lib/bio/db/kegg/reaction.rb +81 -28
  53. data/lib/bio/db/kegg/taxonomy.rb +1 -52
  54. data/lib/bio/db/litdb.rb +1 -16
  55. data/lib/bio/db/phyloxml/phyloxml.xsd +582 -0
  56. data/lib/bio/db/phyloxml/phyloxml_elements.rb +1174 -0
  57. data/lib/bio/db/phyloxml/phyloxml_parser.rb +954 -0
  58. data/lib/bio/db/phyloxml/phyloxml_writer.rb +228 -0
  59. data/lib/bio/db/prosite.rb +2 -95
  60. data/lib/bio/db/rebase.rb +5 -6
  61. data/lib/bio/db/sanger_chromatogram/abif.rb +120 -0
  62. data/lib/bio/db/sanger_chromatogram/chromatogram.rb +133 -0
  63. data/lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb +32 -0
  64. data/lib/bio/db/sanger_chromatogram/scf.rb +210 -0
  65. data/lib/bio/io/das.rb +0 -44
  66. data/lib/bio/io/ddbjxml.rb +1 -181
  67. data/lib/bio/io/flatfile.rb +1 -7
  68. data/lib/bio/io/flatfile/autodetection.rb +6 -0
  69. data/lib/bio/io/keggapi.rb +0 -442
  70. data/lib/bio/io/ncbirest.rb +130 -132
  71. data/lib/bio/io/ncbisoap.rb +2 -1
  72. data/lib/bio/io/pubmed.rb +0 -88
  73. data/lib/bio/location.rb +0 -73
  74. data/lib/bio/pathway.rb +0 -171
  75. data/lib/bio/sequence.rb +18 -1
  76. data/lib/bio/sequence/adapter.rb +3 -0
  77. data/lib/bio/sequence/format.rb +16 -0
  78. data/lib/bio/sequence/quality_score.rb +205 -0
  79. data/lib/bio/tree.rb +70 -5
  80. data/lib/bio/util/restriction_enzyme/single_strand.rb +3 -2
  81. data/lib/bio/util/sirna.rb +1 -23
  82. data/lib/bio/version.rb +1 -1
  83. data/sample/demo_aaindex.rb +67 -0
  84. data/sample/demo_aminoacid.rb +101 -0
  85. data/sample/demo_bl2seq_report.rb +220 -0
  86. data/sample/demo_blast_report.rb +285 -0
  87. data/sample/demo_codontable.rb +119 -0
  88. data/sample/demo_das.rb +105 -0
  89. data/sample/demo_ddbjxml.rb +212 -0
  90. data/sample/demo_fasta_remote.rb +51 -0
  91. data/sample/demo_fastaformat.rb +105 -0
  92. data/sample/demo_genbank.rb +132 -0
  93. data/sample/demo_genscan_report.rb +202 -0
  94. data/sample/demo_gff1.rb +49 -0
  95. data/sample/demo_go.rb +98 -0
  96. data/sample/demo_hmmer_report.rb +149 -0
  97. data/sample/demo_kegg_compound.rb +57 -0
  98. data/sample/demo_kegg_drug.rb +65 -0
  99. data/sample/demo_kegg_genome.rb +74 -0
  100. data/sample/demo_kegg_glycan.rb +72 -0
  101. data/sample/demo_kegg_orthology.rb +62 -0
  102. data/sample/demo_kegg_reaction.rb +66 -0
  103. data/sample/demo_kegg_taxonomy.rb +92 -0
  104. data/sample/demo_keggapi.rb +502 -0
  105. data/sample/demo_litdb.rb +42 -0
  106. data/sample/demo_locations.rb +99 -0
  107. data/sample/demo_ncbi_rest.rb +130 -0
  108. data/sample/demo_nucleicacid.rb +49 -0
  109. data/sample/demo_pathway.rb +196 -0
  110. data/sample/demo_prosite.rb +120 -0
  111. data/sample/demo_psort.rb +138 -0
  112. data/sample/demo_psort_report.rb +70 -0
  113. data/sample/demo_pubmed.rb +118 -0
  114. data/sample/demo_sirna.rb +63 -0
  115. data/sample/demo_sosui_report.rb +89 -0
  116. data/sample/demo_targetp_report.rb +135 -0
  117. data/sample/demo_tmhmm_report.rb +68 -0
  118. data/sample/pmfetch.rb +13 -4
  119. data/sample/pmsearch.rb +15 -4
  120. data/sample/test_phyloxml_big.rb +205 -0
  121. data/test/bioruby_test_helper.rb +61 -0
  122. data/test/data/KEGG/1.1.1.1.enzyme +935 -0
  123. data/test/data/KEGG/C00025.compound +102 -0
  124. data/test/data/KEGG/D00063.drug +104 -0
  125. data/test/data/KEGG/G00024.glycan +47 -0
  126. data/test/data/KEGG/G01366.glycan +18 -0
  127. data/test/data/KEGG/K02338.orthology +902 -0
  128. data/test/data/KEGG/R00006.reaction +14 -0
  129. data/test/data/fastq/README.txt +109 -0
  130. data/test/data/fastq/error_diff_ids.fastq +20 -0
  131. data/test/data/fastq/error_double_qual.fastq +22 -0
  132. data/test/data/fastq/error_double_seq.fastq +22 -0
  133. data/test/data/fastq/error_long_qual.fastq +20 -0
  134. data/test/data/fastq/error_no_qual.fastq +20 -0
  135. data/test/data/fastq/error_qual_del.fastq +20 -0
  136. data/test/data/fastq/error_qual_escape.fastq +20 -0
