| Next changeset 1:9ce7ccd468aa (2018-02-16) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db |
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added:
sequence_format_converter.py sequence_format_converter.xml test-data/fastqTofasta.sorted.fa test-data/fastqTofastaw.sorted.faw test-data/fastqTotabular.sorted.tab test-data/input.fa test-data/input.fastqsanger test-data/input.sorted.fa test-data/output.faw test-data/output.sorted.faw test-data/output.sorted.tab test-data/output.tab test-data/sort.py |
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| diff -r 000000000000 -r a8aacccd79a3 sequence_format_converter.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sequence_format_converter.py Mon Sep 04 07:13:28 2017 -0400 |
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| b'@@ -0,0 +1,208 @@\n+#!/usr/bin/env python\n+#\n+import argparse\n+import logging\n+import sys\n+from collections import defaultdict\n+\n+\n+def Parser():\n+ the_parser = argparse.ArgumentParser()\n+ the_parser.add_argument(\n+ \'--input\', action="store", type=str,\n+ help="input file, accepted format: fastq, fasta, fasta_weigthed, \\\n+ tabular")\n+ the_parser.add_argument(\n+ \'--output\', action="store", type=str, help="output converted file")\n+ the_parser.add_argument(\n+ \'--format\', action="store", type=str,\n+ help="select output format (fasta, fasta_weigthed, tabular")\n+ args = the_parser.parse_args()\n+ return args\n+\n+\n+class Sequencing:\n+\n+ def __init__(self, input, output, format):\n+ self.input = input\n+ self.output = open(output, \'w\')\n+ self.outputformat = format\n+ self.inputformat = self.detectformat(self.input)\n+ self.seqdic = defaultdict(int)\n+ self.read(self.input, self.inputformat)\n+ self.write(self.output, self.outputformat)\n+\n+ def detectformat(self, input):\n+ input = open(input, \'r\')\n+ block = []\n+ reference = [\'A\', \'T\', \'G\', \'C\', \'N\']\n+ format = \'\'\n+ try:\n+ for l in range(4):\n+ block.append(input.readline()[:-1])\n+ except:\n+ logging.info("File hasn\'t at leat four lines !")\n+ sys.exit("File hasn\'t at leat four lines !")\n+ input.close()\n+ line1, line2, line3, line4 = block[0], block[1], block[2], block[3]\n+ if line1[0] == \'>\' and line3[0] == \'>\':\n+ logging.info("\'>\' detected in lines 1 and 3")\n+ sequence = \'\'.join([line2, line4]).upper()\n+ nucleotides = set([base for base in sequence])\n+ for nucleotide in nucleotides:\n+ if nucleotide not in reference:\n+ logging.info("But other nucleotides that A, T, G, C or N")\n+ sys.exit(\'input appears to be Fasta but with \\\n+ unexpected nucleotides\')\n+ format = \'fasta\'\n+ elif line1[0] == \'>\' and line4[0] == \'>\':\n+ logging.info("\'>\' detected in lines 1 and 4")\n+ sequence = \'\'.join([line2, line3]).upper()\n+ nucleotides = set([base for base in sequence])\n+ for nucleotide in nucleotides:\n+ if nucleotide not in reference:\n+ logging.info("But other nucleotides that A, T, G, C or N")\n+ sys.exit(\'input appears to be Fasta but with \\\n+ unexpected nucleotides\')\n+ format = \'fasta\'\n+ elif line1[0] == \'>\':\n+ logging.info("\'>\' detected in lines 1")\n+ sequence = \'\'.join([line2, line3, line4]).upper()\n+ nucleotides = set([base for base in sequence])\n+ for nucleotide in nucleotides:\n+ if nucleotide not in reference:\n+ logging.info("But other nucleotides that A, T, G, C or N")\n+ sys.exit(\'input appears to be Fasta but with \\\n+ unexpected nucleotides\')\n+ format = \'fasta\'\n+ if format == \'fasta\':\n+ try:\n+ for line in block:\n+ if line[0] == \'>\':\n+ int(line.split(\'_\')[-1])\n+ return \'fastaw\'\n+ except:\n+ return \'fasta\'\n+ if line1[0] == \'@\' and line3[0] == \'+\':\n+ nucleotides = set([base for base in line2])\n+ for nucleotide in nucleotides:\n+ if nucleotide not in reference:\n+ logging.info("Looks like fastq input but other nucleotides \\\n+ that A, T, G, C or N")\n+ sys.exit("input appears to be Fastq \\\n+ but with unexpected nucleotides")\n+ return \'fastq\'\n+ for line in block:\n+ if len(line.split(\'\\t\')) !'..b'"No valid format detected")\n+ sys.exit(\'No valid format detected\')\n+ for nucleotide in line.split(\'\\t\')[0]:\n+ if nucleotide not in reference:\n+ logging.info("No valid format detected")\n+ sys.exit(\'No valid format detected\')\n+ return \'tabular\'\n+\n+ def read(self, input, format):\n+ input = open(input, \'r\')\n+ if format == \'fasta\':\n+ try:\n+ self.readfasta(input)\n+ except:\n+ logging.info("an error occured while reading fasta")\n+ elif format == \'fastaw\':\n+ try:\n+ self.readfastaw(input)\n+ except:\n+ logging.info("an error occured while reading fastaw")\n+ elif format == \'tabular\':\n+ try:\n+ self.readtabular(input)\n+ except:\n+ logging.info("an error occured while reading tabular")\n+ elif format == \'fastq\':\n+ try:\n+ self.readfastq(input)\n+ except:\n+ logging.info("an error occured while reading fastq")\n+ else:\n+ logging.info("no valid format detected")\n+ sys.exit(\'No valid format detected\')\n+\n+ def readfastaw(self, input):\n+ for line in input:\n+ if line[0] == ">":\n+ weigth = int(line[:-1].split("_")[-1])\n+ else:\n+ self.seqdic[line[:-1]] += weigth\n+ input.close()\n+\n+ def readfasta(self, input):\n+ \'\'\' this method is able to read multi-line fasta sequence\'\'\'\n+ for line in input:\n+ if line[0] == ">":\n+ try:\n+ # to dump the sequence of the previous item\n+ # try because of first missing stringlist variable\n+ self.seqdic["".join(stringlist)] += 1\n+ except NameError:\n+ pass\n+ stringlist = []\n+ else:\n+ try:\n+ stringlist.append(line[:-1])\n+ except UnboundLocalError:\n+ # if file went through filter and contains only empty lines\n+ logging.info("first line is empty.")\n+ try:\n+ self.seqdic["".join(stringlist)] += 1 # for the last sequence\n+ except NameError:\n+ logging.info("input file has not fasta sequences.")\n+ input.close()\n+\n+ def readtabular(self, input):\n+ for line in input:\n+ fields = line[:-1].split(\'\\t\')\n+ self.seqdic[fields[0]] += int(fields[1])\n+ input.close()\n+\n+ def readfastq(self, input):\n+ linecount = 0\n+ for line in input:\n+ linecount += 1\n+ if linecount % 4 == 2:\n+ self.seqdic[line[:-1]] += 1\n+ input.close()\n+\n+ def write(self, output, format=\'fasta\'):\n+ if format == \'fasta\':\n+ headercount = 0\n+ for seq in sorted(self.seqdic, key=self.seqdic.get, reverse=True):\n+ for i in range(self.seqdic[seq]):\n+ headercount += 1\n+ output.write(\'>%s\\n%s\\n\' % (headercount, seq))\n+ elif format == \'fastaw\':\n+ headercount = 0\n+ for seq in sorted(self.seqdic, key=self.seqdic.get, reverse=True):\n+ headercount += 1\n+ output.write(\'>%s_%s\\n%s\\n\' % (headercount,\n+ self.seqdic[seq], seq))\n+ elif format == \'tabular\':\n+ for seq in sorted(self.seqdic, key=self.seqdic.get, reverse=True):\n+ output.write(\'%s\\t%s\\n\' % (seq, self.seqdic[seq]))\n+ output.close()\n+\n+\n+def main(input, output, format):\n+ Sequencing(input, output, format)\n+\n+\n+if __name__ == "__main__":\n+ args = Parser()\n+ log = logging.getLogger(__name__)\n+ logging.basicConfig(stream=sys.stdout, level=logging.INFO)\n+ main(args.input, args.output, args.format)\n' |
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| diff -r 000000000000 -r a8aacccd79a3 sequence_format_converter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sequence_format_converter.xml Mon Sep 04 07:13:28 2017 -0400 |
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| @@ -0,0 +1,169 @@ +<tool id="sequence_format_converter" name="sequence_format_converter" version="2.0.0"> + <description></description> + <command><![CDATA[ + python '$__tool_directory__'/sequence_format_converter.py + --input '$input' + --output '$output' + --format '$output_format' + ]]></command> + +<inputs> + <param name="input" type="data" format="fasta, fastq, tabular" label="file to convert to tabular (input format is automatically detected)"/> + <param name="output_format" type="select" label="conversion options"> + <option value="tabular" selected="true">tabular</option> + <option value="fasta">Fasta</option> + <option value="fastaw">Weighted fasta</option> + </param> + </inputs> + + <outputs> + <data format="fasta" name="output" label="${output_format} conversion of ${input.name}"> + <change_format> + <when input="output_format" value="tabular" format="tabular"/> + </change_format> + </data> +</outputs> + + <tests> + <test> + <!-- convertion fasta to tabular --> + <param name="output_format" value="tabular" /> + <param ftype="fasta" name="input" value="input.fa" /> + <output file="output.tab" name="output" /> + </test> + <test> + <!-- convertion tabular to fasta --> + <param name="output_format" value="fasta" /> + <param ftype="tabular" name="input" value="output.tab" /> + <output file="input.sorted.fa" name="output" sort="True"/> + </test> + <test> + <!-- convertion fastaw to tabular --> + <param name="output_format" value="tabular" /> + <param ftype="fasta" name="input" value="output.faw" /> + <output file="output.sorted.tab" name="output" sort="True"/> + </test> + <test> + <!-- convertion tabular to fastaw --> + <param name="output_format" value="fastaw" /> + <param ftype="tabular" name="input" value="output.tab" /> + <output file="output.sorted.faw" name="output" sort="True" /> + </test> + <test> + <!-- convertion fasta to fastaw --> + <param name="output_format" value="fastaw" /> + <param ftype="fasta" name="input" value="input.fa" /> + <output file="output.sorted.faw" name="output" sort="True" /> + </test> + <test> + <!-- convertion fastaw to fasta --> + <param name="output_format" value="fasta" /> + <param ftype="fasta" name="input" value="output.faw" /> + <output file="input.sorted.fa" name="output" sort="True" /> + </test> + <test> + <!