bio 1.3.1 → 1.4.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (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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+ 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
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+ +SLXA-B3_649_FC8437_R1_1_1_850_123
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+ YYYYYYYYYYYYYWYYWYYSYYYSY
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+ @SLXA-B3_649_FC8437_R1_1_1_362_549
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+ GGAAACAAAGTTTTTCTCAACATAG
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+ +SLXA-B3_649_FC8437_R1_1_1_362_549
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+ 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/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^