  137. data/test/data/fastq/error_qual_null.fastq +0 -0
  138. data/test/data/fastq/error_qual_space.fastq +21 -0
  139. data/test/data/fastq/error_qual_tab.fastq +21 -0
  140. data/test/data/fastq/error_qual_unit_sep.fastq +20 -0
  141. data/test/data/fastq/error_qual_vtab.fastq +20 -0
  142. data/test/data/fastq/error_short_qual.fastq +20 -0
  143. data/test/data/fastq/error_spaces.fastq +20 -0
  144. data/test/data/fastq/error_tabs.fastq +21 -0
  145. data/test/data/fastq/error_trunc_at_plus.fastq +19 -0
  146. data/test/data/fastq/error_trunc_at_qual.fastq +19 -0
  147. data/test/data/fastq/error_trunc_at_seq.fastq +18 -0
  148. data/test/data/fastq/error_trunc_in_plus.fastq +19 -0
  149. data/test/data/fastq/error_trunc_in_qual.fastq +20 -0
  150. data/test/data/fastq/error_trunc_in_seq.fastq +18 -0
  151. data/test/data/fastq/error_trunc_in_title.fastq +17 -0
  152. data/test/data/fastq/illumina_full_range_as_illumina.fastq +8 -0
  153. data/test/data/fastq/illumina_full_range_as_sanger.fastq +8 -0
  154. data/test/data/fastq/illumina_full_range_as_solexa.fastq +8 -0
  155. data/test/data/fastq/illumina_full_range_original_illumina.fastq +8 -0
  156. data/test/data/fastq/longreads_as_illumina.fastq +40 -0
  157. data/test/data/fastq/longreads_as_sanger.fastq +40 -0
  158. data/test/data/fastq/longreads_as_solexa.fastq +40 -0
  159. data/test/data/fastq/longreads_original_sanger.fastq +120 -0
  160. data/test/data/fastq/misc_dna_as_illumina.fastq +16 -0
  161. data/test/data/fastq/misc_dna_as_sanger.fastq +16 -0
  162. data/test/data/fastq/misc_dna_as_solexa.fastq +16 -0
  163. data/test/data/fastq/misc_dna_original_sanger.fastq +16 -0
  164. data/test/data/fastq/misc_rna_as_illumina.fastq +16 -0
  165. data/test/data/fastq/misc_rna_as_sanger.fastq +16 -0
  166. data/test/data/fastq/misc_rna_as_solexa.fastq +16 -0
  167. data/test/data/fastq/misc_rna_original_sanger.fastq +16 -0
  168. data/test/data/fastq/sanger_full_range_as_illumina.fastq +8 -0
  169. data/test/data/fastq/sanger_full_range_as_sanger.fastq +8 -0
  170. data/test/data/fastq/sanger_full_range_as_solexa.fastq +8 -0
  171. data/test/data/fastq/sanger_full_range_original_sanger.fastq +8 -0
  172. data/test/data/fastq/solexa_full_range_as_illumina.fastq +8 -0
  173. data/test/data/fastq/solexa_full_range_as_sanger.fastq +8 -0
  174. data/test/data/fastq/solexa_full_range_as_solexa.fastq +8 -0
  175. data/test/data/fastq/solexa_full_range_original_solexa.fastq +8 -0
  176. data/test/data/fastq/wrapping_as_illumina.fastq +12 -0
  177. data/test/data/fastq/wrapping_as_sanger.fastq +12 -0
  178. data/test/data/fastq/wrapping_as_solexa.fastq +12 -0
  179. data/test/data/fastq/wrapping_original_sanger.fastq +24 -0
  180. data/test/data/meme/db +0 -0
  181. data/test/data/meme/mast +0 -0
  182. data/test/data/meme/mast.out +13 -0
  183. data/test/data/meme/meme.out +3 -0
  184. data/test/data/phyloxml/apaf.xml +666 -0
  185. data/test/data/phyloxml/bcl_2.xml +2097 -0
  186. data/test/data/phyloxml/made_up.xml +144 -0
  187. data/test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml +65 -0
  188. data/test/data/phyloxml/phyloxml_examples.xml +415 -0
  189. data/test/data/sanger_chromatogram/test_chromatogram_abif.ab1 +0 -0
  190. data/test/data/sanger_chromatogram/test_chromatogram_scf_v2.scf +0 -0
  191. data/test/data/sanger_chromatogram/test_chromatogram_scf_v3.scf +0 -0
  192. data/test/functional/bio/appl/test_pts1.rb +7 -5
  193. data/test/functional/bio/io/test_ensembl.rb +4 -3
  194. data/test/functional/bio/io/test_pubmed.rb +9 -3
  195. data/test/functional/bio/io/test_soapwsdl.rb +5 -4
  196. data/test/functional/bio/io/test_togows.rb +5 -4
  197. data/test/functional/bio/sequence/test_output_embl.rb +6 -4
  198. data/test/functional/bio/test_command.rb +54 -5
  199. data/test/runner.rb +5 -3
  200. data/test/unit/bio/appl/bl2seq/test_report.rb +5 -4
  201. data/test/unit/bio/appl/blast/test_ncbioptions.rb +4 -2
  202. data/test/unit/bio/appl/blast/test_report.rb +5 -4