-- convertion fastq to tabular --> + <param name="output_format" value="tabular" /> + <param ftype="fastq" name="input" value="input.fastqsanger" /> + <output file="fastqTotabular.sorted.tab" name="output" sort="True" /> + </test> + <test> + <!-- convertion fastq to fasta --> + <param name="output_format" value="fasta" /> + <param ftype="fasta" name="input" value="input.fastqsanger" /> + <output file="fastqTofasta.sorted.fa" name="output" sort="True" /> + </test> + <test> + <!-- convertion fastq to fastaw --> + <param name="output_format" value="fastaw" /> + <param ftype="fasta" name="input" value="input.fastqsanger" /> + <output file="fastqTofastaw.sorted.faw" name="output" sort="True" /> + </test> + </tests> + + +<help> + +**What it does** + +The tool performs all pairwise conversions between sequence formats fasta, fastaw and tabular. + +The tool is also able to convert fastq format in any of the formats fasta, fastaw and tabular. + +The format of the input is automatically detected by the tool. + +**Formats** + +*Fasta* + +>id1 + +ATGCATGACCAGATAGGAC + +>id2 + +ATGCATGACCAGATAGGAC + +Note that the tool handles fasta sequences over multiple lines + + +---------- + +*Fastaw* + +Allows to reduce the size of a fasta file of sequence reads: + +>id1_n1 + +ATGCATGACCAGATAGGAC + +>id2_n2 + +ATGCATGACCAGATAGGAC + +etc... + +Here n1 and n2 are integers that indicate the number of reads of the sequence found in the sequencing dataset + +Note that if 2 fastaw files are merged (e.g. by concatenation), the values of the number of reads are wrong. + +These values can simply be re-computed by submitting the merged file to a fastaw conversion with the *sequence_format_converter* tool ! + + +---------- + +*Tabular* + +Is a tabular version of fastaw without fasta headers: + +column 1 column2 + +ATGCATGACCAGATAGGAC n1 + +ATGCATGACCAGATAGGAC n2 + + +---------- + +*Fastq* + +@HWI-1 + +ATGCATGACCAGATAGGAC + +\+ + +BBBA;ACB9ABCBABB@@/ + +@HWI-2 + +ATGCATGACCAGATAGGAC + +\+ + +?03@?82?B>C@B>@CC?0 + + +</help> + +</tool> |
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| diff -r 000000000000 -r a8aacccd79a3 test-data/fastqTofasta.sorted.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastqTofasta.sorted.fa Mon Sep 04 07:13:28 2017 -0400 |
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| @@ -0,0 +1,500 @@ +>1 +>10 +>100 +>101 +>102 +>103 +>104 +>105 +>106 +>107 +>108 +>109 +>11 +>110 +>111 +>112 +>113 +>114 +>115 +>116 +>117 +>118 +>119 +>12 +>120 +>121 +>122 +>123 +>124 +>125 +>126 +>127 +>128 +>129 +>13 +>130 +>131 +>132 +>133 +>134 +>135 +>136 +>137 +>138 +>139 +>14 +>140 +>141 +>142 +>143 +>144 +>145 +>146 +>147 +>148 +>149 +>15 +>150 +>151 +>152 +>153 +>154 +>155 +>156 +>157 +>158 +>159 +>16 +>160 +>161 +>162 +>163 +>164 +>165 +>166 +>167 +>168 +>169 +>17 +>170 +>171 +>172 +>173 +>174 +>175 +>176 +>177 +>178 +>179 +>18 +>180 +>181 +>182 +>183 +>184 +>185 +>186 +>187 +>188 +>189 +>19 +>190 +>191 +>192 +>193 +>194 +>195 +>196 +>197 +>198 +>199 +>2 +>20 +>200 +>201 +>202 +>203 +>204 +>205 +>206 +>207 +>208 +>209 +>21 +>210 +>211 +>212 +>213 +>214 +>215 +>216 +>217 +>218 +>219 +>22 +>220 +>221 +>222 +>223 +>224 +>225 +>226 +>227 +>228 +>229 +>23 +>230 +>231 +>232 +>233 +>234 +>235 +>236 +>237 +>238 +>239 +>24 +>240 +>241 +>242 +>243 +>244 +>245 +>246 +>247 +>248 +>249 +>25 +>250 +>26 +>27 +>28 +>29 +>3 +>30 +>31 +>32 +>33 +>34 +>35 +>36 +>37 +>38 +>39 +>4 +>40 +>41 +>42 +>43 +>44 +>45 +>46 +>47 +>48 +>49 +>5 +>50 +>51 +>52 +>53 +>54 +>55 +>56 +>57 +>58 +>59 +>6 +>60 +>61 +>62 +>63 +>64 +>65 +>66 +>67 +>68 +>69 +>7 +>70 +>71 +>72 +>73 +>74 +>75 +>76 +>77 +>78 +>79 +>8 +>80 +>81 +>82 +>83 +>84 +>85 +>86 +>87 +>88 +>89 +>9 +>90 +>91 +>92 +>93 +>94 +>95 +>96 +>97 +>98 +>99 +AATGGCACTGGAAGAATTCACGG +AATGGCACTGGAAGAATTCACGG +AATGGCACTGGAAGAATTCACGGG +AATGGCACTGGAAGAATTCACGGG +AATGGCACTGGAAGAATTCACGGG +AATGGCACTGGAAGAATTCACGGG +AATGGCACTGGAAGAATTCACGGGT +AATGGCACTGGAAGAATTCACGTG +AATTGCACTAGTCCCGGCCTG +ACTGAATTCTCGTGGGTCTGCAT +AGGACGGGAAGGTGTCAACG +ATAAAGCTAGATTACCAAAGCAT +CAAATTCGGTTCTAGAGAGGTT +CGAATAGCGTTGTGACTGA +CGGACGGTATATGGGTTAATATT +CGGATGATGGTTCACAACGACC +CGGCACATGTTGAAGTACACTCA +CGGCACATGTTGAAGTACACTCA +CGGCACATGTTGAAGTACACTCAA +CGGCACATGTTGAAGTACACTCAA +CTGACTAGATCCACACTCATTA +GGACGGAGAACTGATAAGGGCTCGG +GGCGAACATGGATCTAGTGCACG +GGGAGCGAGACGGGGACTCAC +GGGAGCGAGACGGGGACTCACT +GGGAGCGAGACGGGGACTCACT +TAAAGCTAGATTACCAAAGCAT +TAAAGCTAGATTACCAAAGCAT +TAAAGCTAGATTACCAAAGCAT +TAAGGAAATAGTAGCCGTGAT +TAAGGAAATAGTAGCCGTGAT +TAAGGAAATAGTAGCCGTGAT +TAGCACCACATGATTCGGCT +TAGGAACTTCATACCGTGCTCT +TAGGAACTTCATACCGTGCTCT +TATCACAGCCAGCTTTGAGGAG +TATCACAGCCATTTTGACGAGTT +TATCACAGCCATTTTGACGAGTT +TATTGCACTTGAGACGGCCTTA +TCAGGTACCTGAAGTAGCG +TCAGGTACCTGAAGTAGCGCGCG +TCAGGTACCTGAAGTAGCGCGCG +TCAGGTACCTGAAGTAGCGCGCG +TCAGGTACCTGAAGTAGCGCGCG +TCAGGTACCTGAAGTAGCGCGCG +TCAGGTACCTGAAGTAGCGCGCG +TCAGGTACCTGAAGTAGCGCGCG +TCAGGTACCTGAAGTAGCGCGCG +TCAGGTACCTGAAGTAGCGCGCG +TCAGGTACCTGAAGTAGCGCGCG +TCAGGTACCTGAAGTAGCGCGCGTTAT +TCTTTGGTATTCTAGCTGTAGA +TGACTAGATCCACACTCATTA +TGACTAGATCCACACTCATTAA +TGACTAGATCCACACTCATTAA +TGACTAGATCCACACTCATTAC +TGACTAGATTCACACTCATTA +TGGAATGTAAAGAAGAATGGAG +TGGAATGTAAAGAAGTATGG +TGGAATGTAAAGAAGTATGG +TGGAATGTAAAGAAGTATGGA +TGGAATGTAAAGAAGTATGGA +TGGAATGTAAAGAAGTATGGA +TGGAATGTAAAGAAGTATGGA +TGGAATGTAAAGAAGTATGGA +TGGAATGTAAAGAAGTATGGA +TGGAATGTAAAGAAGTATGGA +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAGA +TGGAATGTAAAGAAGTATGGAGA +TGGAATGTAAAGAAGTATGGAGT +TGGAATGTAAAGAATTATGGAG +TGGAATGTAAAGGAGTATGGAG +TGGACGGAGAACTGATAAGG +TGGACGGAGAACTGATAAGG +TGGACGGAGAACTGATAAGGG +TGGACGGAGAACTGATAAGGG +TGGACGGAGAACTGATAAGGG +TGGACGGAGAACTGATAAGGG +TGGACGGAGAACTGATAAGGG +TGGACGGAGAACTGATAAGGG +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGCA +TGGACGGAGAACTGATAAGGGCA +TGGACGGAGAACTGATAAGGGCA +TGGACGGAGAACTGATAAGGGCA +TGGACGGAGAACTGATAAGGGCA +TGGACGGAGAACTGATAAGGGCA +TGGACGGAGAACTGATAAGGGCA +TGGACGGAGAACTGATAAGGGCA +TGGACGGAGAACTGATAAGGGCAA +TGGACGGAGAACTGATAAGGGCAA +TGGACGGAGAACTGATAAGGGCAA +TGGACGGAGAACTGATAAGGGCAA +TGGACGGAGAACTGATAAGGGCAA +TGGACGGAGAACTGATAAGGGCAA +TGGACGGAGAACTGATAAGGGCAA +TGGACGGAGAACTGATAAGGGCAA +TGGACGGAGAACTGATAAGGGCAA +TGGACGGAGAACTGATAAGGGCAAA +TGGACGGAGAACTGATAAGGGCAT +TGGACGGAGAACTGATAAGGGCT +TGGACGGAGAACTGATAAGGGCTT +TGGACGGAGAACTGATAAGGGT +TGTGATGTGACGTAGTGGAA +TGTGATGTGACGTAGTGGAA +TGTGATGTGACGTAGTGGAA +TGTGATGTGACGTAGTGGAA +TGTGATGTGACGTAGTGGAA +TGTGATGTGACGTAGTGGAA +TGTGATGTGACGTAGTGGAA +TGTGATGTGACGTAGTGGAA +TGTGATGTGACGTAGTGGAA +TGTGATGTGACGTAGTGGAA +TGTGATGTGACGTAGTGGAA +TGTGATGTGACGTAGTGGAA +TGTGATGTGACGTAGTGGAA +TGTGATGTGACGTAGTGGAA +TGTGATGTGACGTAGTGGAA +TGTGATGTGACGTAGTGGAA +TGTGATGTGACGTAGTGGAAA +TGTGATGTGACGTAGTGGAAA +TGTGATGTGACGTAGTGGAAC |
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| diff -r 000000000000 -r a8aacccd79a3 test-data/fastqTofastaw.sorted.faw --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastqTofastaw.sorted.faw Mon Sep 04 07:13:28 2017 -0400 |
| b |
| @@ -0,0 +1,110 @@ +>10_3 +>11_3 +>12_2 +>13_2 +>14_2 +>15_2 +>16_2 +>17_2 +>18_2 +>19_2 +>1_86 +>20_2 +>21_2 +>22_2 +>23_1 +>24_1 +>25_1 +>26_1 +>27_1 +>28_1 +>29_1 +>2_43 +>30_1 +>31_1 +>32_1 +>33_1 +>34_1 +>35_1 +>36_1 +>37_1 +>38_1 +>39_1 +>3_16 +>40_1 +>41_1 +>42_1 +>43_1 +>44_1 +>45_1 +>46_1 +>47_1 +>48_1 +>49_1 +>4_10 +>50_1 +>51_1 +>52_1 +>53_1 +>54_1 +>55_1 +>5_9 +>6_8 +>7_7 +>8_6 +>9_4 +AATGGCACTGGAAGAATTCACGG +AATGGCACTGGAAGAATTCACGGG +AATGGCACTGGAAGAATTCACGGGT +AATGGCACTGGAAGAATTCACGTG +AATTGCACTAGTCCCGGCCTG +ACTGAATTCTCGTGGGTCTGCAT +AGGACGGGAAGGTGTCAACG +ATAAAGCTAGATTACCAAAGCAT +CAAATTCGGTTCTAGAGAGGTT +CGAATAGCGTTGTGACTGA +CGGACGGTATATGGGTTAATATT +CGGATGATGGTTCACAACGACC +CGGCACATGTTGAAGTACACTCA +CGGCACATGTTGAAGTACACTCAA +CTGACTAGATCCACACTCATTA +GGACGGAGAACTGATAAGGGCTCGG +GGCGAACATGGATCTAGTGCACG +GGGAGCGAGACGGGGACTCAC +GGGAGCGAGACGGGGACTCACT +TAAAGCTAGATTACCAAAGCAT +TAAGGAAATAGTAGCCGTGAT +TAGCACCACATGATTCGGCT +TAGGAACTTCATACCGTGCTCT +TATCACAGCCAGCTTTGAGGAG +TATCACAGCCATTTTGACGAGTT +TATTGCACTTGAGACGGCCTTA +TCAGGTACCTGAAGTAGCG +TCAGGTACCTGAAGTAGCGCGCG +TCAGGTACCTGAAGTAGCGCGCGTTAT +TCTTTGGTATTCTAGCTGTAGA +TGACTAGATCCACACTCATTA +TGACTAGATCCACACTCATTAA +TGACTAGATCCACACTCATTAC +TGACTAGATTCACACTCATTA +TGGAATGTAAAGAAGAATGGAG +TGGAATGTAAAGAAGTATGG +TGGAATGTAAAGAAGTATGGA +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAGA +TGGAATGTAAAGAAGTATGGAGT +TGGAATGTAAAGAATTATGGAG +TGGAATGTAAAGGAGTATGGAG +TGGACGGAGAACTGATAAGG +TGGACGGAGAACTGATAAGGG +TGGACGGAGAACTGATAAGGGC +TGGACGGAGAACTGATAAGGGCA +TGGACGGAGAACTGATAAGGGCAA +TGGACGGAGAACTGATAAGGGCAAA +TGGACGGAGAACTGATAAGGGCAT +TGGACGGAGAACTGATAAGGGCT +TGGACGGAGAACTGATAAGGGCTT +TGGACGGAGAACTGATAAGGGT +TGTGATGTGACGTAGTGGAA +TGTGATGTGACGTAGTGGAAA +TGTGATGTGACGTAGTGGAAC |
| b |
| diff -r 000000000000 -r a8aacccd79a3 test-data/fastqTotabular.sorted.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastqTotabular.sorted.tab Mon Sep 04 07:13:28 2017 -0400 |
| b |