  203. data/test/unit/bio/appl/blast/test_rpsblast.rb +5 -4
  204. data/test/unit/bio/appl/gcg/test_msf.rb +5 -5
  205. data/test/unit/bio/appl/genscan/test_report.rb +8 -9
  206. data/test/unit/bio/appl/hmmer/test_report.rb +5 -4
  207. data/test/unit/bio/appl/iprscan/test_report.rb +6 -5
  208. data/test/unit/bio/appl/mafft/test_report.rb +6 -5
  209. data/test/unit/bio/appl/meme/mast/test_report.rb +46 -0
  210. data/test/unit/bio/appl/meme/test_mast.rb +103 -0
  211. data/test/unit/bio/appl/meme/test_motif.rb +38 -0
  212. data/test/unit/bio/appl/paml/codeml/test_rates.rb +5 -4
  213. data/test/unit/bio/appl/paml/codeml/test_report.rb +5 -4
  214. data/test/unit/bio/appl/paml/test_codeml.rb +5 -4
  215. data/test/unit/bio/appl/sim4/test_report.rb +5 -4
  216. data/test/unit/bio/appl/sosui/test_report.rb +6 -5
  217. data/test/unit/bio/appl/targetp/test_report.rb +5 -3
  218. data/test/unit/bio/appl/test_blast.rb +5 -4
  219. data/test/unit/bio/appl/test_fasta.rb +4 -2
  220. data/test/unit/bio/appl/test_pts1.rb +4 -2
  221. data/test/unit/bio/appl/tmhmm/test_report.rb +6 -5
  222. data/test/unit/bio/data/test_aa.rb +5 -3
  223. data/test/unit/bio/data/test_codontable.rb +5 -4
  224. data/test/unit/bio/data/test_na.rb +5 -3
  225. data/test/unit/bio/db/biosql/tc_biosql.rb +5 -1
  226. data/test/unit/bio/db/embl/test_common.rb +4 -2
  227. data/test/unit/bio/db/embl/test_embl.rb +6 -6
  228. data/test/unit/bio/db/embl/test_embl_rel89.rb +6 -6
  229. data/test/unit/bio/db/embl/test_embl_to_bioseq.rb +7 -8
  230. data/test/unit/bio/db/embl/test_sptr.rb +6 -8
  231. data/test/unit/bio/db/embl/test_uniprot.rb +6 -5
  232. data/test/unit/bio/db/fasta/test_format_qual.rb +346 -0
  233. data/test/unit/bio/db/kegg/test_compound.rb +146 -0
  234. data/test/unit/bio/db/kegg/test_drug.rb +194 -0
  235. data/test/unit/bio/db/kegg/test_enzyme.rb +241 -0
  236. data/test/unit/bio/db/kegg/test_genes.rb +32 -4
  237. data/test/unit/bio/db/kegg/test_glycan.rb +260 -0
  238. data/test/unit/bio/db/kegg/test_orthology.rb +50 -0
  239. data/test/unit/bio/db/kegg/test_reaction.rb +96 -0
  240. data/test/unit/bio/db/pdb/test_pdb.rb +4 -2
  241. data/test/unit/bio/db/sanger_chromatogram/test_abif.rb +76 -0
  242. data/test/unit/bio/db/sanger_chromatogram/test_scf.rb +98 -0
  243. data/test/unit/bio/db/test_aaindex.rb +6 -6
  244. data/test/unit/bio/db/test_fasta.rb +5 -46
  245. data/test/unit/bio/db/test_fastq.rb +829 -0
  246. data/test/unit/bio/db/test_gff.rb +4 -2
  247. data/test/unit/bio/db/test_lasergene.rb +7 -5
  248. data/test/unit/bio/db/test_medline.rb +4 -2
  249. data/test/unit/bio/db/test_newick.rb +6 -6
  250. data/test/unit/bio/db/test_nexus.rb +4 -2
  251. data/test/unit/bio/db/test_phyloxml.rb +769 -0
  252. data/test/unit/bio/db/test_phyloxml_writer.rb +328 -0
  253. data/test/unit/bio/db/test_prosite.rb +6 -5
  254. data/test/unit/bio/db/test_qual.rb +63 -0
  255. data/test/unit/bio/db/test_rebase.rb +5 -3
  256. data/test/unit/bio/db/test_soft.rb +7 -6
  257. data/test/unit/bio/io/flatfile/test_autodetection.rb +6 -7
  258. data/test/unit/bio/io/flatfile/test_buffer.rb +6 -5
  259. data/test/unit/bio/io/flatfile/test_splitter.rb +4 -4
  260. data/test/unit/bio/io/test_ddbjxml.rb +4 -3
  261. data/test/unit/bio/io/test_ensembl.rb +5 -3
  262. data/test/unit/bio/io/test_fastacmd.rb +4 -3
  263. data/test/unit/bio/io/test_flatfile.rb +6 -5
  264. data/test/unit/bio/io/test_soapwsdl.rb +4 -3
  265. data/test/unit/bio/io/test_togows.rb +4 -2
  266. data/test/unit/bio/sequence/test_aa.rb +5 -3
  267. data/test/unit/bio/sequence/test_common.rb +4 -2
  268. data/test/unit/bio/sequence/test_compat.rb +4 -2
  269. data/test/unit/bio/sequence/test_dblink.rb +5 -3
  270. data/test/unit/bio/sequence/test_na.rb +4 -2
  271. data/test/unit/bio/sequence/test_quality_score.rb +330 -0
  272. data/test/unit/bio/shell/plugin/test_seq.rb +5 -3
  273. data/test/unit/bio/test_alignment.rb +5 -3
  274. data/test/unit/bio/test_command.rb +4 -3