| @@ -0,0 +1,55 @@ +AATGGCACTGGAAGAATTCACGG 2 +AATGGCACTGGAAGAATTCACGGG 4 +AATGGCACTGGAAGAATTCACGGGT 1 +AATGGCACTGGAAGAATTCACGTG 1 +AATTGCACTAGTCCCGGCCTG 1 +ACTGAATTCTCGTGGGTCTGCAT 1 +AGGACGGGAAGGTGTCAACG 1 +ATAAAGCTAGATTACCAAAGCAT 1 +CAAATTCGGTTCTAGAGAGGTT 1 +CGAATAGCGTTGTGACTGA 1 +CGGACGGTATATGGGTTAATATT 1 +CGGATGATGGTTCACAACGACC 1 +CGGCACATGTTGAAGTACACTCA 2 +CGGCACATGTTGAAGTACACTCAA 2 +CTGACTAGATCCACACTCATTA 1 +GGACGGAGAACTGATAAGGGCTCGG 1 +GGCGAACATGGATCTAGTGCACG 1 +GGGAGCGAGACGGGGACTCAC 1 +GGGAGCGAGACGGGGACTCACT 2 +TAAAGCTAGATTACCAAAGCAT 3 +TAAGGAAATAGTAGCCGTGAT 3 +TAGCACCACATGATTCGGCT 1 +TAGGAACTTCATACCGTGCTCT 2 +TATCACAGCCAGCTTTGAGGAG 1 +TATCACAGCCATTTTGACGAGTT 2 +TATTGCACTTGAGACGGCCTTA 1 +TCAGGTACCTGAAGTAGCG 1 +TCAGGTACCTGAAGTAGCGCGCG 10 +TCAGGTACCTGAAGTAGCGCGCGTTAT 1 +TCTTTGGTATTCTAGCTGTAGA 1 +TGACTAGATCCACACTCATTA 1 +TGACTAGATCCACACTCATTAA 2 +TGACTAGATCCACACTCATTAC 1 +TGACTAGATTCACACTCATTA 1 +TGGAATGTAAAGAAGAATGGAG 1 +TGGAATGTAAAGAAGTATGG 2 +TGGAATGTAAAGAAGTATGGA 7 +TGGAATGTAAAGAAGTATGGAG 43 +TGGAATGTAAAGAAGTATGGAGA 2 +TGGAATGTAAAGAAGTATGGAGT 1 +TGGAATGTAAAGAATTATGGAG 1 +TGGAATGTAAAGGAGTATGGAG 1 +TGGACGGAGAACTGATAAGG 2 +TGGACGGAGAACTGATAAGGG 6 +TGGACGGAGAACTGATAAGGGC 86 +TGGACGGAGAACTGATAAGGGCA 8 +TGGACGGAGAACTGATAAGGGCAA 9 +TGGACGGAGAACTGATAAGGGCAAA 1 +TGGACGGAGAACTGATAAGGGCAT 1 +TGGACGGAGAACTGATAAGGGCT 1 +TGGACGGAGAACTGATAAGGGCTT 1 +TGGACGGAGAACTGATAAGGGT 1 +TGTGATGTGACGTAGTGGAA 16 +TGTGATGTGACGTAGTGGAAA 2 +TGTGATGTGACGTAGTGGAAC 1 |
| b |
| diff -r 000000000000 -r a8aacccd79a3 test-data/input.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.fa Mon Sep 04 07:13:28 2017 -0400 |
| b |
| @@ -0,0 +1,500 @@ +>1 +TAGTTACCTTCATATCTCTCTTTA +>2 +TCTATTCATACAAAACACTAATACCC +>3 +ACAACCTCAACTCATATTT +>4 +TATAATTTTATTTTATATTTTCTCT +>5 +TCTTCTATATAATCCTTTATTATAA +>6 +TAAAATAAACCAAAACCCAAAAAT +>7 +AATCTACAATTTCCATTACGACTCC +>8 +TTTCCGACAAATACACCATCTTC +>9 +CAGATTCACTGATTTTCTTACGCC +>10 +CAAGAATACAAAAAATACTAATTA +>11 +AACTCTCTAATTTAACTTTGTGC +>12 +AAAAACACACAGACACAAGCAGCAAT +>13 +TTACTAGATCCACCCTCATTA +>14 +ATGTTATTTACTTTTTCCCCTTATA +>15 +CGATATTTTCTCCTCTTACC +>16 +TACAGAGAAATATACAACACTCACC +>17 +ATGAAATTCGAACAATACGTC +>18 +GAGAATAAATATTTCAATGGTCTATTG +>19 +TGCTTTTACTACATATTTTTTATTTTTTTA +>20 +CATACCTTAAATTATCTCTTTCTT +>21 +TTTGTTTTTCATTTTTTTATCTTT +>22 +TTATTATCTATTTTAATTTTTCTTAA +>23 +TATTATCATCTCGTTCTTCCTTCTC +>24 +TCAACTGGCAAGAATTTTTGAAAATT +>25 +TACAAATTTTTTTTTCTTTCTTAT +>26 +TTTTCTTTTTTTCATTTTCTCTTTTA +>27 +AAGATGGAGTAGTTTTTT +>28 +TCTCATCTTACAATTTTTTAAAACTT +>29 +CATACCTACAAAAAAGCTTCTCTTAC +>30 +TTTTATATTTCCTTATATCTTTACTA +>31 +GGAGATTGTAGAACGAAAGGAAAAT +>32 +TCTATTTCTTTATTTTTTTTATTAT +>33 +CGGACGGTATATTTTTTAATATAA +>34 +TTCTTGGACTACACATTTTTTATTGTTTTA +>35 +TACTATATACTTCTTCAAATCACA +>36 +ATTTTACTTCATCATTTTC +>37 +TATTTCCAACCTTCAACCTCAAATAA +>38 +CACGACTTTATTCTTTTTATCTCA +>39 +TTCTTTTACTACATATTTTTTATTTTTTTA +>40 +TTTATTACAACCCTATCTTACCTCAA +>41 +CGATATTTTCTCCTCGTACC +>42 +TAATTACCATTGCTAACTATCCA +>43 +CATTAATTCATCCATTTAAACTAA +>44 +GAAACAAACAACACATACCCTCTGGC +>45 +TACTTTTTTCTTAATTTTTTATTAAAC +>46 +TAACTTTAACTTTTTTACT +>47 +TTCTTTTACTACATATTGTTTATTTTTTTA +>48 +TCTAGTCTGAGCGTAGTACCAGATTG +>49 +TTTTTTATCAATTTTCACCATTCAT +>50 +AATGACACACTCTTCATCAAC +>51 +TAACATAAATTTTAATCATAAATTG +>52 +TCTATATTATTTTTATCAATTTTCACC +>53 +TCCCAACCCTCGAGCATCATTTTC +>54 +TAGTCATACATACCTAATTATACATA +>55 +TACAAAAAATGCGAAAATTGACCCT +>56 +GAGAACTTTTAATCATTTTAC +>57 +TCTTATTTTAATCTTCCAATTTC +>58 +CGGCACATGTTGAATTACACTCA +>59 +CAGTTTCACAAAAGATCTTTTAA +>60 +GCCAACGACCATACCACGA +>61 +CAAATAACAAACTGAATAAACGAAA +>62 +TAGTTTCACTACTTTATTCTTTTTA +>63 +TGAGGAAAACAGAAAAATGAGAGACA +>64 +TATATAAATCTTCAACATCAA +>65 +TGATTTACTTACATTCTTTTTTT +>66 +CTTCTTTTACTACATATTTTTTATTTTTTTA +>67 +TACTGAAAACGGGCGCATATCAGTGG +>68 +TATTCAATCACTCCATTATATATAACA +>69 +TATATTGCCTCCCCATAATCCTT +>70 +TCGCCGTAAAGCCAGTCGTTCTCC +>71 +TTTAAACACTTCCTACATCAAATTTC +>72 +TTTGTTTTTTACTATATTT +>73 +TCTTTTTTTTAATACTTATTTTCATT +>74 +TAAGTTTTTAATCATTTTTTTT +>75 +TGAGAATGACTTCTTCACGATCTCTT +>76 +AATTTATTTAATTTATATTCTAACTAA +>77 +AAAAAATATCTTTTTTAACTCGTGGCC +>78 +AAGACAACAATGACATATAAGACG +>79 +TGAGCTAGAACTGCACCCACTCCA +>80 +ACTAAACTTTTCTTACCATATTTCTA +>81 +TATTTCACTTTATACTTCCTTAA +>82 +TATCTATCTTTGATCTTCTTTTCA +>83 +TTTTTATCAATTTTCACCATTC +>84 +TAAAAATAATTGTCTTTAATTTCA +>85 +TTAAAGACGCAACAACTAACATT +>86 +TAACCTTGCAGAACTATACGATTCAAA +>87 +TACTATTTTATTATACATACATACATTA +>88 +TAGTGGACTTTAAAAAAAAAAAAAAAAAA +>89 +AATGTCACTTGAAGAATTCACGT +>90 +TAATAAGAAACTGTTCAAACAATCCAC +>91 +AAGCACGCCTTACCACAATTTATAA +>92 +CCATATATGACTGACTCATTTCAC +>93 +TTAATATGTAATTTCATACCTCAC +>94 +AGGATTTTTAAGCCCATATGTTTCC +>95 +ACAGCAGGACGGTGATCA +>96 +TGATGACGGGCAGCAGGGATTTTC +>97 +TTGTAAAACATTCTTTCTCCTGAC +>98 +TTCTTCCTTTTATCCTCTCTTAA +>99 +ATTATTAATAAATTATTATAA +>100 +CTGGAAACTATTGATCAAATT +>101 +TACAACTAACATCCTTTCTTCTTCC +>102 +TCAAATGCAAATTGGATTTATGA +>103 +TCCTGAGGACGAGGGGCGTTTAGC +>104 +TACACAGACTTACAAAACACATCCTTC +>105 +GAAAGGAAGGGAAGAAAGCGAAAGGA +>106 +TTAAACAATTTGGAATTAATT +>107 +TAGCCTTTACTAGGCTTTTTCTAA +>108 +CGATATTTTCTCCTCTTACCT +>109 +TGGAATGTAAAGAAGTATGGAG +>110 +TTTTTAACTCCCATCATTTTTCCTC +>111 +TTTTTTATCATTTTTCACCTAAAAAA +>112 +GAACAATTTTTCAATTTTTTACATTA +>113 +TATGGATTATTTCAAAATTTTTTTTT +>114 +TAACGGAGCACGAGAACGAAGTGG +>115 +CAATTTTTAATTCCTTTTTTCTTCTT +>116 +AGATGTTGATCTAAACTCTCCCA +>117 +TGAGCGGAGAACCAGAGTTGATGAGC +>118 +TAACAAATAGAACGTTCTAATTTAAA +>119 +CTAGACAAGATGCTATAAATTTTAAA +>120 +TTTTCTTTACCCATCTTTACTTTCCC +>121 +TACACACTCATCAACCAAAGGACG +>122 +TCTTATTATCATTTTTTTATCCCTT +>123 +TCAGAGTTCTACAGGTCCTACGATT +>124 +TTTATTACTTAGTCATAATTCCAA +>125 +GCCGGGGCGTGAGATGTCTGCATTA +>126 +GACGAAACGCAACAACAAAATGGACG +>127 +TAGACTTTCTACTCATTATTAC +>128 +AAATTGCAAAGATGGAAAATAAAACT +>129 +CCTTACTCAACATACTTAATCATACTTA +>130 +TGCTTGGACTACATATGGTTGAGTG +>131 +GAATGATCGCACCACCACCTCAACGTT +>132 +TCCACCTATTTATCTTTTCTT +>133 +TGGACAAGAACCACGCGACGGGTGT +>134 +CAAGATATGAACAAAGCAAAGACAC +>135 +CAAACGGAACAAGACATCACCATC +>136 +NATTCTTACTCCATTTCAATTTACT +>137 +TAGAACTCGAACCAGAGCTCC +>138 +CGGAAAAGAATGTAGACCATTTAA +>139 +TACAAACGGAACTTTCGTCATAA +>140 +GGTATCTTTATATTTTAATTTTCTT +>141 +TATTCCGACAATACCTTCTTTAC +>142 +AACTTTAAATTTTTAATAACCTT +>143 +CATAATATAAACTTATCTT +>144 +TATTTATAAATTTTTTCTTGAGAC +>145 +TTTTTTTTTTGTTTTTATTTTTATCAT +>146 +TATTATACATAGAATAACAAATCTTT +>147 +TGGAGTAGCACAGTCGTCTGAAATC +>148 +TATTTCTTTTTTAACTTCTTTTC +>149 +TTATAATCACGGCACCCTATACA +>150 +TTCTTTTACTACATATTTTTTATTTTT +>151 +TAGCGAGATGGACCAACGTGCTGT +>152 +CCAGAAAACAATACAACATCCTCA +>153 +TCCGAAAACAAGGCCCGTCGCT +>154 +TACTCAATAGAACTCTACTCACTCATA +>155 +AACGGGGAATAAGGGTTCG +>156 +TCAGTCTTTTTTTCTCTCCTA +>157 +AATATAAAAATACAATCAACCATTGCA +>158 +GGACGGAGAACTGATAAGGGCA +>159 +TAAAGAAGAAGAATTGATTTTAAT +>160 +TCATTACACTTCTTACAAAAC +>161 +CCGCGATCTGCTTATTTATAATCTT +>162 +TCTAAACACCCACGAAAATCTCTTAC +>163 +AACAGGAAAAACAGAAGGATTTCTA +>164 +TCTCTTTTATTTTTATCTTTCCTT +>165 +AACATTTTATCAATTATACATTA +>166 +GCAGATAGAAATCAATACAAAAATC +>167 +TTAATGACACACGGGAAAAACACCG +>168 +TACAGACAACACATACGGACTTAAGT +>169 +TCCACAACAACTCTATCTAAAGCATT +>170 +ATAAAGCTAGATTACCAAAGCAT +>171 +TACCTCTTTATTAACCTCCACCTCTA +>172 +TACACCTCTTTTTACTTTTTTATT +>173 +CACCGAACCGGGAAGGCGAACAAC +>174 +TAGGTACTTACCTTTTTTTTACACAA +>175 +AGGAATATGATGAAATAAAAAAAT +>176 +TATTATTTTTTTATTCCATTCATAT +>177 +TAAAATAAATAAGTCCGACGACAA +>178 +TCTGTATTTGACTTATTACTTTCTCC +>179 +AAGGAATTAAAGCAATAATTCTAA +>180 +TTCATTTTATTTTTAAATATCTTTTTT +>181 +TTAGTATTAATCTTCACTTAA +>182 +TATGGAGAAACAGCGATATAAGTCA +>183 +CCCGAAAAGCCGAGGACGACTTA +>184 +CACAGACTGAGGCAGAAAAAACAA +>185 +TCAAGCCTTTTGAAGAACTGACCTAAA +>186 +TAAGAAACTGAGCTAACGCAATGTACC +>187 +CGATATTTTCTCCTCTGACC +>188 +TAACTACTTTTACATTAATACTAA +>189 +ACCAGCACCTTCCGACTCAACGTCAAA +>190 +TCAAAGAACAATGTAAAGCCGCGAC +>191 +TTGATTCTTCTTTTTCACAAAA +>192 +TACAAAACAAACAAATTACAATCTAAA +>193 +GAAACCATTATCTTATCTTTATACA +>194 +CTATATTTTCTCTCTTACC +>195 +TCAGAAGAACAGAGAATTGATTTT +>196 +TAATAAATTATTAAATAAAAAAAAAA +>197 +CCGACCGAGCAAATAAACACAGGAACG +>198 +AAGTGAAGAAGTAGTTTTT +>199 +TGGACGGAGAACTGATAAGGGC +>200 +TGCTTGGACTACATATGGTTGAGGG +>201 +TACAAGACTAAAACAAACGTGAAGT +>202 +TGAAACTGAAACTAACATACAAAATATT +>203 +TATCTGATCAACAATCTTTTCCCAT +>204 +TTTAAGACTTATGAGCTTG +>205 +CAAGGCTCAGAAGAACATCACCAAGACC +>206 +TTCAAGTAGATTGCATTTTTTAATA +>207 +CGCAACCAGCAGCAACTCCTAGCAT +>208 +TACAAACGGAACTTTCTTCATAACTTC +>209 +ACAAATCATAAATTTTTTTTTACT +>210 +TCCGAAAAATCGTAGGACCCGGGCA +>211 +CGCCGCAAGATGAATACTCTAATGA +>212 +TGACCAAAGACAAACAAACAATAAATA +>213 +AAAAGGAAAAACAGAAAAATTGGG +>214 +TTCTTGATAACGCATCTTCTACAT +>215 +TACTGAAACAAGGAAACACAAGC +>216 +TCAAAAAGTAATAGGGATCGTTA +>217 +TGGAATGTAAAGAAGTATGGAG +>218 +TAAAATTGTAATATTTAAATAATAT +>219 +GAGGATTAAAAGAACGGTTTATAA +>220 +TTCTTTGACTACATATTTTTTATT +>221 +TACAAACGTAATTTTCGCATAACATC +>222 +AGAACAATTAAATAAAATAGCATA +>223 +TAATAATTTAAATAAATATAAATTT +>224 +AATTGCAACAGAGACTGGAA +>225 +TTAAGTTTTAGACATAATCTATTACAA +>226 +TGAAAGGAAAAACAGGACACGGGA +>227 +AACAGGGAGATCAACAGCGTTGACA +>228 +GGACGGAGAACTGATAATGGC +>229 +TGTGTAATCTTTCTACTTCTTCTAC +>230 +TTTACCAGAGGAGTCGAGTTTTT +>231 +AAAATCGACTGCCGAAAACATTTTAA +>232 +TGCTTGGACTACATATGGTTGAGTG +>233 +TACAGACAACACATACGGACTTAA +>234 +GAAGAGGAGGAGGAGTTTGTAAG +>235 +TTACAATCTACTATTCTTTTATTA +>236 +TTATTACATCGTCCACATATAACAAAA +>237 +TTTTTAACTCATTTTACAATTAAAC +>238 +AAAACCCGGACAAACCATCGGAGGA +>239 +CAACACATGACGCGACAATTCTTG +>240 +TACACACTCATCAACCAAAGTACGTA +>241 +TTTTCATTTCTTCTTCAAATCCTTT +>242 +AACAACTGCAAACATCTACCACA +>243 +TAGTTTTAAATATTTCTTTTTTTC +>244 +AAAGACAAAAGAAATACAGGCACT +>245 +TTTGATACCTTTATACCATACCTATT +>246 +ACAGCAGGACGGTGATCA +>247 +TTCTAGCACAACACGCACACATATA +>248 +TAATCAAAAAACTCTTCATTTTTA +>249 +TAGGAACTTCATACCGGTCTC +>250 +TATTTCAGCAACAGACTAAGACTAA |
| b |
| diff -r 000000000000 -r a8aacccd79a3 test-data/input.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.fastqsanger Mon Sep 04 07:13:28 2017 -0400 |
| b |