  275. data/test/unit/bio/test_db.rb +5 -3
  276. data/test/unit/bio/test_feature.rb +4 -2
  277. data/test/unit/bio/test_location.rb +4 -2
  278. data/test/unit/bio/test_map.rb +5 -3
  279. data/test/unit/bio/test_pathway.rb +4 -2
  280. data/test/unit/bio/test_reference.rb +4 -2
  281. data/test/unit/bio/test_sequence.rb +5 -3
  282. data/test/unit/bio/test_shell.rb +5 -3
  283. data/test/unit/bio/test_tree.rb +6 -6
  284. data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb +4 -2
  285. data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb +4 -2
  286. data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb +4 -2
  287. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb +4 -2
  288. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb +4 -2
  289. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +4 -2
  290. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb +4 -2
  291. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +4 -2
  292. data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +4 -2
  293. data/test/unit/bio/util/restriction_enzyme/test_analysis.rb +4 -2
  294. data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb +4 -2
  295. data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb +4 -2
  296. data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb +17 -13
  297. data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb +17 -13
  298. data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb +4 -2
  299. data/test/unit/bio/util/test_color_scheme.rb +5 -3
  300. data/test/unit/bio/util/test_contingency_table.rb +5 -3
  301. data/test/unit/bio/util/test_restriction_enzyme.rb +4 -2
  302. data/test/unit/bio/util/test_sirna.rb +6 -4
  303. metadata +147 -2
data/test/data/fastq/error_trunc_at_qual.fastq ADDED
@@ -0,0 +1,19 @@
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+ @SLXA-B3_649_FC8437_R1_1_1_610_79
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+ GATGTGCAATACCTTTGTAGAGGAA
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+ +SLXA-B3_649_FC8437_R1_1_1_610_79
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+ YYYYYYYYYYYYYYYYYYWYWYYSU
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+ @SLXA-B3_649_FC8437_R1_1_1_397_389
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+ GGTTTGAGAAAGAGAAATGAGATAA
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+ +SLXA-B3_649_FC8437_R1_1_1_397_389
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+ YYYYYYYYYWYYYYWWYYYWYWYWW
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+ @SLXA-B3_649_FC8437_R1_1_1_850_123
10
+ GAGGGTGTTGATCATGATGATGGCG
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+ +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
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+ @SLXA-B3_649_FC8437_R1_1_1_183_714
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+ GTATTATTTAATGGCATACACTCAA
19
+ +SLXA-B3_649_FC8437_R1_1_1_183_714
data/test/data/fastq/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/fastq/error_trunc_in_plus.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_FC
data/test/data/fastq/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/fastq/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/fastq/error_trunc_in_title.fastq ADDED
@@ -0,0 +1,17 @@
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_
data/test/data/fastq/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`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@
data/test/data/fastq/illumina_full_range_as_sanger.fastq ADDED
@@ -0,0 +1,8 @@
1
+ @FAKE0005 Original version has PHRED scores from 0 to 62 inclusive (in that order)
2
+ ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG
3
+ +
4
+ !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_
5
+ @FAKE0006 Original version has PHRED scores from 62 to 0 inclusive (in that order)
6
+ GCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
7
+ +
8
+ _^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"!
data/test/data/fastq/illumina_full_range_as_solexa.fastq ADDED
@@ -0,0 +1,8 @@
1
+ @FAKE0005 Original version has PHRED scores from 0 to 62 inclusive (in that order)
2
+ ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG
3
+ +
4
+ ;;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
5
+ @FAKE0006 Original version has PHRED scores from 62 to 0 inclusive (in that order)
6
+ GCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
7
+ +
8
+ ~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJHGFECB@>;;
data/test/data/fastq/illumina_full_range_original_illumina.fastq ADDED
@@ -0,0 +1,8 @@
1
+ @FAKE0005 Original version has PHRED scores from 0 to 62 inclusive (in that order)
2
+ ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG
3
+ +
4
+ @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`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/fastq/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/fastq/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/fastq/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/fastq/longreads_original_sanger.fastq ADDED
@@ -0,0 +1,120 @@
1
+ @FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95]
2
+ tcagTTAAGATGGGATAATATCCTCAGATTGCGTGATGAACTTTGTTCTGGTGGAGGAGAAGGAAGTGCATTCGACGTAT
3
+ GCCCGTTTGTCGATATTTGtatttaaagtaatccgtcacaaatcagtgacataaatattatttagatttcgggagcaact
4
+ ttatttattccacaagcaggtttaaattttaaatttaaattattgcagaagactttaaattaacctcgttgtcggagtca
5
+ tttgttcggttattggtcgaaagtaaccncgggaagtgccgaaaactaacaaacaaaagaagatagtgaaattttaatta
6
+ aaanaaatagccaaacgtaactaactaaaacggacccgtcgaggaactgccaacggacgacacagggagtagnnn
7
+ +FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95]
8
+ FFFDDDDDDDA666?688FFHGGIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIGHGFFFFF====DFFFFFFFFFFFFFF
9
+ D???:3104/76=:5...4.3,,,366////4<ABBAAA=CCFDDDDDDDD:666CDFFFF=<ABA=;:333111<===9
10
+ 9;B889FFFFFFDDBDBDDD=8844231..,,,-,,,,,,,,1133..---17111,,,,,22555131121.--.,333
11
+ 11,.,,3--,,.,,--,3511123..--!,,,,--,----9,,,,8=,,-,,,-,,,,---26:9:5-..1,,,,11//,
12
+ ,,,!,,1917--,,,,-3.,--,,17,,,,---+11113.030000,,,044400036;96662.//;7><;!!!
13
+ @FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74]
14
+ tcagCCAGCAATTCCGACTTAATTGTTCTTCTTCCATCATTCATCTCGACTAACAGTTCTACGATTAATGAGTTTGGCtt
15
+ taatttgttgttcattattgtcacaattacactactgagactgccaaggcacncagggataggnn
16
+ +FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74]
17
+ FFFFFFFFFDDDDFFFFGFDDDDBAAAAA=<4444@@B=555:BBBBB@@?8:8<?<89898<84442;==3,,,514,,
18
+ ,11,,,.,,21777555513,..--1115758.//34488><<;;;;9944/!/4,,,57855!!