| b"@@ -0,0 +1,1000 @@\n+@HWI-49\n+TAAAGCTAGATTACCAAAGCAT\n++\n+BBBA;ACB9ABCBABB@@/?BB\n+@HWI-119\n+TGGACGGAGAACTGATAAGGGC\n++\n+?03@?82?B>C@B>@CC?032<\n+@HWI-127\n+TGGACGGAGAACTGATAAGGGC\n++\n+A>9@>;9>:=@3A7@BB#####\n+@HWI-135\n+TGGACGGAGAACTGATAAGGGC\n++\n+BB6BA5AC+BBBCC6@B>C<'<\n+@HWI-136\n+TGGACGGAGAACTGATAAGGGC\n++\n+B22<A?85=CBCB?;BB===88\n+@HWI-161\n+TGGACGGAGAACTGATAAGGGC\n++\n+B@>>A=?;7:;BB>=C@>)1(:\n+@HWI-166\n+CGGCACATGTTGAAGTACACTCAA\n++\n+B<2>BCBCACC@C@3@BBCBCCCB\n+@HWI-187\n+TGGACGGAGAACTGATAAGGGC\n++\n+B;>@B82:4;B?B?@BB=5:2<\n+@HWI-199\n+GGGAGCGAGACGGGGACTCAC\n++\n+@?@@8?6;@AB=72;;=<AB>\n+@HWI-36\n+ATAAAGCTAGATTACCAAAGCAT\n++\n+BBBB?AAAA9AABA>7@@:-9AB\n+@HWI-39\n+AATGGCACTGGAAGAATTCACGG\n++\n+54=4440)@0365:83:<;5###\n+@HWI-227\n+TGGAATGTAAAGAAGTATGGAG\n++\n+BB>ACCBCCC@9@A4>CA66@>\n+@HWI-249\n+TGGAATGTAAAGAAGTATGGAG\n++\n+A9>?BA2@AA>5<<4<BA5.:)\n+@HWI-252\n+TGGAATGTAAAGAAGTATGGAG\n++\n+>A?:BB:BBA?9<;4?B>3-78\n+@HWI-254\n+TGGAATGTAAAGAAGTATGGAG\n++\n+B>A=B@1>B?47<?B9A?09?0\n+@HWI-278\n+TGGACGGAGAACTGATAAGGGC\n++\n+A54;A<3:?9A@A7<BA?755=\n+@HWI-216\n+TGGACGGAGAACTGATAAGGGCA\n++\n+?34@><6=A<B?@5=A?<30./;\n+@HWI-307\n+TGGACGGAGAACTGATAAGGGC\n++\n+B>??BB;@<@BABB@CC==:0?\n+@HWI-332\n+TGGACGGAGAACTGATAAGGGC\n++\n+B?8@A>B;BAB@BA?CB@A731\n+@HWI-211\n+TGGAATGTAAAGAAGTATGGAGA\n++\n+A61=BA;7B@BBA:9:B?;;@2=\n+@HWI-333\n+TGGAATGTAAAGAAGTATGGA\n++\n+BA>>AB8@BB?=>@98BBA>#\n+@HWI-355\n+TGGAATGTAAAGAAGTATGGAG\n++\n+B>8BBA7@CBA;>A2?BB2.>8\n+@HWI-282\n+TGGAATGTAAAGAATTATGGAG\n++\n+B>8>@A7@8=>>997-8A72##\n+@HWI-378\n+TGGAATGTAAAGAAGTATGGAG\n++\n+B7=;AA8=A@@5=;4>BB31:2\n+@HWI-372\n+AATGGCACTGGAAGAATTCACGGG\n++\n+BBA;@;>A@;@=?@:?B@######\n+@HWI-388\n+TGGAATGTAAAGAAGTATGGAG\n++\n+BA@?BB?BBB??A?0:BA53<>\n+@HWI-399\n+TGGAATGTAAAGAAGTATGGAG\n++\n+A;*>?B9@B<+1<@<4B@7)@-\n+@HWI-109\n+TGGACGGAGAACTGATAAGGGC\n++\n+BC@CBCC@CBB9@8?CCC>AA;\n+@HWI-421\n+TGGACGGAGAACTGATAAGGGC\n++\n+A66?A;0<@;B?A;?BB>38-7\n+@HWI-412\n+TGTGATGTGACGTAGTGGAA\n++\n+BA=?>B<>9><09?0=656=\n+@HWI-432\n+TGGACGGAGAACTGATAAGGGC\n++\n+A;;B>=;=2@?0@@>?CBA@2=\n+@HWI-442\n+TGGACGGAGAACTGATAAGGGC\n++\n+BBA?=;;>B6??@07AA#####\n+@HWI-470\n+TGGAATGTAAAGAAGTATGGAG\n++\n+B?3>AC>:AA?AA<)7BA;7=:\n+@HWI-499\n+TGGACGGAGAACTGATAAGGGC\n++\n+BA>??=:;B=B8A>>B9=/55=\n+@HWI-100\n+TGGACGGAGAACTGATAAGGGC\n++\n+A;6@@96@;?A@BBABC?3<5>\n+@HWI-514\n+TGACTAGATCCACACTCATTAA\n++\n+BAABC?7@C@ABABBBBABBBB\n+@HWI-521\n+TGGACGGAGAACTGATAAGGGC\n++\n+A2=A5=2=>@B;C>:7A>>:1.\n+@HWI-545\n+TGGACGGAGAACTGATAAGGGC\n++\n+BA?BBBAABAB@B>?BB@>A><\n+@HWI-549\n+TGGACGGAGAACTGATAAGGGC\n++\n+A66<;;0<>:@4A1<>>#####\n+@HWI-431\n+TATCACAGCCAGCTTTGAGGAG\n++\n+B>B?B?@A?69?38<@5902;9\n+@HWI-579\n+TGGAATGTAAAGAAGTATGGA\n++\n+BBB@A@BB>B=1<?>>BA###\n+@HWI-583\n+TGGACGGAGAACTGATAAGGGC\n++\n+BB:@BCB>>BBAB@>@BA8;00\n+@HWI-587\n+TAGCACCACATGATTCGGCT\n++\n+BA;/A;;A1BA:@BB>=4;?\n+@HWI-516\n+TGGACGGAGAACTGATAAGGGCA\n++\n+B??>>AA>A9A3A69B?;64779\n+@HWI-113\n+TGGACGGAGAACTGATAAGGGCA\n++\n+BBC@@;>BCBCBB*BCC@95**C\n+@HWI-592\n+TGGAATGTAAAGAAGTATGGAG\n++\n+BBBBBB?ABA;9@@2=B@)1=4\n+@HWI-602\n+TGGACGGAGAACTGATAAGGGC\n++\n+BA;>A@>=8=@?BB>B?:0906\n+@HWI-608\n+TGGACGGAGAACTGATAAGGGC\n++\n+BBC>CC9>??CAA9=B@=::36\n+@HWI-590\n+GGGAGCGAGACGGGGACTCACT\n++\n+=B=AAAA?CBAB@=A95=%:0;\n+@HWI-612\n+CGGCACATGTTGAAGTACACTCA\n++\n+B?>BBBCBABCCA=7@AAABBAA\n+@HWI-610\n+TCAGGTACCTGAAGTAGCGCGCG\n++\n+BB@;@2>;>?66>963#######\n+@HWI-629\n+TGGACGGAGAACTGATAAGGGCA\n++\n+A68@?;6<0<A=A99BB;'--8;\n+@HWI-170\n+TGGACGGAGAACTGATAAGGGC\n++\n+BABCB;;=;=B@BAACB@)80?\n+@HWI-382\n+TGGACGGAGAACTGATAAGGGCAT\n++\n+BB>C39>;B4B@CB73@@;<(>BB\n+@HWI-648\n+TGGACGGAGAACTGATAAGGGC\n++\n+A8=A?@9<A=A?A;=B>=275<\n+@HWI-377\n+TGGACGGAGAACTGATAAGGGCAA\n++\n+B>5>4?A?A;>0:9<=0;;:0.88\n+@HWI-658\n+TGGAATGTAAAGAAGTATGGAG\n++\n+B>8>AB9@B?AA>=;>AA82<8\n+@HWI-677\n+TGGAATGTAAAGAAGTATGG\n++\n+A:0<B>)<BB@2=>2=AB<4\n+@HWI-684\n+TGGAATGTAAAGAAGTATGGAG\n++\n+BAA?BBA@BA==?>8@B?02:)\n+@HWI-699\n+TGGACGGAGAACTGATAAGGGC\n++\n+B??B@>;<;>B?BB?AB>####\n+@HWI-707\n+TGGAATGTAAAGAAGAATGGAG\n++\n+BBAB9*===@7;;:(.,B??@;\n+@HWI-710\n+TGGACGGAGAACTGATAAGGGC\n++\n+BA?AA?8>A=B?BA>AA?####\n+@HWI-700\n+TGGACGGAGAACTGATAAGGGC\n++\n+BCB>4BB@8<A<A>=CB>130-\n+@HWI-780\n+TGGACGGAGAACTGATAAGGGC\n++\n+BBAABCAA<ABAB@?A>>0/29\n+@HWI-766\n+TGGACGGAGAACTGATAAGGGCAA\n++\n+A;3=C@-<A@CCA;@CC<00;@A"..b"\n++\n+BB@B@AA?A@B?B:>AB@943\n+@HWI-1780\n+TGGACGGAGAACTGATAAGGGCAA\n++\n+B;;BA@9?BAB?=-<@>@3:4>;?\n+@HWI-1800\n+TGGAATGTAAAGAAGTATGGAG\n++\n+BAB?BBA@B@:)9=AAB@34?0\n+@HWI-1806\n+TGGAATGTAAAGAAGTATGGA\n++\n+BBBBCCABCCA=AA<;CB@2>\n+@HWI-1821\n+TGGAATGTAAAGAAGTATGGAG\n++\n+B@8?AB;@BB>;>>;;@@:2=7\n+@HWI-1766\n+TGGACGGAGAACTGATAAGGGC\n++\n+BCACCCC?:C@7BAAACB6>2<\n+@HWI-1830\n+TGGACGGAGAACTGATAAGGGC\n++\n+BA@BB>@>>@B@A5>@B@866;\n+@HWI-1846\n+TGGACGGAGAACTGATAAGGGC\n++\n+BB?;5BA?@8B;>>@A9<####\n+@HWI-1851\n+TGGAATGTAAAGAAGTATGGA\n++\n+BBB@BBBABB@3??A@AB###\n+@HWI-1856\n+TGGAATGTAAAGAAGTATGGAG\n++\n+B@:=@B?BBB=:>@@>BB=:>;\n+@HWI-1873\n+TGGAATGTAAAGAAGTATGGAG\n++\n+BB@?BB@BBB???=>=B@2)<=\n+@HWI-1876\n+TGGACGGAGAACTGATAAGGGC\n++\n+A==B@?B;?>B=72;B==/<##\n+@HWI-1885\n+TGGAATGTAAAGAAGTATGGAG\n++\n+A74@BCBABAA:<?03BB:3=2\n+@HWI-1888\n+TGTGATGTGACGTAGTGGAA\n++\n+B@@:>>1<:62;?=7928=@\n+@HWI-1889\n+TGGACGGAGAACTGATAAGGGC\n++\n+A>;@B@;@=@CAB;@BB?330:\n+@HWI-1894\n+TAAGGAAATAGTAGCCGTGAT\n++\n+BAA>><AAA=<<>########\n+@HWI-1912\n+TGGACGGAGAACTGATAAGGG\n++\n+=<??67;8B>A4?A=)>1@?:\n+@HWI-1914\n+TAAGGAAATAGTAGCCGTGAT\n++\n+BBBB7BB>9B;=AA:A>####\n+@HWI-1915\n+TAGGAACTTCATACCGTGCTCT\n++\n+BC=9@BBCCBCBCBA*?3?BAB\n+@HWI-1931\n+TGGACGGAGAACTGATAAGGGCAA\n++\n+A6;@B=5@=@BBCB?B@A13)=9@\n+@HWI-1940\n+TGGAATGTAAAGAAGTATGGAG\n++\n+BC@BBBCBBAA@;?7<BA67?B\n+@HWI-1939\n+TGTGATGTGACGTAGTGGAA\n++\n+B?B??B<B??=8A=8>757:\n+@HWI-1943\n+TGTGATGTGACGTAGTGGAA\n++\n+BA<:<B<;5;94:<-<7###\n+@HWI-1949\n+TGTGATGTGACGTAGTGGAA\n++\n+BA?>7BB>>=?AA<9?>>5;\n+@HWI-1955\n+TGGAATGTAAAGAAGTATGGAG\n++\n+B?;>AB;>BA???>49BA92=2\n+@HWI-1884\n+TGGACGGAGAACTGATAAGGGC\n++\n+B==A=3<AB@B<A;AB@=5/5?\n+@HWI-1973\n+TGTGATGTGACGTAGTGGAAA\n++\n+A9><=B>;8877><9?:####\n+@HWI-1983\n+TGGACGGAGAACTGATAAGGGC\n++\n+B=1@B@6:B@B@BB=BBBA@;@\n+@HWI-1980\n+TGGACGGAGAACTGATAAGGGC\n++\n+BABBB=>>6?C@BBBBA=(52@\n+@HWI-1992\n+TGTGATGTGACGTAGTGGAA\n++\n+BA@9=@7@A?<>>?:@7:9>\n+@HWI-1995\n+CAAATTCGGTTCTAGAGAGGTT\n++\n+B<ABACBCA<C@A@==;=BBAB\n+@HWI-2007\n+TGGACGGAGAACTGATAAGGGT\n++\n+B?BBBA6ABBB?CBACB?AA?>\n+@HWI-2011\n+ACTGAATTCTCGTGGGTCTGCAT\n++\n+BAB==B?B@A@8;/.(:?A>:<?\n+@HWI-2017\n+TCAGGTACCTGAAGTAGCGCGCG\n++\n+BC@?727=B@5<<##########\n+@HWI-2013\n+AATTGCACTAGTCCCGGCCTG\n++\n+BCA>5;A=A>?=B@@4:?@8'\n+@HWI-2040\n+TGGACGGAGAACTGATAAGGGC\n++\n+BBBBB=BBB9BBB@?BB:88>=\n+@HWI-2049\n+TGGAATGTAAAGAAGTATGGAG\n++\n+BA>=ABAABB>5><0;@?.-94\n+@HWI-2053\n+TATCACAGCCATTTTGACGAGTT\n++\n+BCBBCBC>A@ABCBC@@=;</:C\n+@HWI-2055\n+TATTGCACTTGAGACGGCCTTA\n++\n+BBCC>BCBCBAA;<B</-=@2:\n+@HWI-2104\n+TGGACGGAGAACTGATAAGGGC\n++\n+A9@B@AA>A?A?BAACA=805;\n+@HWI-2106\n+TGGACGGAGAACTGATAAGGGCT\n++\n+A:5;BA8;A=A@?4;BA93-0:=\n+@HWI-2100\n+TCAGGTACCTGAAGTAGCGCGCGTTAT\n++\n+BB@579A@B<3;=07615830,6>=##\n+@HWI-2072\n+GGACGGAGAACTGATAAGGGCTCGG\n++\n+ABCBBA.3@@:A=@B=@@0<;@;.<\n+@HWI-2124\n+TGGACGGAGAACTGATAAGGGC\n++\n+?00@B@1>?AB@>9;B?>503?\n+@HWI-2136\n+TGGACGGAGAACTGATAAGGGC\n++\n+BBBBBBCABB@>BB?CBB?>>:\n+@HWI-2137\n+TGTGATGTGACGTAGTGGAA\n++\n+B>=<:<-149;8>8.93379\n+@HWI-2141\n+TGTGATGTGACGTAGTGGAAA\n++\n+BB@AAB<@8>=+=@1=/5=B?\n+@HWI-2117\n+CGGCACATGTTGAAGTACACTCA\n++\n+B>ABBABA>@?)=?0>CABABBB\n+@HWI-2146\n+TGGACGGAGAACTGATAAGGGC\n++\n+B;;BB4=ABBCBB8@CC;/5;B\n+@HWI-2148\n+TGGACGGAGAACTGATAAGGGC\n++\n+BBABA??@@AA:B@@AB@6=8=\n+@HWI-2151\n+TGGACGGAGAACTGATAAGGGC\n++\n+BCA@>BCB?3ABBA?B?A7@6B\n+@HWI-2145\n+TGTGATGTGACGTAGTGGAA\n++\n+B>?BBB>A>A;9<@1@559<\n+@HWI-2158\n+AATGGCACTGGAAGAATTCACGGG\n++\n+BCBABBBB?50=?8;A=>9>;###\n+@HWI-2142\n+TGGACGGAGAACTGATAAGGGC\n++\n+A4;@<@?=<@>@BB>BB8<0:7\n+@HWI-2140\n+TCAGGTACCTGAAGTAGCGCGCG\n++\n+BBABB?B=>=0<@>7<394:4:4\n+@HWI-2191\n+AATGGCACTGGAAGAATTCACGTG\n++\n+ABB?A@ABA;5;>8<??#######\n+@HWI-2183\n+TGGACGGAGAACTGATAAGGGC\n++\n+BAA?@>@>:;>=A>>BA:3107\n+@HWI-2203\n+TGGAATGTAAAGGAGTATGGAG\n++\n+BBABBC@?@A83?A>BBB>7?:\n+@HWI-2200\n+TCTTTGGTATTCTAGCTGTAGA\n++\n+BBCBCC@BACC?CB:AB5@###\n+@HWI-2209\n+TGGACGGAGAACTGATAAGGGC\n++\n+BAAA?A>>=;@;B;>@@>5/94\n+@HWI-2218\n+TGGAATGTAAAGAAGTATGGAG\n++\n+BC>BBCBBBC?A?@<>BB2);7\n+@HWI-2222\n+TGGACGGAGAACTGATAAGGGCA\n++\n+BCABBB?@BBCBBAABB@94;@@\n+@HWI-2227\n+TGGACGGAGAACTGATAAGGGC\n++\n+BBBBBBB?B@BAA;>BBA:0;>\n+@HWI-2225\n+AATGGCACTGGAAGAATTCACGG\n++\n+ABBA@?B@:6>;?@9@@B=?::?\n+@HWI-2230\n+TGGACGGAGAACTGATAAGGGC\n++\n+BBBB@CB@?>B?A;>=@>2/7;\n" |
| b |
| diff -r 000000000000 -r a8aacccd79a3 test-data/input.sorted.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.sorted.fa Mon Sep 04 07:13:28 2017 -0400 |
| b |
| @@ -0,0 +1,500 @@ +>1 +>10 +>100 +>101 +>102 +>103 +>104 +>105 +>106 +>107 +>108 +>109 +>11 +>110 +>111 +>112 +>113 +>114 +>115 +>116 +>117 +>118 +>119 +>12 +>120 +>121 +>122 +>123 +>124 +>125 +>126 +>127 +>128 +>129 +>13 +>130 +>131 +>132 +>133 +>134 +>135 +>136 +>137 +>138 +>139 +>14 +>140 +>141 +>142 +>143 +>144 +>145 +>146 +>147 +>148 +>149 +>15 +>150 +>151 +>152 +>153 +>154 +>155 +>156 +>157 +>158 +>159 +>16 +>160 +>161 +>162 +>163 +>164 +>165 +>166 +>167 +>168 +>169 +>17 +>170 +>171 +>172 +>173 +>174 +>175 +>176 +>177 +>178 +>179 +>18 +>180 +>181 +>182 +>183 +>184 +>185 +>186 +>187 +>188 +>189 +>19 +>190 +>191 +>192 +>193 +>194 +>195 +>196 +>197 +>198 +>199 +>2 +>20 +>200 +>201 +>202 +>203 +>204 +>205 +>206 +>207 +>208 +>209 +>21 +>210 +>211 +>212 +>213 +>214 +>215 +>216 +>217 +>218 +>219 +>22 +>220 +>221 +>222 +>223 +>224 +>225 +>226 +>227 +>228 +>229 +>23 +>230 +>231 +>232 +>233 +>234 +>235 +>236 +>237 +>238 +>239 +>24 +>240 +>241 +>242 +>243 +>244 +>245 +>246 +>247 +>248 +>249 +>25 +>250 +>26 +>27 +>28 +>29 +>3 +>30 +>31 +>32 +>33 +>34 +>35 +>36 +>37 +>38 +>39 +>4 +>40 +>41 +>42 +>43 +>44 +>45 +>46 +>47 +>48 +>49 +>5 +>50 +>51 +>52 +>53 +>54 +>55 +>56 +>57 +>58 +>59 +>6 +>60 +>61 +>62 +>63 +>64 +>65 +>66 +>67 +>68 +>69 +>7 +>70 +>71 +>72 +>73 +>74 +>75 +>76 +>77 +>78 +>79 +>8 +>80 +>81 +>82 +>83 +>84 +>85 +>86 +>87 +>88 +>89 +>9 +>90 +>91 +>92 +>93 +>94 +>95 +>96 +>97 +>98 +>99 +AAAAAATATCTTTTTTAACTCGTGGCC +AAAAACACACAGACACAAGCAGCAAT +AAAACCCGGACAAACCATCGGAGGA +AAAAGGAAAAACAGAAAAATTGGG +AAAATCGACTGCCGAAAACATTTTAA +AAAGACAAAAGAAATACAGGCACT +AAATTGCAAAGATGGAAAATAAAACT +AACAACTGCAAACATCTACCACA +AACAGGAAAAACAGAAGGATTTCTA +AACAGGGAGATCAACAGCGTTGACA +AACATTTTATCAATTATACATTA +AACGGGGAATAAGGGTTCG +AACTCTCTAATTTAACTTTGTGC +AACTTTAAATTTTTAATAACCTT +AAGACAACAATGACATATAAGACG +AAGATGGAGTAGTTTTTT +AAGCACGCCTTACCACAATTTATAA +AAGGAATTAAAGCAATAATTCTAA +AAGTGAAGAAGTAGTTTTT +AATATAAAAATACAATCAACCATTGCA +AATCTACAATTTCCATTACGACTCC +AATGACACACTCTTCATCAAC +AATGTCACTTGAAGAATTCACGT +AATTGCAACAGAGACTGGAA +AATTTATTTAATTTATATTCTAACTAA +ACAAATCATAAATTTTTTTTTACT +ACAACCTCAACTCATATTT +ACAGCAGGACGGTGATCA +ACAGCAGGACGGTGATCA +ACCAGCACCTTCCGACTCAACGTCAAA +ACTAAACTTTTCTTACCATATTTCTA +AGAACAATTAAATAAAATAGCATA +AGATGTTGATCTAAACTCTCCCA +AGGAATATGATGAAATAAAAAAAT +AGGATTTTTAAGCCCATATGTTTCC +ATAAAGCTAGATTACCAAAGCAT +ATGAAATTCGAACAATACGTC +ATGTTATTTACTTTTTCCCCTTATA +ATTATTAATAAATTATTATAA +ATTTTACTTCATCATTTTC +CAAACGGAACAAGACATCACCATC +CAAATAACAAACTGAATAAACGAAA +CAACACATGACGCGACAATTCTTG +CAAGAATACAAAAAATACTAATTA +CAAGATATGAACAAAGCAAAGACAC +CAAGGCTCAGAAGAACATCACCAAGACC +CAATTTTTAATTCCTTTTTTCTTCTT +CACAGACTGAGGCAGAAAAAACAA +CACCGAACCGGGAAGGCGAACAAC +CACGACTTTATTCTTTTTATCTCA +CAGATTCACTGATTTTCTTACGCC +CAGTTTCACAAAAGATCTTTTAA +CATAATATAAACTTATCTT +CATACCTACAAAAAAGCTTCTCTTAC +CATACCTTAAATTATCTCTTTCTT +CATTAATTCATCCATTTAAACTAA +CCAGAAAACAATACAACATCCTCA +CCATATATGACTGACTCATTTCAC +CCCGAAAAGCCGAGGACGACTTA +CCGACCGAGCAAATAAACACAGGAACG +CCGCGATCTGCTTATTTATAATCTT +CCTTACTCAACATACTTAATCATACTTA +CGATATTTTCTCCTCGTACC +CGATATTTTCTCCTCTGACC +CGATATTTTCTCCTCTTACC +CGATATTTTCTCCTCTTACCT +CGCAACCAGCAGCAACTCCTAGCAT +CGCCGCAAGATGAATACTCTAATGA +CGGAAAAGAATGTAGACCATTTAA +CGGACGGTATATTTTTTAATATAA +CGGCACATGTTGAATTACACTCA +CTAGACAAGATGCTATAAATTTTAAA +CTATATTTTCTCTCTTACC +CTGGAAACTATTGATCAAATT +CTTCTTTTACTACATATTTTTTATTTTTTTA +GAAACAAACAACACATACCCTCTGGC +GAAACCATTATCTTATCTTTATACA +GAAAGGAAGGGAAGAAAGCGAAAGGA +GAACAATTTTTCAATTTTTTACATTA +GAAGAGGAGGAGGAGTTTGTAAG +GAATGATCGCACCACCACCTCAACGTT +GACGAAACGCAACAACAAAATGGACG +GAGAACTTTTAATCATTTTAC +GAGAATAAATATTTCAATGGTCTATTG +GAGGATTAAAAGAACGGTTTATAA +GCAGATAGAAATCAATACAAAAATC +GCCAACGACCATACCACGA +GCCGGGGCGTGAGATGTCTGCATTA +GGACGGAGAACTGATAAGGGCA +GGACGGAGAACTGATAATGGC +GGAGATTGTAGAACGAAAGGAAAAT +GGTATCTTTATATTTTAATTTTCTT +NATTCTTACTCCATTTCAATTTACT +TAAAAATAATTGTCTTTAATTTCA +TAAAATAAACCAAAACCCAAAAAT +TAAAATAAATAAGTCCGACGACAA +TAAAATTGTAATATTTAAATAATAT +TAAAGAAGAAGAATTGATTTTAAT +TAACAAATAGAACGTTCTAATTTAAA +TAACATAAATTTTAATCATAAATTG +TAACCTTGCAGAACTATACGATTCAAA +TAACGGAGCACGAGAACGAAGTGG +TAACTACTTTTACATTAATACTAA +TAACTTTAACTTTTTTACT +TAAGAAACTGAGCTAACGCAATGTACC +TAAGTTTTTAATCATTTTTTTT +TAATAAATTATTAAATAAAAAAAAAA +TAATAAGAAACTGTTCAAACAATCCAC +TAATAATTTAAATAAATATAAATTT +TAATCAAAAAACTCTTCATTTTTA +TAATTACCATTGCTAACTATCCA +TACAAAAAATGCGAAAATTGACCCT +TACAAAACAAACAAATTACAATCTAAA +TACAAACGGAACTTTCGTCATAA +TACAAACGGAACTTTCTTCATAACTTC +TACAAACGTAATTTTCGCATAACATC +TACAAATTTTTTTTTCTTTCTTAT +TACAACTAACATCCTTTCTTCTTCC +TACAAGACTAAAACAAACGTGAAGT +TACACACTCATCAACCAAAGGACG +TACACACTCATCAACCAAAGTACGTA +TACACAGACTTACAAAACACATCCTTC +TACACCTCTTTTTACTTTTTTATT +TACAGACAACACATACGGACTTAA +TACAGACAACACATACGGACTTAAGT +TACAGAGAAATATACAACACTCACC +TACCTCTTTATTAACCTCCACCTCTA +TACTATATACTTCTTCAAATCACA +TACTATTTTATTATACATACATACATTA +TACTCAATAGAACTCTACTCACTCATA +TACTGAAAACGGGCGCATATCAGTGG +TACTGAAACAAGGAAACACAAGC +TACTTTTTTCTTAATTTTTTATTAAAC +TAGAACTCGAACCAGAGCTCC +TAGACTTTCTACTCATTATTAC +TAGCCTTTACTAGGCTTTTTCTAA +TAGCGAGATGGACCAACGTGCTGT +TAGGAACTTCATACCGGTCTC +TAGGTACTTACCTTTTTTTTACACAA +TAGTCATACATACCTAATTATACATA +TAGTGGACTTTAAAAAAAAAAAAAAAAAA +TAGTTACCTTCATATCTCTCTTTA +TAGTTTCACTACTTTATTCTTTTTA +TAGTTTTAAATATTTCTTTTTTTC +TATAATTTTATTTTATATTTTCTCT +TATATAAATCTTCAACATCAA +TATATTGCCTCCCCATAATCCTT +TATCTATCTTTGATCTTCTTTTCA +TATCTGATCAACAATCTTTTCCCAT +TATGGAGAAACAGCGATATAAGTCA +TATGGATTATTTCAAAATTTTTTTTT +TATTATACATAGAATAACAAATCTTT +TATTATCATCTCGTTCTTCCTTCTC +TATTATTTTTTTATTCCATTCATAT +TATTCAATCACTCCATTATATATAACA +TATTCCGACAATACCTTCTTTAC +TATTTATAAATTTTTTCTTGAGAC +TATTTCACTTTATACTTCCTTAA +TATTTCAGCAACAGACTAAGACTAA +TATTTCCAACCTTCAACCTCAAATAA +TATTTCTTTTTTAACTTCTTTTC +TCAAAAAGTAATAGGGATCGTTA +TCAAAGAACAATGTAAAGCCGCGAC +TCAAATGCAAATTGGATTTATGA +TCAACTGGCAAGAATTTTTGAAAATT +TCAAGCCTTTTGAAGAACTGACCTAAA +TCAGAAGAACAGAGAATTGATTTT +TCAGAGTTCTACAGGTCCTACGATT +TCAGTCTTTTTTTCTCTCCTA +TCATTACACTTCTTACAAAAC +TCCACAACAACTCTATCTAAAGCATT +TCCACCTATTTATCTTTTCTT +TCCCAACCCTCGAGCATCATTTTC +TCCGAAAAATCGTAGGACCCGGGCA +TCCGAAAACAAGGCCCGTCGCT +TCCTGAGGACGAGGGGCGTTTAGC +TCGCCGTAAAGCCAGTCGTTCTCC +TCTAAACACCCACGAAAATCTCTTAC +TCTAGTCTGAGCGTAGTACCAGATTG +TCTATATTATTTTTATCAATTTTCACC +TCTATTCATACAAAACACTAATACCC +TCTATTTCTTTATTTTTTTTATTAT +TCTCATCTTACAATTTTTTAAAACTT +TCTCTTTTATTTTTATCTTTCCTT +TCTGTATTTGACTTATTACTTTCTCC +TCTTATTATCATTTTTTTATCCCTT +TCTTATTTTAATCTTCCAATTTC +TCTTCTATATAATCCTTTATTATAA +TCTTTTTTTTAATACTTATTTTCATT +TGAAACTGAAACTAACATACAAAATATT +TGAAAGGAAAAACAGGACACGGGA +TGACCAAAGACAAACAAACAATAAATA +TGAGAATGACTTCTTCACGATCTCTT +TGAGCGGAGAACCAGAGTTGATGAGC +TGAGCTAGAACTGCACCCACTCCA +TGAGGAAAACAGAAAAATGAGAGACA +TGATGACGGGCAGCAGGGATTTTC +TGATTTACTTACATTCTTTTTTT +TGCTTGGACTACATATGGTTGAGGG +TGCTTGGACTACATATGGTTGAGTG +TGCTTGGACTACATATGGTTGAGTG +TGCTTTTACTACATATTTTTTATTTTTTTA +TGGAATGTAAAGAAGTATGGAG +TGGAATGTAAAGAAGTATGGAG +TGGACAAGAACCACGCGACGGGTGT +TGGACGGAGAACTGATAAGGGC +TGGAGTAGCACAGTCGTCTGAAATC +TGTGTAATCTTTCTACTTCTTCTAC +TTAAACAATTTGGAATTAATT +TTAAAGACGCAACAACTAACATT +TTAAGTTTTAGACATAATCTATTACAA +TTAATATGTAATTTCATACCTCAC +TTAATGACACACGGGAAAAACACCG +TTACAATCTACTATTCTTTTATTA +TTACTAGATCCACCCTCATTA +TTAGTATTAATCTTCACTTAA +TTATAATCACGGCACCCTATACA +TTATTACATCGTCCACATATAACAAAA +TTATTATCTATTTTAATTTTTCTTAA +TTCAAGTAGATTGCATTTTTTAATA +TTCATTTTATTTTTAAATATCTTTTTT +TTCTAGCACAACACGCACACATATA +TTCTTCCTTTTATCCTCTCTTAA +TTCTTGATAACGCATCTTCTACAT +TTCTTGGACTACACATTTTTTATTGTTTTA +TTCTTTGACTACATATTTTTTATT +TTCTTTTACTACATATTGTTTATTTTTTTA +TTCTTTTACTACATATTTTTTATTTTT +TTCTTTTACTACATATTTTTTATTTTTTTA +TTGATTCTTCTTTTTCACAAAA +TTGTAAAACATTCTTTCTCCTGAC +TTTAAACACTTCCTACATCAAATTTC +TTTAAGACTTATGAGCTTG +TTTACCAGAGGAGTCGAGTTTTT +TTTATTACAACCCTATCTTACCTCAA +TTTATTACTTAGTCATAATTCCAA +TTTCCGACAAATACACCATCTTC +TTTGATACCTTTATACCATACCTATT +TTTGTTTTTCATTTTTTTATCTTT +TTTGTTTTTTACTATATTT +TTTTATATTTCCTTATATCTTTACTA +TTTTCATTTCTTCTTCAAATCCTTT +TTTTCTTTACCCATCTTTACTTTCCC +TTTTCTTTTTTTCATTTTCTCTTTTA +TTTTTAACTCATTTTACAATTAAAC +TTTTTAACTCCCATCATTTTTCCTC +TTTTTATCAATTTTCACCATTC +TTTTTTATCAATTTTCACCATTCAT +TTTTTTATCATTTTTCACCTAAAAAA +TTTTTTTTTTGTTTTTATTTTTATCAT |
| b |
| diff -r 000000000000 -r a8aacccd79a3 test-data/output.faw --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.faw Mon Sep 04 07:13:28 2017 -0400 |
| b |
| b'@@ -0,0 +1,494 @@\n+>1_2\n+ACAGCAGGACGGTGATCA\n+>2_2\n+TGCTTGGACTACATATGGTTGAGTG\n+>3_2\n+TGGAATGTAAAGAAGTATGGAG\n+>4_1\n+AATTTATTTAATTTATATTCTAACTAA\n+>5_1\n+TTATAATCACGGCACCCTATACA\n+>6_1\n+TCCGAAAAATCGTAGGACCCGGGCA\n+>7_1\n+TCCCAACCCTCGAGCATCATTTTC\n+>8_1\n+TTGATTCTTCTTTTTCACAAAA\n+>9_1\n+AGAACAATTAAATAAAATAGCATA\n+>10_1\n+CCAGAAAACAATACAACATCCTCA\n+>11_1\n+TCTAGTCTGAGCGTAGTACCAGATTG\n+>12_1\n+TTTTTAACTCCCATCATTTTTCCTC\n+>13_1\n+GCAGATAGAAATCAATACAAAAATC\n+>14_1\n+AAGTGAAGAAGTAGTTTTT\n+>15_1\n+AATGTCACTTGAAGAATTCACGT\n+>16_1\n+TTTACCAGAGGAGTCGAGTTTTT\n+>17_1\n+GGTATCTTTATATTTTAATTTTCTT\n+>18_1\n+TTACTAGATCCACCCTCATTA\n+>19_1\n+TATATAAATCTTCAACATCAA\n+>20_1\n+GAAACCATTATCTTATCTTTATACA\n+>21_1\n+GGAGATTGTAGAACGAAAGGAAAAT\n+>22_1\n+ACTAAACTTTTCTTACCATATTTCTA\n+>23_1\n+TCAAGCCTTTTGAAGAACTGACCTAAA\n+>24_1\n+TAACATAAATTTTAATCATAAATTG\n+>25_1\n+TAGCGAGATGGACCAACGTGCTGT\n+>26_1\n+TACAAACGTAATTTTCGCATAACATC\n+>27_1\n+CGGAAAAGAATGTAGACCATTTAA\n+>28_1\n+GAAAGGAAGGGAAGAAAGCGAAAGGA\n+>29_1\n+CAAGAATACAAAAAATACTAATTA\n+>30_1\n+CATACCTACAAAAAAGCTTCTCTTAC\n+>31_1\n+TAAAATAAATAAGTCCGACGACAA\n+>32_1\n+AGGAATATGATGAAATAAAAAAAT\n+>33_1\n+TTTTTTTTTTGTTTTTATTTTTATCAT\n+>34_1\n+TTTTTAACTCATTTTACAATTAAAC\n+>35_1\n+CCGCGATCTGCTTATTTATAATCTT\n+>36_1\n+TAGGTACTTACCTTTTTTTTACACAA\n+>37_1\n+TCATTACACTTCTTACAAAAC\n+>38_1\n+TATTATACATAGAATAACAAATCTTT\n+>39_1\n+ATGTTATTTACTTTTTCCCCTTATA\n+>40_1\n+TCCGAAAACAAGGCCCGTCGCT\n+>41_1\n+TGCTTTTACTACATATTTTTTATTTTTTTA\n+>42_1\n+GAACAATTTTTCAATTTTTTACATTA\n+>43_1\n+AACATTTTATCAATTATACATTA\n+>44_1\n+TATCTGATCAACAATCTTTTCCCAT\n+>45_1\n+AATTGCAACAGAGACTGGAA\n+>46_1\n+TATTCAATCACTCCATTATATATAACA\n+>47_1\n+CAAACGGAACAAGACATCACCATC\n+>48_1\n+TCTTCTATATAATCCTTTATTATAA\n+>49_1\n+TGATGACGGGCAGCAGGGATTTTC\n+>50_1\n+TTTATTACAACCCTATCTTACCTCAA\n+>51_1\n+AACAGGAAAAACAGAAGGATTTCTA\n+>52_1\n+CGATATTTTCTCCTCGTACC\n+>53_1\n+AAATTGCAAAGATGGAAAATAAAACT\n+>54_1\n+TACACACTCATCAACCAAAGGACG\n+>55_1\n+TATATTGCCTCCCCATAATCCTT\n+>56_1\n+TACAAACGGAACTTTCTTCATAACTTC\n+>57_1\n+GGACGGAGAACTGATAATGGC\n+>58_1\n+TTCTTTGACTACATATTTTTTATT\n+>59_1\n+TCTTTTTTTTAATACTTATTTTCATT\n+>60_1\n+TACTTTTTTCTTAATTTTTTATTAAAC\n+>61_1\n+AATATAAAAATACAATCAACCATTGCA\n+>62_1\n+CAGTTTCACAAAAGATCTTTTAA\n+>63_1\n+GAAACAAACAACACATACCCTCTGGC\n+>64_1\n+AATGACACACTCTTCATCAAC\n+>65_1\n+AAGATGGAGTAGTTTTTT\n+>66_1\n+ACAACCTCAACTCATATTT\n+>67_1\n+TTAAACAATTTGGAATTAATT\n+>68_1\n+TACAAAAAATGCGAAAATTGACCCT\n+>69_1\n+GGACGGAGAACTGATAAGGGCA\n+>70_1\n+TTAAGTTTTAGACATAATCTATTACAA\n+>71_1\n+TTATTATCTATTTTAATTTTTCTTAA\n+>72_1\n+CACCGAACCGGGAAGGCGAACAAC\n+>73_1\n+TCCACCTATTTATCTTTTCTT\n+>74_1\n+TCGCCGTAAAGCCAGTCGTTCTCC\n+>75_1\n+TCAAAGAACAATGTAAAGCCGCGAC\n+>76_1\n+TGGACAAGAACCACGCGACGGGTGT\n+>77_1\n+CCCGAAAAGCCGAGGACGACTTA\n+>78_1\n+TTTTTTATCATTTTTCACCTAAAAAA\n+>79_1\n+TAGAACTCGAACCAGAGCTCC\n+>80_1\n+TCTATATTATTTTTATCAATTTTCACC\n+>81_1\n+TCTATTTCTTTATTTTTTTTATTAT\n+>82_1\n+TTTGATACCTTTATACCATACCTATT\n+>83_1\n+ATAAAGCTAGATTACCAAAGCAT\