19
+ @FSRRS4401B64ST [length=382] [gc=40.58] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=346]
20
+ tcagTTTTCTTAAATTACTTGAATCTGTTGAAGTGGATGTCCACTTTTGTATGCCAAATATGCCCAGCGTATACGATCTT
21
+ GGCCACATCTCCACATAATCATCAGTCGGATGCAAAAAGCGATTAAACTAAAAATGAATGCGTTTTTAGATGAGTAAATA
22
+ GGTAATACTTTGTTTAAATAATAAATGTCACAAACAGAACGCGGATTACAGTACCTGAAAATAGTTGTACTGTATCTGTG
23
+ CCGGCACTTCCTCGGCCCTGAGAAGTTGTCCCGTTGTTTCCATTCGCACCATCCAATGGCCAAAGTTTGCGAAGAATCTG
24
+ TTCCGTTCCATTACCAATTGTTTTTCCATGctgagactgccaaggcacacaggggataggnn
25
+ +FSRRS4401B64ST [length=382] [gc=40.58] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=346]
26
+ IIIICCCCI??666IIIIIIIIIIIIIIIIIIIIIIIIIIIIII6666IAIIIII???IIIICCCIIIIIIIIIIIIIII
27
+ IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII66333EICE::338=/----,8=>>??:2-////7>CEEIEIHHHII
28
+ IIIIIIIE;;9911199B???IBCHIIIIIIHHHIIHHHIIIIIIIIIIIIIIIIIIBBCCIIIIIIIIIIIIIIIIIII
29
+ IIIIIIIIIIIIIIIGGGIIIIIIIIID?===DIIIHHHIIIIIIIIIHHHIIIIIIIIIIHHHIHHHIIIIIIIIIIII
30
+ IIIIIIIIII?>;9988==5----.@@AEGIIIIIIIIIHH????EIIIFF999;EIIBB!!
31
+ @FSRRS4401EJ0YH [length=381] [gc=48.29] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=343]
32
+ tcagTTTTTGGAGAATTCCGTCAGGGACGGCATGGCATATTTGTGGGTTCGGCACGGCGTCCTGGCCAAGAAGAAGAAGA
33
+ CGAATTAGCCCGTTAATTTAATGACACCTTCCCCAATTTTGCAGCAATGATTGGTTCATTCTTGGCGGTGCGTTTTTGTG
34
+ CTTCGTCGAATTGTTGGCCATTTTGGTCCACCGGCCATCATCTTTACGCTATCCGACTGATTGGAAATCACCGCCTAGCA
35
+ TTTTGCCGAAGATTGTTGCGTTGTACGGCCATGTGCTGATTGTTTACATTGGCATTCTTGGCAATTTGTCCTTGGTCGGC
36
+ TTTGACGGCAAATTTGCGGTGTTAAGTctgagactgccaaggcacacagggggatagggnn
37
+ +FSRRS4401EJ0YH [length=381] [gc=48.29] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=343]
38
+ IIII?????IIIIIIIIIIIIIIHHHIIIIIIIIIIIIIHHHIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
39
+ IIIIIIIIHHHIIIIIHHHIIIIIIIIIIIAAAAII>>>>IIIIIIIIIIIIIIIIIIIIIIIIIIEEIEE;33333D7I
40
+ IIIIIIIIIIIIIIIIIIIICC@@HHIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIII
41
+ BBBBIHCDCHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIHHCCDIIIIIIHHHIICCCH=CCIIIIIIIII
42
+ GGGIIIIIIHHHHHHIIIIIIIIIIIIIIIHHHIIHHE??>>?EFEE?/////;:80--!!
43
+ @FSRRS4401BK0IB [length=507] [gc=49.31] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=208]
44
+ tcagTTGACCGGCGTTGTGTAACAATAATTCATTATTCTGAGACGATGCCAATGTAATCGACGGTTTATGCCCAATTATT
45
+ CCCATCTATGCTTAACTGATCAAATACTATTTGCATTACGTCACGAAATTGCGCGAACACCGCCGGCCGACAATAATTTA
46
+ TACCGGACATACCGGAGTTGATGGTAATCGGTAAAGAGTTTTATTTAATTATntattatcnctattaattattgttanca
47
+ acaatgtgcacgctntgccgcccgccgccgccgtgtcggtaggaccccggacggacccggacccggttcgggtacccgtt
48
+ ttcgggttcccggaaccgtttttcgggtacccggttttttcggggggccccccggtaaaaaaccggggaaccccctaaaa
49
+ cgggtaaacgtaccgtaagggaccccctaaacgggggccccgaaaaaccgggacccaaaccggggggaaacggttaaagg
50
+ ggggggaagtaggngnnnnnnnnnnnn
51
+ +FSRRS4401BK0IB [length=507] [gc=49.31] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=208]
52
+ FFFA@@FFFFFFFFFFHHB:::@BFFFFGGHIHIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFF?=BA@11188011<<
53
+ 88;?AABDDC???DDAAAADA666D?DDD=====AA>?>><<<=<11188<<???AA?9555=ABBB@@?=>>?@@1114
54
+ 2::DDA???DFFFFFFFFFFFFFBAAAA<<0000.22=////8,--111111!23--/24!37:6666<;822/..4!46
55
+ 521177553.-.23!231121112,,-,,211==5------,12,,,,,,-,,,-1,,,,-,,155--,,,,13111.,,
56
+ ,,,,,,++111..11..1,,,,,,,,,+3,,,,,--22-----//----55//**/--22--**,,,,**,,,,,,.1.,
57
+ *,,,,***,,,,,,,,,,,,,,,,,,,,,,,),,-,,,,,,),,,,,**//.),,,///,,,,,,,,,,,.))33---,,
58
+ ,,,,,,,,(0,,,!.!!!!!!!!!!!!
59
+ @FSRRS4401ARCCB [length=258] [gc=46.90] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=193]
60
+ tcagTTATTGCAGTCGTTCCGCGCCATCGCCGGTAACCGTCCGCGTGTTATTCTGTGTATCGGCCAACCTTCGTATAACT
61
+ TCGTATAATGTATGCTATACGAAGTTATTACGATCTATACCGGCGAAACTCAGCCGAAAGGTCTCGCGGTAGAGCCTATG
62
+ AGCTGCCCGACCGATGCATTTAAATTTCCGGGGATCGtcgctgatctgagactgccaaaggcacactagggggataggnn
63
+ nnnnnnnnnnnnnnnnnn
64
+ +FSRRS4401ARCCB [length=258] [gc=46.90] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=193]
65
+ FFF<8::@DFFFFFFFGGFDCAAAAAB@@000046<;66322366762243348<<=??4445::>ABAAA@<<==B=:5
66
+ 55:BBD??=BDDDDFFFCCCCCCCFFCDDDFFFFFDBAA==88880004><<<99688;889<889?BBBBA=???DDBB
67
+ B@@??88889---237771,,,,,,,,--1152<<00158A@><<<<<43277711,,,--37===75,----34666!!
68
+ !!!!!!!!!!!!!!!!!!
69
+ @FSRRS4401CM938 [length=453] [gc=44.15] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=418]
70
+ tcagGTTTTAAATCGCTTTCCAAGGAATTTGAGTCTAAATCCGGTGGATCCCATCAGTACAAATGCGGCGACAAGGCCGT
71
+ GAAAACACTGCTTAATTCTTTGCACTTTTTGGCCACCTTTTTGGAAATGTTGTTTTGTGTTCTCAAAATTTTCCATCTCA
72
+ GAACAAACATTCCATCGGGCTGATGTTGTGGCTTTTGGCGCGCGAAGTGCTGCTACTGCGCGGCAAAATCAGTCGCCAGA
73
+ CCGGTTTTGTTGTGGACGACAAAGTGATCATGCCTGACTTGTACTTCTACCGCGATCCGCAAGCGCGAATTGGTCACATA
74
+ GTTATAGAATTTTTGAGCCTTTTTCTTGACATAAAAAGTGTGGTTTTAAAAATTTCCTGGCAGGACCCACGCCAACGTTC
75
+ AGGAATAATATCTTTTAAAAAGctgagactgccaaggcacacaggggataggn
76
+ +FSRRS4401CM938 [length=453] [gc=44.15] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=418]
77
+ IIIIICC>>666IIIICCCIIIIIIIIHHHIIIIIG666IIIIIIIIIIHHHIIIIIIIICCCIIIIIIIIIIIIIIIII
78
+ I@@@@IIIIIIIIIIIIIHHHIIII???=;IIEEI:://///7544:?IBB72244E8EECEBC=@@@@@@@HHIIIIII
79
+ IIIIBBBIIIIIIIIIHHHIIIIIIIIIIIIICCCCIIIIIIIIIIIIIIIIIIIIIIIIIIII6666DEIIHEB??D@7
80
+ 77772222D89EEIIIIIIIHHHIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIII
81
+ IIIIIIIII==?==IIIII???=;I63DDD82--,,,38==::----,,---+++33066;@6380008/:889<:BGII
82
+ IIIIIIIFE<?F5500-----5:;;;:>?@C<<7999EEEEEE@@@@EEEEE!