n+>84_1\n+GCCAACGACCATACCACGA\n+>85_1\n+CGGCACATGTTGAATTACACTCA\n+>86_1\n+TACTATTTTATTATACATACATACATTA\n+>87_1\n+TTAATGACACACGGGAAAAACACCG\n+>88_1\n+TAGTTTCACTACTTTATTCTTTTTA\n+>89_1\n+AACAGGGAGATCAACAGCGTTGACA\n+>90_1\n+CGATATTTTCTCCTCTGACC\n+>91_1\n+ACCAGCACCTTCCGACTCAACGTCAAA\n+>92_1\n+AAGGAATTAAAGCAATAATTCTAA\n+>93_1\n+TACAAAACAAACAAATTACAATCTAAA\n+>94_1\n+CAATTTTTAATTCCTTTTTTCTTCTT\n+>95_1\n+TACAGACAACACATACGGACTTAA\n+>96_1\n+TCTGTATTTGACTTATTACTTTCTCC\n+>97_1\n+TGAGCTAGAACTGCACCCACTCCA\n+>98_1\n+CGCCGCAAGATGAATACTCTAATGA\n+>99_1\n+TATTTCTTTTTTAACTTCTTTTC\n+>100_1\n+TTACAATCTACTATTCTTTTATTA\n+>101_1\n+TTTAAACACTTCCTACATCAAATTTC\n+>102_1\n+TGTGTAATCTTTCTACTTCTTCTAC\n+>103_1\n+TCTATTCATACAAAACACTAATACCC\n+>104_1\n+TGGAGTAGCACAGTCGTCTGAAATC\n+>105_1\n+AAGCACGCCTTACCACAATTTATAA\n+>106_1\n+CTGGAAACTATTGATCAAATT\n+>107_1\n+TACACAGACTTACAAAACACATCCTTC\n+>108_1\n+TTCAAGTAGATTGCATTTTTTAATA\n+>109_1\n+TTATTACATCGTCCACATATAACAAAA\n+>110_1\n+CAAGGCTCAGAAGAACATCACCAAGACC\n+>111_1\n+TGAGGAAAACAGAAAAATGAGAGACA\n+>112_1\n+TCAAAAAGTAATAGGGATCGTTA\n+>113_1\n+TAACTTTAACTTTTTTACT\n+>114_1\n+TATTCCGACAATACCTTCTTTAC\n+>115_1\n+TTTGTTTTTTACTATATTT\n+>116_1\n+TTCATTTTATTTTTAAATATCTTTTTT\n+>117_1\n+TACTCAATAGAACTCTACTCACTCATA\n+>118_1\n+TGAAAGGAAAAACAGGACACGGGA\n+>119_1\n+AAAATCGACTGCCGAAAACATTTTAA\n+>120_1\n+TAC'..b'>132_1\n+CAAATAACAAACTGAATAAACGAAA\n+>133_1\n+TGAGAATGACTTCTTCACGATCTCTT\n+>134_1\n+TCTTATTATCATTTTTTTATCCCTT\n+>135_1\n+TCAAATGCAAATTGGATTTATGA\n+>136_1\n+CCTTACTCAACATACTTAATCATACTTA\n+>137_1\n+TAGACTTTCTACTCATTATTAC\n+>138_1\n+TGAAACTGAAACTAACATACAAAATATT\n+>139_1\n+AAAACCCGGACAAACCATCGGAGGA\n+>140_1\n+TACAGACAACACATACGGACTTAAGT\n+>141_1\n+TATTTCAGCAACAGACTAAGACTAA\n+>142_1\n+AACTTTAAATTTTTAATAACCTT\n+>143_1\n+TATTTATAAATTTTTTCTTGAGAC\n+>144_1\n+TTAATATGTAATTTCATACCTCAC\n+>145_1\n+CACAGACTGAGGCAGAAAAAACAA\n+>146_1\n+TAAAGAAGAAGAATTGATTTTAAT\n+>147_1\n+TACTGAAAACGGGCGCATATCAGTGG\n+>148_1\n+TCAGTCTTTTTTTCTCTCCTA\n+>149_1\n+TATAATTTTATTTTATATTTTCTCT\n+>150_1\n+NATTCTTACTCCATTTCAATTTACT\n+>151_1\n+TTGTAAAACATTCTTTCTCCTGAC\n+>152_1\n+TAATTACCATTGCTAACTATCCA\n+>153_1\n+TTCTTCCTTTTATCCTCTCTTAA\n+>154_1\n+TCTAAACACCCACGAAAATCTCTTAC\n+>155_1\n+AAAAACACACAGACACAAGCAGCAAT\n+>156_1\n+CGGACGGTATATTTTTTAATATAA\n+>157_1\n+TATGGAGAAACAGCGATATAAGTCA\n+>158_1\n+TACAACTAACATCCTTTCTTCTTCC\n+>159_1\n+AACTCTCTAATTTAACTTTGTGC\n+>160_1\n+TCCTGAGGACGAGGGGCGTTTAGC\n+>161_1\n+TATTTCCAACCTTCAACCTCAAATAA\n+>162_1\n+TGGACGGAGAACTGATAAGGGC\n+>163_1\n+TTTAAGACTTATGAGCTTG\n+>164_1\n+TTAAAGACGCAACAACTAACATT\n+>165_1\n+TAGGAACTTCATACCGGTCTC\n+>166_1\n+CGATATTTTCTCCTCTTACC\n+>167_1\n+GAGGATTAAAAGAACGGTTTATAA\n+>168_1\n+GAATGATCGCACCACCACCTCAACGTT\n+>169_1\n+TTTTCTTTACCCATCTTTACTTTCCC\n+>170_1\n+AAGACAACAATGACATATAAGACG\n+>171_1\n+TAATAATTTAAATAAATATAAATTT\n+>172_1\n+TACTGAAACAAGGAAACACAAGC\n+>173_1\n+TCAGAAGAACAGAGAATTGATTTT\n+>174_1\n+CATACCTTAAATTATCTCTTTCTT\n+>175_1\n+TTCTTTTACTACATATTTTTTATTTTT\n+>176_1\n+AAAAAATATCTTTTTTAACTCGTGGCC\n+>177_1\n+TAACAAATAGAACGTTCTAATTTAAA\n+>178_1\n+TAGTTACCTTCATATCTCTCTTTA\n+>179_1\n+TAAAATTGTAATATTTAAATAATAT\n+>180_1\n+AAAAGGAAAAACAGAAAAATTGGG\n+>181_1\n+AGATGTTGATCTAAACTCTCCCA\n+>182_1\n+TACCTCTTTATTAACCTCCACCTCTA\n+>183_1\n+TTTCCGACAAATACACCATCTTC\n+>184_1\n+ACAAATCATAAATTTTTTTTTACT\n+>185_1\n+GACGAAACGCAACAACAAAATGGACG\n+>186_1\n+TACAAATTTTTTTTTCTTTCTTAT\n+>187_1\n+TACACCTCTTTTTACTTTTTTATT\n+>188_1\n+TATGGATTATTTCAAAATTTTTTTTT\n+>189_1\n+TTCTAGCACAACACGCACACATATA\n+>190_1\n+TAACTACTTTTACATTAATACTAA\n+>191_1\n+TCTCATCTTACAATTTTTTAAAACTT\n+>192_1\n+TTCTTGGACTACACATTTTTTATTGTTTTA\n+>193_1\n+TACACACTCATCAACCAAAGTACGTA\n+>194_1\n+TACTATATACTTCTTCAAATCACA\n+>195_1\n+TCAGAGTTCTACAGGTCCTACGATT\n+>196_1\n+TGATTTACTTACATTCTTTTTTT\n+>197_1\n+CCATATATGACTGACTCATTTCAC\n+>198_1\n+GAAGAGGAGGAGGAGTTTGTAAG\n+>199_1\n+AAAGACAAAAGAAATACAGGCACT\n+>200_1\n+TACAAGACTAAAACAAACGTGAAGT\n+>201_1\n+TAACGGAGCACGAGAACGAAGTGG\n+>202_1\n+CTTCTTTTACTACATATTTTTTATTTTTTTA\n+>203_1\n+TAATAAGAAACTGTTCAAACAATCCAC\n+>204_1\n+TGAGCGGAGAACCAGAGTTGATGAGC\n+>205_1\n+TATTATTTTTTTATTCCATTCATAT\n+>206_1\n+TTTATTACTTAGTCATAATTCCAA\n+>207_1\n+TTTTATATTTCCTTATATCTTTACTA\n+>208_1\n+AACGGGGAATAAGGGTTCG\n+>209_1\n+AATCTACAATTTCCATTACGACTCC\n+>210_1\n+CCGACCGAGCAAATAAACACAGGAACG\n+>211_1\n+TCCACAACAACTCTATCTAAAGCATT\n+>212_1\n+TTCTTGATAACGCATCTTCTACAT\n+>213_1\n+TGCTTGGACTACATATGGTTGAGGG\n+>214_1\n+CAGATTCACTGATTTTCTTACGCC\n+>215_1\n+TTTGTTTTTCATTTTTTTATCTTT\n+>216_1\n+CTATATTTTCTCTCTTACC\n+>217_1\n+TAACCTTGCAGAACTATACGATTCAAA\n+>218_1\n+TAAGAAACTGAGCTAACGCAATGTACC\n+>219_1\n+TTCTTTTACTACATATTTTTTATTTTTTTA\n+>220_1\n+TATCTATCTTTGATCTTCTTTTCA\n+>221_1\n+TAATAAATTATTAAATAAAAAAAAAA\n+>222_1\n+TTTTTTATCAATTTTCACCATTCAT\n+>223_1\n+TATTTCACTTTATACTTCCTTAA\n+>224_1\n+TAGTTTTAAATATTTCTTTTTTTC\n+>225_1\n+TTCTTTTACTACATATTGTTTATTTTTTTA\n+>226_1\n+GAGAATAAATATTTCAATGGTCTATTG\n+>227_1\n+CGATATTTTCTCCTCTTACCT\n+>228_1\n+CACGACTTTATTCTTTTTATCTCA\n+>229_1\n+TAGTGGACTTTAAAAAAAAAAAAAAAAAA\n+>230_1\n+CATAATATAAACTTATCTT\n+>231_1\n+ATGAAATTCGAACAATACGTC\n+>232_1\n+AACAACTGCAAACATCTACCACA\n+>233_1\n+TAAAAATAATTGTCTTTAATTTCA\n+>234_1\n+CGCAACCAGCAGCAACTCCTAGCAT\n+>235_1\n+ATTATTAATAAATTATTATAA\n+>236_1\n+CATTAATTCATCCATTTAAACTAA\n+>237_1\n+TCTTATTTTAATCTTCCAATTTC\n+>238_1\n+CTAGACAAGATGCTATAAATTTTAAA\n+>239_1\n+TGACCAAAGACAAACAAACAATAAATA\n+>240_1\n+TTTTTATCAATTTTCACCATTC\n+>241_1\n+TAAGTTTTTAATCATTTTTTTT\n+>242_1\n+TAATCAAAAAACTCTTCATTTTTA\n+>243_1\n+TACAAACGGAACTTTCGTCATAA\n+>244_1\n+TTTTCTTTTTTTCATTTTCTCTTTTA\n+>245_1\n+TAGCCTTTACTAGGCTTTTTCTAA\n+>246_1\n+TTAGTATTAATCTTCACTTAA\n+>247_1\n+TAAAATAAACCAAAACCCAAAAAT\n' |
| b |
| diff -r 000000000000 -r a8aacccd79a3 test-data/output.sorted.faw --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.sorted.faw Mon Sep 04 07:13:28 2017 -0400 |
| b |
| b'@@ -0,0 +1,494 @@\n+>100_1\n+>101_1\n+>102_1\n+>103_1\n+>104_1\n+>105_1\n+>106_1\n+>107_1\n+>108_1\n+>109_1\n+>10_1\n+>110_1\n+>111_1\n+>112_1\n+>113_1\n+>114_1\n+>115_1\n+>116_1\n+>117_1\n+>118_1\n+>119_1\n+>11_1\n+>120_1\n+>121_1\n+>122_1\n+>123_1\n+>124_1\n+>125_1\n+>126_1\n+>127_1\n+>128_1\n+>129_1\n+>12_1\n+>130_1\n+>131_1\n+>132_1\n+>133_1\n+>134_1\n+>135_1\n+>136_1\n+>137_1\n+>138_1\n+>139_1\n+>13_1\n+>140_1\n+>141_1\n+>142_1\n+>143_1\n+>144_1\n+>145_1\n+>146_1\n+>147_1\n+>148_1\n+>149_1\n+>14_1\n+>150_1\n+>151_1\n+>152_1\n+>153_1\n+>154_1\n+>155_1\n+>156_1\n+>157_1\n+>158_1\n+>159_1\n+>15_1\n+>160_1\n+>161_1\n+>162_1\n+>163_1\n+>164_1\n+>165_1\n+>166_1\n+>167_1\n+>168_1\n+>169_1\n+>16_1\n+>170_1\n+>171_1\n+>172_1\n+>173_1\n+>174_1\n+>175_1\n+>176_1\n+>177_1\n+>178_1\n+>179_1\n+>17_1\n+>180_1\n+>181_1\n+>182_1\n+>183_1\n+>184_1\n+>185_1\n+>186_1\n+>187_1\n+>188_1\n+>189_1\n+>18_1\n+>190_1\n+>191_1\n+>192_1\n+>193_1\n+>194_1\n+>195_1\n+>196_1\n+>197_1\n+>198_1\n+>199_1\n+>19_1\n+>1_2\n+>200_1\n+>201_1\n+>202_1\n+>203_1\n+>204_1\n+>205_1\n+>206_1\n+>207_1\n+>208_1\n+>209_1\n+>20_1\n+>210_1\n+>211_1\n+>212_1\n+>213_1\n+>214_1\n+>215_1\n+>216_1\n+>217_1\n+>218_1\n+>219_1\n+>21_1\n+>220_1\n+>221_1\n+>222_1\n+>223_1\n+>224_1\n+>225_1\n+>226_1\n+>227_1\n+>228_1\n+>229_1\n+>22_1\n+>230_1\n+>231_1\n+>232_1\n+>233_1\n+>234_1\n+>235_1\n+>236_1\n+>237_1\n+>238_1\n+>239_1\n+>23_1\n+>240_1\n+>241_1\n+>242_1\n+>243_1\n+>244_1\n+>245_1\n+>246_1\n+>247_1\n+>24_1\n+>25_1\n+>26_1\n+>27_1\n+>28_1\n+>29_1\n+>2_2\n+>30_1\n+>31_1\n+>32_1\n+>33_1\n+>34_1\n+>35_1\n+>36_1\n+>37_1\n+>38_1\n+>39_1\n+>3_2\n+>40_1\n+>41_1\n+>42_1\n+>43_1\n+>44_1\n+>45_1\n+>46_1\n+>47_1\n+>48_1\n+>49_1\n+>4_1\n+>50_1\n+>51_1\n+>52_1\n+>53_1\n+>54_1\n+>55_1\n+>56_1\n+>57_1\n+>58_1\n+>59_1\n+>5_1\n+>60_1\n+>61_1\n+>62_1\n+>63_1\n+>64_1\n+>65_1\n+>66_1\n+>67_1\n+>68_1\n+>69_1\n+>6_1\n+>70_1\n+>71_1\n+>72_1\n+>73_1\n+>74_1\n+>75_1\n+>76_1\n+>77_1\n+>78_1\n+>79_1\n+>7_1\n+>80_1\n+>81_1\n+>82_1\n+>83_1\n+>84_1\n+>85_1\n+>86_1\n+>87_1\n+>88_1\n+>89_1\n+>8_1\n+>90_1\n+>91_1\n+>92_1\n+>93_1\n+>94_1\n+>95_1\n+>96_1\n+>97_1\n+>98_1\n+>99_1\n+>9_1\n+AAAAAATATCTTTTTTAACTCGTGGCC\n+AAAAACACACAGACACAAGCAGCAAT\n+AAAACCCGGACAAACCATCGGAGGA\n+AAAAGGAAAAACAGAAAAATTGGG\n+AAAATCGACTGCCGAAAACATTTTAA\n+AAAGACAAAAGAAATACAGGCACT\n+AAATTGCAAAGATGGAAAATAAAACT\n+AACAACTGCAAACATCTACCACA\n+AACAGGAAAAACAGAAGGATTTCTA\n+AACAGGGAGATCAACAGCGTTGACA\n+AACATTTTATCAATTATACATTA\n+AACGGGGAATAAGGGTTCG\n+AACTCTCTAATTTAACTTTGTGC\n+AACTTTAAATTTTTAATAACCTT\n+AAGACAACAATGACATATAAGACG\n+AAGATGGAGTAGTTTTTT\n+AAGCACGCCTTACCACAATTTATAA\n+AAGGAATTAAAGCAATAATTCTAA\n+AAGTGAAGAAGTAGTTTTT\n+AATATAAAAATACAATCAACCATTGCA\n+AATCTACAATTTCCATTACGACTCC\n+AATGACACACTCTTCATCAAC\n+AATGTCACTTGAAGAATTCACGT\n+AATTGCAACAGAGACTGGAA\n+AATTTATTTAATTTATATTCTAACTAA\n+ACAAATCATAAATTTTTTTTTACT\n+ACAACCTCAACTCATATTT\n+ACAGCAGGACGGTGATCA\n+ACCAGCACCTTCCGACTCAACGTCAAA\n+ACTAAACTTTTCTTACCATATTTCTA\n+AGAACAATTAAATAAAATAGCATA\n+AGATGTTGATCTAAACTCTCCCA\n+AGGAATATGATGAAATAAAAAAAT\n+AGGATTTTTAAGCCCATATGTTTCC\n+ATAAAGCTAGATTACCAAAGCAT\n+ATGAAATTCGAACAATACGTC\n+ATGTTATTTACTTTTTCCCCTTATA\n+ATTATTAATAAATTATTATAA\n+ATTTTACTTCATCATTTTC\n+CAAACGGAACAAGACATCACCATC\n+CAAATAACAAACTGAATAAACGAAA\n+CAACACATGACGCGACAATTCTTG\n+CAAGAATACAAAAAATACTAATTA\n+CAAGATATGAACAAAGCAAAGACAC\n+CAAGGCTCAGAAGAACATCACCAAGACC\n+CAATTTTTAATTCCTTTTTTCTTCTT\n+CACAGACTGAGGCAGAAAAAACAA\n+CACCGAACCGGGAAGGCGAACAAC\n+CACGACTTTATTCTTTTTATCTCA\n+CAGATTCACTGATTTTCTTACGCC\n+CAGTTTCACAAAAGATCTTTTAA\n+CATAATATAAACTTATCTT\n+CATACCTACAAAAAAGCTTCTCTTAC\n+CATACCTTAAATTATCTCTTTCTT\n+CATTAATTCATCCATTTAAACTAA\n+CCAGAAAACAATACAACATCCTCA\n+CCATATATGACTGACTCATTTCAC\n+CCCGAAAAGCCGAGGACGACTTA\n+CCGACCGAGCAAATAAACACAGGAACG\n+CCGCGATCTGCTTATTTATAATCTT\n+CCTTACTCAACATACTTAATCATACTTA\n+CGATATTTTCTCCTCGTACC\n+CGATATTTTCTCCTCTGACC\n+CGATATTTTCTCCTCTTACC\n+CGATATTTTCTCCTCTTACCT\n+CGCAACCAGCAGCAACTCCTAGCAT\n+CGCCGCAAGATGAATACTCTAATGA\n+CGGAAAAGAATGTAGACCATTTAA\n+CGGACGGTATATTTTTTAATATAA\n+CGGCACATGTTGAATTACACTCA\n+CTAGACAAGATGCTATAAATTTTAAA\n+CTATATTTTCTCTCTTACC\n+CTGGAAACTATTGATCAAATT\n+CTTCTTTTACTACATATTTTTTATTTTTTTA\n+GAAACAAACAACACATACCCTCTGGC\n+GAAACCATTATCTTATCTTTATACA\n+GAAAGGAAGGGAAGAAAGCGAAAGGA\n+GAACAATTTTTCAATTTTTTACATTA\n+GAAGAGGAGGAGGAGTTTGTAAG\n+GAATGATCGCACCACCACCTCAACGTT\n+GACGAAACGCAACAACAAAATGGACG\n+GAGAACTTTTAATCATTTTAC\n'..b'GAACGTTCTAATTTAAA\n+TAACATAAATTTTAATCATAAATTG\n+TAACCTTGCAGAACTATACGATTCAAA\n+TAACGGAGCACGAGAACGAAGTGG\n+TAACTACTTTTACATTAATACTAA\n+TAACTTTAACTTTTTTACT\n+TAAGAAACTGAGCTAACGCAATGTACC\n+TAAGTTTTTAATCATTTTTTTT\n+TAATAAATTATTAAATAAAAAAAAAA\n+TAATAAGAAACTGTTCAAACAATCCAC\n+TAATAATTTAAATAAATATAAATTT\n+TAATCAAAAAACTCTTCATTTTTA\n+TAATTACCATTGCTAACTATCCA\n+TACAAAAAATGCGAAAATTGACCCT\n+TACAAAACAAACAAATTACAATCTAAA\n+TACAAACGGAACTTTCGTCATAA\n+TACAAACGGAACTTTCTTCATAACTTC\n+TACAAACGTAATTTTCGCATAACATC\n+TACAAATTTTTTTTTCTTTCTTAT\n+TACAACTAACATCCTTTCTTCTTCC\n+TACAAGACTAAAACAAACGTGAAGT\n+TACACACTCATCAACCAAAGGACG\n+TACACACTCATCAACCAAAGTACGTA\n+TACACAGACTTACAAAACACATCCTTC\n+TACACCTCTTTTTACTTTTTTATT\n+TACAGACAACACATACGGACTTAA\n+TACAGACAACACATACGGACTTAAGT\n+TACAGAGAAATATACAACACTCACC\n+TACCTCTTTATTAACCTCCACCTCTA\n+TACTATATACTTCTTCAAATCACA\n+TACTATTTTATTATACATACATACATTA\n+TACTCAATAGAACTCTACTCACTCATA\n+TACTGAAAACGGGCGCATATCAGTGG\n+TACTGAAACAAGGAAACACAAGC\n+TACTTTTTTCTTAATTTTTTATTAAAC\n+TAGAACTCGAACCAGAGCTCC\n+TAGACTTTCTACTCATTATTAC\n+TAGCCTTTACTAGGCTTTTTCTAA\n+TAGCGAGATGGACCAACGTGCTGT\n+TAGGAACTTCATACCGGTCTC\n+TAGGTACTTACCTTTTTTTTACACAA\n+TAGTCATACATACCTAATTATACATA\n+TAGTGGACTTTAAAAAAAAAAAAAAAAAA\n+TAGTTACCTTCATATCTCTCTTTA\n+TAGTTTCACTACTTTATTCTTTTTA\n+TAGTTTTAAATATTTCTTTTTTTC\n+TATAATTTTATTTTATATTTTCTCT\n+TATATAAATCTTCAACATCAA\n+TATATTGCCTCCCCATAATCCTT\n+TATCTATCTTTGATCTTCTTTTCA\n+TATCTGATCAACAATCTTTTCCCAT\n+TATGGAGAAACAGCGATATAAGTCA\n+TATGGATTATTTCAAAATTTTTTTTT\n+TATTATACATAGAATAACAAATCTTT\n+TATTATCATCTCGTTCTTCCTTCTC\n+TATTATTTTTTTATTCCATTCATAT\n+TATTCAATCACTCCATTATATATAACA\n+TATTCCGACAATACCTTCTTTAC\n+TATTTATAAATTTTTTCTTGAGAC\n+TATTTCACTTTATACTTCCTTAA\n+TATTTCAGCAACAGACTAAGACTAA\n+TATTTCCAACCTTCAACCTCAAATAA\n+TATTTCTTTTTTAACTTCTTTTC\n+TCAAAAAGTAATAGGGATCGTTA\n+TCAAAGAACAATGTAAAGCCGCGAC\n+TCAAATGCAAATTGGATTTATGA\n+TCAACTGGCAAGAATTTTTGAAAATT\n+TCAAGCCTTTTGAAGAACTGACCTAAA\n+TCAGAAGAACAGAGAATTGATTTT\n+TCAGAGTTCTACAGGTCCTACGATT\n+TCAGTCTTTTTTTCTCTCCTA\n+TCATTACACTTCTTACAAAAC\n+TCCACAACAACTCTATCTAAAGCATT\n+TCCACCTATTTATCTTTTCTT\n+TCCCAACCCTCGAGCATCATTTTC\n+TCCGAAAAATCGTAGGACCCGGGCA\n+TCCGAAAACAAGGCCCGTCGCT\n+TCCTGAGGACGAGGGGCGTTTAGC\n+TCGCCGTAAAGCCAGTCGTTCTCC\n+TCTAAACACCCACGAAAATCTCTTAC\n+TCTAGTCTGAGCGTAGTACCAGATTG\n+TCTATATTATTTTTATCAATTTTCACC\n+TCTATTCATACAAAACACTAATACCC\n+TCTATTTCTTTATTTTTTTTATTAT\n+TCTCATCTTACAATTTTTTAAAACTT\n+TCTCTTTTATTTTTATCTTTCCTT\n+TCTGTATTTGACTTATTACTTTCTCC\n+TCTTATTATCATTTTTTTATCCCTT\n+TCTTATTTTAATCTTCCAATTTC\n+TCTTCTATATAATCCTTTATTATAA\n+TCTTTTTTTTAATACTTATTTTCATT\n+TGAAACTGAAACTAACATACAAAATATT\n+TGAAAGGAAAAACAGGACACGGGA\n+TGACCAAAGACAAACAAACAATAAATA\n+TGAGAATGACTTCTTCACGATCTCTT\n+TGAGCGGAGAACCAGAGTTGATGAGC\n+TGAGCTAGAACTGCACCCACTCCA\n+TGAGGAAAACAGAAAAATGAGAGACA\n+TGATGACGGGCAGCAGGGATTTTC\n+TGATTTACTTACATTCTTTTTTT\n+TGCTTGGACTACATATGGTTGAGGG\n+TGCTTGGACTACATATGGTTGAGTG\n+TGCTTTTACTACATATTTTTTATTTTTTTA\n+TGGAATGTAAAGAAGTATGGAG\n+TGGACAAGAACCACGCGACGGGTGT\n+TGGACGGAGAACTGATAAGGGC\n+TGGAGTAGCACAGTCGTCTGAAATC\n+TGTGTAATCTTTCTACTTCTTCTAC\n+TTAAACAATTTGGAATTAATT\n+TTAAAGACGCAACAACTAACATT\n+TTAAGTTTTAGACATAATCTATTACAA\n+TTAATATGTAATTTCATACCTCAC\n+TTAATGACACACGGGAAAAACACCG\n+TTACAATCTACTATTCTTTTATTA\n+TTACTAGATCCACCCTCATTA\n+TTAGTATTAATCTTCACTTAA\n+TTATAATCACGGCACCCTATACA\n+TTATTACATCGTCCACATATAACAAAA\n+TTATTATCTATTTTAATTTTTCTTAA\n+TTCAAGTAGATTGCATTTTTTAATA\n+TTCATTTTATTTTTAAATATCTTTTTT\n+TTCTAGCACAACACGCACACATATA\n+TTCTTCCTTTTATCCTCTCTTAA\n+TTCTTGATAACGCATCTTCTACAT\n+TTCTTGGACTACACATTTTTTATTGTTTTA\n+TTCTTTGACTACATATTTTTTATT\n+TTCTTTTACTACATATTGTTTATTTTTTTA\n+TTCTTTTACTACATATTTTTTATTTTT\n+TTCTTTTACTACATATTTTTTATTTTTTTA\n+TTGATTCTTCTTTTTCACAAAA\n+TTGTAAAACATTCTTTCTCCTGAC\n+TTTAAACACTTCCTACATCAAATTTC\n+TTTAAGACTTATGAGCTTG\n+TTTACCAGAGGAGTCGAGTTTTT\n+TTTATTACAACCCTATCTTACCTCAA\n+TTTATTACTTAGTCATAATTCCAA\n+TTTCCGACAAATACACCATCTTC\n+TTTGATACCTTTATACCATACCTATT\n+TTTGTTTTTCATTTTTTTATCTTT\n+TTTGTTTTTTACTATATTT\n+TTTTATATTTCCTTATATCTTTACTA\n+TTTTCATTTCTTCTTCAAATCCTTT\n+TTTTCTTTACCCATCTTTACTTTCCC\n+TTTTCTTTTTTTCATTTTCTCTTTTA\n+TTTTTAACTCATTTTACAATTAAAC\n+TTTTTAACTCCCATCATTTTTCCTC\n+TTTTTATCAATTTTCACCATTC\n+TTTTTTATCAATTTTCACCATTCAT\n+TTTTTTATCATTTTTCACCTAAAAAA\n+TTTTTTTTTTGTTTTTATTTTTATCAT\n' |
| b |
| diff -r 000000000000 -r a8aacccd79a3 test-data/output.sorted.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.sorted.tab Mon Sep 04 07:13:28 2017 -0400 |
| b |
| @@ -0,0 +1,247 @@ +AAAAAATATCTTTTTTAACTCGTGGCC 1 +AAAAACACACAGACACAAGCAGCAAT 1 +AAAACCCGGACAAACCATCGGAGGA 1 +AAAAGGAAAAACAGAAAAATTGGG 1 +AAAATCGACTGCCGAAAACATTTTAA 1 +AAAGACAAAAGAAATACAGGCACT 1 +AAATTGCAAAGATGGAAAATAAAACT 1 +AACAACTGCAAACATCTACCACA 1 +AACAGGAAAAACAGAAGGATTTCTA 1 +AACAGGGAGATCAACAGCGTTGACA 1 +AACATTTTATCAATTATACATTA 1 +AACGGGGAATAAGGGTTCG 1 +AACTCTCTAATTTAACTTTGTGC 1 +AACTTTAAATTTTTAATAACCTT 1 +AAGACAACAATGACATATAAGACG 1 +AAGATGGAGTAGTTTTTT 1 +AAGCACGCCTTACCACAATTTATAA 1 +AAGGAATTAAAGCAATAATTCTAA 1 +AAGTGAAGAAGTAGTTTTT 1 +AATATAAAAATACAATCAACCATTGCA 1 +AATCTACAATTTCCATTACGACTCC 1 +AATGACACACTCTTCATCAAC 1 +AATGTCACTTGAAGAATTCACGT 1 +AATTGCAACAGAGACTGGAA 1 +AATTTATTTAATTTATATTCTAACTAA 1 +ACAAATCATAAATTTTTTTTTACT 1 +ACAACCTCAACTCATATTT 1 +ACAGCAGGACGGTGATCA 2 +ACCAGCACCTTCCGACTCAACGTCAAA 1 +ACTAAACTTTTCTTACCATATTTCTA 1 +AGAACAATTAAATAAAATAGCATA 1 +AGATGTTGATCTAAACTCTCCCA 1 +AGGAATATGATGAAATAAAAAAAT 1 +AGGATTTTTAAGCCCATATGTTTCC 1 +ATAAAGCTAGATTACCAAAGCAT 1 +ATGAAATTCGAACAATACGTC 1 +ATGTTATTTACTTTTTCCCCTTATA 1 +ATTATTAATAAATTATTATAA 1 +ATTTTACTTCATCATTTTC 1 +CAAACGGAACAAGACATCACCATC 1 +CAAATAACAAACTGAATAAACGAAA 1 +CAACACATGACGCGACAATTCTTG 1 +CAAGAATACAAAAAATACTAATTA 1 +CAAGATATGAACAAAGCAAAGACAC 1 +CAAGGCTCAGAAGAACATCACCAAGACC 1 +CAATTTTTAATTCCTTTTTTCTTCTT 1 +CACAGACTGAGGCAGAAAAAACAA 1 +CACCGAACCGGGAAGGCGAACAAC 1 +CACGACTTTATTCTTTTTATCTCA 1 +CAGATTCACTGATTTTCTTACGCC 1 +CAGTTTCACAAAAGATCTTTTAA 1 +CATAATATAAACTTATCTT 1 +CATACCTACAAAAAAGCTTCTCTTAC 1 +CATACCTTAAATTATCTCTTTCTT 1 +CATTAATTCATCCATTTAAACTAA 1 +CCAGAAAACAATACAACATCCTCA 1 +CCATATATGACTGACTCATTTCAC 1 +CCCGAAAAGCCGAGGACGACTTA 1 +CCGACCGAGCAAATAAACACAGGAACG 1 +CCGCGATCTGCTTATTTATAATCTT 1 +CCTTACTCAACATACTTAATCATACTTA 1 +CGATATTTTCTCCTCGTACC 1 +CGATATTTTCTCCTCTGACC 1 +CGATATTTTCTCCTCTTACC 1 +CGATATTTTCTCCTCTTACCT 1 +CGCAACCAGCAGCAACTCCTAGCAT 1 +CGCCGCAAGATGAATACTCTAATGA 1 +CGGAAAAGAATGTAGACCATTTAA 1 +CGGACGGTATATTTTTTAATATAA 1 +CGGCACATGTTGAATTACACTCA 1 +CTAGACAAGATGCTATAAATTTTAAA 1 +CTATATTTTCTCTCTTACC 1 +CTGGAAACTATTGATCAAATT 1 +CTTCTTTTACTACATATTTTTTATTTTTTTA 1 +GAAACAAACAACACATACCCTCTGGC 1 +GAAACCATTATCTTATCTTTATACA 1 +GAAAGGAAGGGAAGAAAGCGAAAGGA 1 +GAACAATTTTTCAATTTTTTACATTA 1 +GAAGAGGAGGAGGAGTTTGTAAG 1 +GAATGATCGCACCACCACCTCAACGTT 1 +GACGAAACGCAACAACAAAATGGACG 1 +GAGAACTTTTAATCATTTTAC 1 +GAGAATAAATATTTCAATGGTCTATTG 1 +GAGGATTAAAAGAACGGTTTATAA 1 +GCAGATAGAAATCAATACAAAAATC 1 +GCCAACGACCATACCACGA 1 +GCCGGGGCGTGAGATGTCTGCATTA 1 +GGACGGAGAACTGATAAGGGCA 1 +GGACGGAGAACTGATAATGGC 1 +GGAGATTGTAGAACGAAAGGAAAAT 1 +GGTATCTTTATATTTTAATTTTCTT 1 +NATTCTTACTCCATTTCAATTTACT 1 +TAAAAATAATTGTCTTTAATTTCA 1 +TAAAATAAACCAAAACCCAAAAAT 1 +TAAAATAAATAAGTCCGACGACAA 1 +TAAAATTGTAATATTTAAATAATAT 1 +TAAAGAAGAAGAATTGATTTTAAT 1 +TAACAAATAGAACGTTCTAATTTAAA 1 +TAACATAAATTTTAATCATAAATTG 1 +TAACCTTGCAGAACTATACGATTCAAA 1 +TAACGGAGCACGAGAACGAAGTGG 1 +TAACTACTTTTACATTAATACTAA 1 +TAACTTTAACTTTTTTACT 1 +TAAGAAACTGAGCTAACGCAATGTACC 1 +TAAGTTTTTAATCATTTTTTTT 1 +TAATAAATTATTAAATAAAAAAAAAA 1 +TAATAAGAAACTGTTCAAACAATCCAC 1 +TAATAATTTAAATAAATATAAATTT 1 +TAATCAAAAAACTCTTCATTTTTA 1 +TAATTACCATTGCTAACTATCCA 1 +TACAAAAAATGCGAAAATTGACCCT 1 +TACAAAACAAACAAATTACAATCTAAA 1 +TACAAACGGAACTTTCGTCATAA 1 +TACAAACGGAACTTTCTTCATAACTTC 1 +TACAAACGTAATTTTCGCATAACATC 1 +TACAAATTTTTTTTTCTTTCTTAT 1 +TACAACTAACATCCTTTCTTCTTCC 1 +TACAAGACTAAAACAAACGTGAAGT 1 +TACACACTCATCAACCAAAGGACG 1 +TACACACTCATCAACCAAAGTACGTA 1 +TACACAGACTTACAAAACACATCCTTC 1 +TACACCTCTTTTTACTTTTTTATT 1 +TACAGACAACACATACGGACTTAA 1 +TACAGACAACACATACGGACTTAAGT 1 +TACAGAGAAATATACAACACTCACC 1 +TACCTCTTTATTAACCTCCACCTCTA 1 +TACTATATACTTCTTCAAATCACA 1 +TACTATTTTATTATACATACATACATTA 1 +TACTCAATAGAACTCTACTCACTCATA 1 +TACTGAAAACGGGCGCATATCAGTGG 1 +TACTGAAACAAGGAAACACAAGC 1 +TACTTTTTTCTTAATTTTTTATTAAAC 1 +TAGAACTCGAACCAGAGCTCC 1 +TAGACTTTCTACTCATTATTAC 1 +TAGCCTTTACTAGGCTTTTTCTAA 1 +TAGCGAGATGGACCAACGTGCTGT 1 +TAGGAACTTCATACCGGTCTC 1 +TAGGTACTTACCTTTTTTTTACACAA 1 +TAGTCATACATACCTAATTATACATA 1 +TAGTGGACTTTAAAAAAAAAAAAAAAAAA 1 +TAGTTACCTTCATATCTCTCTTTA 1 +TAGTTTCACTACTTTATTCTTTTTA 1 +TAGTTTTAAATATTTCTTTTTTTC 1 +TATAATTTTATTTTATATTTTCTCT 1 +TATATAAATCTTCAACATCAA 1 +TATATTGCCTCCCCATAATCCTT 1 +TATCTATCTTTGATCTTCTTTTCA 1 +TATCTGATCAACAATCTTTTCCCAT 1 +TATGGAGAAACAGCGATATAAGTCA 1 +TATGGATTATTTCAAAATTTTTTTTT 1 +TATTATACATAGAATAACAAATCTTT 1 +TATTATCATCTCGTTCTTCCTTCTC 1 +TATTATTTTTTTATTCCATTCATAT 1 +TATTCAATCACTCCATTATATATAACA 1 +TATTCCGACAATACCTTCTTTAC 1 +TATTTATAAATTTTTTCTTGAGAC 1 +TATTTCACTTTATACTTCCTTAA 1 +TATTTCAGCAACAGACTAAGACTAA 1 +TATTTCCAACCTTCAACCTCAAATAA 1 +TATTTCTTTTTTAACTTCTTTTC 1 +TCAAAAAGTAATAGGGATCGTTA 1 +TCAAAGAACAATGTAAAGCCGCGAC 1 +TCAAATGCAAATTGGATTTATGA 1 +TCAACTGGCAAGAATTTTTGAAAATT 1 +TCAAGCCTTTTGAAGAACTGACCTAAA 1 +TCAGAAGAACAGAGAATTGATTTT 1 +TCAGAGTTCTACAGGTCCTACGATT 1 +TCAGTCTTTTTTTCTCTCCTA 1 +TCATTACACTTCTTACAAAAC 1 +TCCACAACAACTCTATCTAAAGCATT 1 +TCCACCTATTTATCTTTTCTT 1 +TCCCAACCCTCGAGCATCATTTTC 1 +TCCGAAAAATCGTAGGACCCGGGCA 