83
+ @FSRRS4401EQLIK [length=411] [gc=34.31] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=374]
84
+ tcagTTTAATTTGGTGCTTCCTTTCAATTCCTTAGTTTAAACTTGGCACTGAAGTCTCGCATTTATAACTAGAGCCCGGA
85
+ TTTTAGAGGCTAAAAAGTTTTCCAGATTTCAAAATTTATTTCGAAACTATTTTTCTGATTGTGATGTGACGGATTTCTAA
86
+ ATTAAATCGAAATGATGTGTATTGAACTTAACAAGTGATTTTTATCAGATTTTGTCAATGAATAAATTTTAATTTAAATC
87
+ TCTTTCTAACACTTTCATGATTAAAATCTAACAAAGCGCGACCAGTATGTGAGAAGAGCAAAAACAACAAAAAGTGCTAG
88
+ CACTAAAGAAGGTTCGAACCCAACACATAACGTAAGAGTTACCGGGAAGAAAACCACTctgagactgccaaggcacacag
89
+ ggggataggnn
90
+ +FSRRS4401EQLIK [length=411] [gc=34.31] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=374]
91
+ III?666??HHHIIIIIIIIIGGGIIIIIIIIIIIGGGHHHIIIIIIIIIIIIIIIIIIIIGGGIIIIIIIIIIHHHIII
92
+ @@@@IIIIEIE111100----22?=8---:-------,,,,33---5:3,----:1BBEEEHIIIIIIIIIIIB??A122
93
+ 000...:?=024GIIIIIIIIIIIIIIIIIIECCHHB=//-,,21??<5-002=6FBB?:9<=11/4444//-//77??G
94
+ EIEEHIACCIIIHHHIIIIIIICCCAIIIHHHHHHIIIIIIIIIIIIIIIIIIIIIIEE1//--822;----.777@EII
95
+ IIII???IIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIII994227775555AE;IEEEEEIIIII??9755>@==:3,
96
+ ,,,,33336!!
97
+ @FSRRS4401AOV6A [length=309] [gc=22.98] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=273]
98
+ tcagTTTTCAAATTTTCCGAAATTTGCTGTTTGGTAGAAGGCAAATTATTTGATTGAATTTTGTATTTATTTAAAACAAT
99
+ TTATTTTAAAATAATAATTTTCCATTGACTTTTTACATTTAATTGATTTTATTATGCATTTTATATTTGTTTTCTAAATA
100
+ TTCGTTTGCAAACTCACGTTGAAATTGTATTAAACTCGAAATTAGAGTTTTTGAAATTAATTTTTATGTAGCATAATATT
101
+ TTAAACATATTGGAATTTTATAAAACATTATATTTTTctgagactgccaaggcacacagggggataggn
102
+ +FSRRS4401AOV6A [length=309] [gc=22.98] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=273]
103
+ IIIICCCCI;;;CCCCIII???HHHIIIIHHHIIIIIIIIIIHHHIIIHHHIIIIIII@@@@IFICCCICAA;;;;ED?B
104
+ @@D66445555<<<GII>>AAIIIIIIII;;;::III???CCCIII;;;;IFFIIIIICCCBIBIEEDC4444?4BBBE?
105
+ EIIICHHII;;;HIIIIIIHH;;;HHIIIII;;;IIIIHHHIIIIII>>??>IEEBGG::1111/46FBFBB?=;=A?97
106
+ 771119:EAAADDBD7777=/111122DA@@B68;;;I8HHIIIII;;;;?>IECCCB/////;745=!
107
+ @FSRRS4401EG0ZW [length=424] [gc=23.82] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=389]
108
+ tcagTTTTGATCTTTTAATAATGAATTTTAATGTGTTAAAATGATTGCATTGATGGCATAACCGCATTTAAATTAATTAC
109
+ ATGAAGTGTAAGTATGAAATTTTCCTTTCCAAATTGCAAAAACTAAAATTTAAAATTTATCGTAAAAATTAACATATATT
110
+ TTAAACGATTTTAAGAAACATTTGTAAATTATATTTTTGTGAAGCGTTCAAACAAAAATAAACAATAAAATATTTTTCTA
111
+ TTTAATAGCAAAACATTTGACGATGAAAAGGAAAATGCGGGTTTGAAAATGGGCTTTGCCATGCTATTTTCATAATAACA
112
+ TATTTTTATTATGAATAATAAATTTACATACAATATATACAGTCTTAAATTTATTCATAATATTTTTGAGAATctgagac
113
+ tgccaaggcacacaggggataggn
114
+ +FSRRS4401EG0ZW [length=424] [gc=23.82] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=389]
115
+ IIA94445EEII===>IIIIIIIIICCCCIIHIIICC;;;;IIIIIIIIIIIIIIIIIIIIIIIIIF;;666DDIIIIII
116
+ IIIIIIIIIIIIIEE94442244@@666CC<<BDDA=-----2<,,,,659//00===8CIII;>>==HH;;IIIIIICC
117
+ @@???III@@@@IC?666HIDDCI?B??CC<EE11111B4BDDCB;=@B777>////-=323?423,,,/=1,,,,-:4E
118
+ ;??EIIIIICCCCI>;;;IIIIIII<<@@?=////7=A99988<<4455IEEEIIIIIIIIIIIII<999HIIIIIIIII
119
+ II?????IIIIIIIIIIICAC;55539EIIIIIIIIIIIIIIIIHH999HHHIA=AEEFF@=.....AD@@@DDEEEEFI
120
+ II;;;977FFCCC@24449?FDD!
data/test/data/fastq/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/fastq/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/fastq/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^