1 +TCCGAAAACAAGGCCCGTCGCT 1 +TCCTGAGGACGAGGGGCGTTTAGC 1 +TCGCCGTAAAGCCAGTCGTTCTCC 1 +TCTAAACACCCACGAAAATCTCTTAC 1 +TCTAGTCTGAGCGTAGTACCAGATTG 1 +TCTATATTATTTTTATCAATTTTCACC 1 +TCTATTCATACAAAACACTAATACCC 1 +TCTATTTCTTTATTTTTTTTATTAT 1 +TCTCATCTTACAATTTTTTAAAACTT 1 +TCTCTTTTATTTTTATCTTTCCTT 1 +TCTGTATTTGACTTATTACTTTCTCC 1 +TCTTATTATCATTTTTTTATCCCTT 1 +TCTTATTTTAATCTTCCAATTTC 1 +TCTTCTATATAATCCTTTATTATAA 1 +TCTTTTTTTTAATACTTATTTTCATT 1 +TGAAACTGAAACTAACATACAAAATATT 1 +TGAAAGGAAAAACAGGACACGGGA 1 +TGACCAAAGACAAACAAACAATAAATA 1 +TGAGAATGACTTCTTCACGATCTCTT 1 +TGAGCGGAGAACCAGAGTTGATGAGC 1 +TGAGCTAGAACTGCACCCACTCCA 1 +TGAGGAAAACAGAAAAATGAGAGACA 1 +TGATGACGGGCAGCAGGGATTTTC 1 +TGATTTACTTACATTCTTTTTTT 1 +TGCTTGGACTACATATGGTTGAGGG 1 +TGCTTGGACTACATATGGTTGAGTG 2 +TGCTTTTACTACATATTTTTTATTTTTTTA 1 +TGGAATGTAAAGAAGTATGGAG 2 +TGGACAAGAACCACGCGACGGGTGT 1 +TGGACGGAGAACTGATAAGGGC 1 +TGGAGTAGCACAGTCGTCTGAAATC 1 +TGTGTAATCTTTCTACTTCTTCTAC 1 +TTAAACAATTTGGAATTAATT 1 +TTAAAGACGCAACAACTAACATT 1 +TTAAGTTTTAGACATAATCTATTACAA 1 +TTAATATGTAATTTCATACCTCAC 1 +TTAATGACACACGGGAAAAACACCG 1 +TTACAATCTACTATTCTTTTATTA 1 +TTACTAGATCCACCCTCATTA 1 +TTAGTATTAATCTTCACTTAA 1 +TTATAATCACGGCACCCTATACA 1 +TTATTACATCGTCCACATATAACAAAA 1 +TTATTATCTATTTTAATTTTTCTTAA 1 +TTCAAGTAGATTGCATTTTTTAATA 1 +TTCATTTTATTTTTAAATATCTTTTTT 1 +TTCTAGCACAACACGCACACATATA 1 +TTCTTCCTTTTATCCTCTCTTAA 1 +TTCTTGATAACGCATCTTCTACAT 1 +TTCTTGGACTACACATTTTTTATTGTTTTA 1 +TTCTTTGACTACATATTTTTTATT 1 +TTCTTTTACTACATATTGTTTATTTTTTTA 1 +TTCTTTTACTACATATTTTTTATTTTT 1 +TTCTTTTACTACATATTTTTTATTTTTTTA 1 +TTGATTCTTCTTTTTCACAAAA 1 +TTGTAAAACATTCTTTCTCCTGAC 1 +TTTAAACACTTCCTACATCAAATTTC 1 +TTTAAGACTTATGAGCTTG 1 +TTTACCAGAGGAGTCGAGTTTTT 1 +TTTATTACAACCCTATCTTACCTCAA 1 +TTTATTACTTAGTCATAATTCCAA 1 +TTTCCGACAAATACACCATCTTC 1 +TTTGATACCTTTATACCATACCTATT 1 +TTTGTTTTTCATTTTTTTATCTTT 1 +TTTGTTTTTTACTATATTT 1 +TTTTATATTTCCTTATATCTTTACTA 1 +TTTTCATTTCTTCTTCAAATCCTTT 1 +TTTTCTTTACCCATCTTTACTTTCCC 1 +TTTTCTTTTTTTCATTTTCTCTTTTA 1 +TTTTTAACTCATTTTACAATTAAAC 1 +TTTTTAACTCCCATCATTTTTCCTC 1 +TTTTTATCAATTTTCACCATTC 1 +TTTTTTATCAATTTTCACCATTCAT 1 +TTTTTTATCATTTTTCACCTAAAAAA 1 +TTTTTTTTTTGTTTTTATTTTTATCAT 1 |
| b |
| diff -r 000000000000 -r a8aacccd79a3 test-data/output.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.tab Mon Sep 04 07:13:28 2017 -0400 |
| b |
| @@ -0,0 +1,247 @@ +ACAGCAGGACGGTGATCA 2 +TGCTTGGACTACATATGGTTGAGTG 2 +TGGAATGTAAAGAAGTATGGAG 2 +AATTTATTTAATTTATATTCTAACTAA 1 +TTATAATCACGGCACCCTATACA 1 +TCCGAAAAATCGTAGGACCCGGGCA 1 +TCCCAACCCTCGAGCATCATTTTC 1 +TTGATTCTTCTTTTTCACAAAA 1 +AGAACAATTAAATAAAATAGCATA 1 +CCAGAAAACAATACAACATCCTCA 1 +TCTAGTCTGAGCGTAGTACCAGATTG 1 +TTTTTAACTCCCATCATTTTTCCTC 1 +GCAGATAGAAATCAATACAAAAATC 1 +AAGTGAAGAAGTAGTTTTT 1 +AATGTCACTTGAAGAATTCACGT 1 +TTTACCAGAGGAGTCGAGTTTTT 1 +GGTATCTTTATATTTTAATTTTCTT 1 +TTACTAGATCCACCCTCATTA 1 +TATATAAATCTTCAACATCAA 1 +GAAACCATTATCTTATCTTTATACA 1 +GGAGATTGTAGAACGAAAGGAAAAT 1 +ACTAAACTTTTCTTACCATATTTCTA 1 +TCAAGCCTTTTGAAGAACTGACCTAAA 1 +TAACATAAATTTTAATCATAAATTG 1 +TAGCGAGATGGACCAACGTGCTGT 1 +TACAAACGTAATTTTCGCATAACATC 1 +CGGAAAAGAATGTAGACCATTTAA 1 +GAAAGGAAGGGAAGAAAGCGAAAGGA 1 +CAAGAATACAAAAAATACTAATTA 1 +CATACCTACAAAAAAGCTTCTCTTAC 1 +TAAAATAAATAAGTCCGACGACAA 1 +AGGAATATGATGAAATAAAAAAAT 1 +TTTTTTTTTTGTTTTTATTTTTATCAT 1 +TTTTTAACTCATTTTACAATTAAAC 1 +CCGCGATCTGCTTATTTATAATCTT 1 +TAGGTACTTACCTTTTTTTTACACAA 1 +TCATTACACTTCTTACAAAAC 1 +TATTATACATAGAATAACAAATCTTT 1 +ATGTTATTTACTTTTTCCCCTTATA 1 +TCCGAAAACAAGGCCCGTCGCT 1 +TGCTTTTACTACATATTTTTTATTTTTTTA 1 +GAACAATTTTTCAATTTTTTACATTA 1 +AACATTTTATCAATTATACATTA 1 +TATCTGATCAACAATCTTTTCCCAT 1 +AATTGCAACAGAGACTGGAA 1 +TATTCAATCACTCCATTATATATAACA 1 +CAAACGGAACAAGACATCACCATC 1 +TCTTCTATATAATCCTTTATTATAA 1 +TGATGACGGGCAGCAGGGATTTTC 1 +TTTATTACAACCCTATCTTACCTCAA 1 +AACAGGAAAAACAGAAGGATTTCTA 1 +CGATATTTTCTCCTCGTACC 1 +AAATTGCAAAGATGGAAAATAAAACT 1 +TACACACTCATCAACCAAAGGACG 1 +TATATTGCCTCCCCATAATCCTT 1 +TACAAACGGAACTTTCTTCATAACTTC 1 +GGACGGAGAACTGATAATGGC 1 +TTCTTTGACTACATATTTTTTATT 1 +TCTTTTTTTTAATACTTATTTTCATT 1 +TACTTTTTTCTTAATTTTTTATTAAAC 1 +AATATAAAAATACAATCAACCATTGCA 1 +CAGTTTCACAAAAGATCTTTTAA 1 +GAAACAAACAACACATACCCTCTGGC 1 +AATGACACACTCTTCATCAAC 1 +AAGATGGAGTAGTTTTTT 1 +ACAACCTCAACTCATATTT 1 +TTAAACAATTTGGAATTAATT 1 +TACAAAAAATGCGAAAATTGACCCT 1 +GGACGGAGAACTGATAAGGGCA 1 +TTAAGTTTTAGACATAATCTATTACAA 1 +TTATTATCTATTTTAATTTTTCTTAA 1 +CACCGAACCGGGAAGGCGAACAAC 1 +TCCACCTATTTATCTTTTCTT 1 +TCGCCGTAAAGCCAGTCGTTCTCC 1 +TCAAAGAACAATGTAAAGCCGCGAC 1 +TGGACAAGAACCACGCGACGGGTGT 1 +CCCGAAAAGCCGAGGACGACTTA 1 +TTTTTTATCATTTTTCACCTAAAAAA 1 +TAGAACTCGAACCAGAGCTCC 1 +TCTATATTATTTTTATCAATTTTCACC 1 +TCTATTTCTTTATTTTTTTTATTAT 1 +TTTGATACCTTTATACCATACCTATT 1 +ATAAAGCTAGATTACCAAAGCAT 1 +GCCAACGACCATACCACGA 1 +CGGCACATGTTGAATTACACTCA 1 +TACTATTTTATTATACATACATACATTA 1 +TTAATGACACACGGGAAAAACACCG 1 +TAGTTTCACTACTTTATTCTTTTTA 1 +AACAGGGAGATCAACAGCGTTGACA 1 +CGATATTTTCTCCTCTGACC 1 +ACCAGCACCTTCCGACTCAACGTCAAA 1 +AAGGAATTAAAGCAATAATTCTAA 1 +TACAAAACAAACAAATTACAATCTAAA 1 +CAATTTTTAATTCCTTTTTTCTTCTT 1 +TACAGACAACACATACGGACTTAA 1 +TCTGTATTTGACTTATTACTTTCTCC 1 +TGAGCTAGAACTGCACCCACTCCA 1 +CGCCGCAAGATGAATACTCTAATGA 1 +TATTTCTTTTTTAACTTCTTTTC 1 +TTACAATCTACTATTCTTTTATTA 1 +TTTAAACACTTCCTACATCAAATTTC 1 +TGTGTAATCTTTCTACTTCTTCTAC 1 +TCTATTCATACAAAACACTAATACCC 1 +TGGAGTAGCACAGTCGTCTGAAATC 1 +AAGCACGCCTTACCACAATTTATAA 1 +CTGGAAACTATTGATCAAATT 1 +TACACAGACTTACAAAACACATCCTTC 1 +TTCAAGTAGATTGCATTTTTTAATA 1 +TTATTACATCGTCCACATATAACAAAA 1 +CAAGGCTCAGAAGAACATCACCAAGACC 1 +TGAGGAAAACAGAAAAATGAGAGACA 1 +TCAAAAAGTAATAGGGATCGTTA 1 +TAACTTTAACTTTTTTACT 1 +TATTCCGACAATACCTTCTTTAC 1 +TTTGTTTTTTACTATATTT 1 +TTCATTTTATTTTTAAATATCTTTTTT 1 +TACTCAATAGAACTCTACTCACTCATA 1 +TGAAAGGAAAAACAGGACACGGGA 1 +AAAATCGACTGCCGAAAACATTTTAA 1 +TACAGAGAAATATACAACACTCACC 1 +TCAACTGGCAAGAATTTTTGAAAATT 1 +GAGAACTTTTAATCATTTTAC 1 +TATTATCATCTCGTTCTTCCTTCTC 1 +TTTTCATTTCTTCTTCAAATCCTTT 1 +TAGTCATACATACCTAATTATACATA 1 +ATTTTACTTCATCATTTTC 1 +TCTCTTTTATTTTTATCTTTCCTT 1 +GCCGGGGCGTGAGATGTCTGCATTA 1 +AGGATTTTTAAGCCCATATGTTTCC 1 +CAAGATATGAACAAAGCAAAGACAC 1 +CAACACATGACGCGACAATTCTTG 1 +CAAATAACAAACTGAATAAACGAAA 1 +TGAGAATGACTTCTTCACGATCTCTT 1 +TCTTATTATCATTTTTTTATCCCTT 1 +TCAAATGCAAATTGGATTTATGA 1 +CCTTACTCAACATACTTAATCATACTTA 1 +TAGACTTTCTACTCATTATTAC 1 +TGAAACTGAAACTAACATACAAAATATT 1 +AAAACCCGGACAAACCATCGGAGGA 1 +TACAGACAACACATACGGACTTAAGT 1 +TATTTCAGCAACAGACTAAGACTAA 1 +AACTTTAAATTTTTAATAACCTT 1 +TATTTATAAATTTTTTCTTGAGAC 1 +TTAATATGTAATTTCATACCTCAC 1 +CACAGACTGAGGCAGAAAAAACAA 1 +TAAAGAAGAAGAATTGATTTTAAT 1 +TACTGAAAACGGGCGCATATCAGTGG 1 +TCAGTCTTTTTTTCTCTCCTA 1 +TATAATTTTATTTTATATTTTCTCT 1 +NATTCTTACTCCATTTCAATTTACT 1 +TTGTAAAACATTCTTTCTCCTGAC 1 +TAATTACCATTGCTAACTATCCA 1 +TTCTTCCTTTTATCCTCTCTTAA 1 +TCTAAACACCCACGAAAATCTCTTAC 1 +AAAAACACACAGACACAAGCAGCAAT 1 +CGGACGGTATATTTTTTAATATAA 1 +TATGGAGAAACAGCGATATAAGTCA 1 +TACAACTAACATCCTTTCTTCTTCC 1 +AACTCTCTAATTTAACTTTGTGC 1 +TCCTGAGGACGAGGGGCGTTTAGC 1 +TATTTCCAACCTTCAACCTCAAATAA 1 +TGGACGGAGAACTGATAAGGGC 1 +TTTAAGACTTATGAGCTTG 1 +TTAAAGACGCAACAACTAACATT 1 +TAGGAACTTCATACCGGTCTC 1 +CGATATTTTCTCCTCTTACC 1 +GAGGATTAAAAGAACGGTTTATAA 1 +GAATGATCGCACCACCACCTCAACGTT 1 +TTTTCTTTACCCATCTTTACTTTCCC 1 +AAGACAACAATGACATATAAGACG 1 +TAATAATTTAAATAAATATAAATTT 1 +TACTGAAACAAGGAAACACAAGC 1 +TCAGAAGAACAGAGAATTGATTTT 1 +CATACCTTAAATTATCTCTTTCTT 1 +TTCTTTTACTACATATTTTTTATTTTT 1 +AAAAAATATCTTTTTTAACTCGTGGCC 1 +TAACAAATAGAACGTTCTAATTTAAA 1 +TAGTTACCTTCATATCTCTCTTTA 1 +TAAAATTGTAATATTTAAATAATAT 1 +AAAAGGAAAAACAGAAAAATTGGG 1 +AGATGTTGATCTAAACTCTCCCA 1 +TACCTCTTTATTAACCTCCACCTCTA 1 +TTTCCGACAAATACACCATCTTC 1 +ACAAATCATAAATTTTTTTTTACT 1 +GACGAAACGCAACAACAAAATGGACG 1 +TACAAATTTTTTTTTCTTTCTTAT 1 +TACACCTCTTTTTACTTTTTTATT 1 +TATGGATTATTTCAAAATTTTTTTTT 1 +TTCTAGCACAACACGCACACATATA 1 +TAACTACTTTTACATTAATACTAA 1 +TCTCATCTTACAATTTTTTAAAACTT 1 +TTCTTGGACTACACATTTTTTATTGTTTTA 1 +TACACACTCATCAACCAAAGTACGTA 1 +TACTATATACTTCTTCAAATCACA 1 +TCAGAGTTCTACAGGTCCTACGATT 1 +TGATTTACTTACATTCTTTTTTT 1 +CCATATATGACTGACTCATTTCAC 1 +GAAGAGGAGGAGGAGTTTGTAAG 1 +AAAGACAAAAGAAATACAGGCACT 1 +TACAAGACTAAAACAAACGTGAAGT 1 +TAACGGAGCACGAGAACGAAGTGG 1 +CTTCTTTTACTACATATTTTTTATTTTTTTA 1 +TAATAAGAAACTGTTCAAACAATCCAC 1 +TGAGCGGAGAACCAGAGTTGATGAGC 1 +TATTATTTTTTTATTCCATTCATAT 1 +TTTATTACTTAGTCATAATTCCAA 1 +TTTTATATTTCCTTATATCTTTACTA 1 +AACGGGGAATAAGGGTTCG 1 +AATCTACAATTTCCATTACGACTCC 1 +CCGACCGAGCAAATAAACACAGGAACG 1 +TCCACAACAACTCTATCTAAAGCATT 1 +TTCTTGATAACGCATCTTCTACAT 1 +TGCTTGGACTACATATGGTTGAGGG 1 +CAGATTCACTGATTTTCTTACGCC 1 +TTTGTTTTTCATTTTTTTATCTTT 1 +CTATATTTTCTCTCTTACC 1 +TAACCTTGCAGAACTATACGATTCAAA 1 +TAAGAAACTGAGCTAACGCAATGTACC 1 +TTCTTTTACTACATATTTTTTATTTTTTTA 1 +TATCTATCTTTGATCTTCTTTTCA 1 +TAATAAATTATTAAATAAAAAAAAAA 1 +TTTTTTATCAATTTTCACCATTCAT 1 +TATTTCACTTTATACTTCCTTAA 1 +TAGTTTTAAATATTTCTTTTTTTC 1 +TTCTTTTACTACATATTGTTTATTTTTTTA 1 +GAGAATAAATATTTCAATGGTCTATTG 1 +CGATATTTTCTCCTCTTACCT 1 +CACGACTTTATTCTTTTTATCTCA 1 +TAGTGGACTTTAAAAAAAAAAAAAAAAAA 1 +CATAATATAAACTTATCTT 1 +ATGAAATTCGAACAATACGTC 1 +AACAACTGCAAACATCTACCACA 1 +TAAAAATAATTGTCTTTAATTTCA 1 +CGCAACCAGCAGCAACTCCTAGCAT 1 +ATTATTAATAAATTATTATAA 1 +CATTAATTCATCCATTTAAACTAA 1 +TCTTATTTTAATCTTCCAATTTC 1 +CTAGACAAGATGCTATAAATTTTAAA 1 +TGACCAAAGACAAACAAACAATAAATA 1 +TTTTTATCAATTTTCACCATTC 1 +TAAGTTTTTAATCATTTTTTTT 1 +TAATCAAAAAACTCTTCATTTTTA 1 +TACAAACGGAACTTTCGTCATAA 1 +TTTTCTTTTTTTCATTTTCTCTTTTA 1 +TAGCCTTTACTAGGCTTTTTCTAA 1 +TTAGTATTAATCTTCACTTAA 1 +TAAAATAAACCAAAACCCAAAAAT 1 |
| b |
| diff -r 000000000000 -r a8aacccd79a3 test-data/sort.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sort.py Mon Sep 04 07:13:28 2017 -0400 |
| [ |
| @@ -0,0 +1,8 @@ +import sys + +F = open(sys.argv[1], 'r') +lines = F.readlines() +lines = [line[:-1] for line in lines] +for line in sorted(lines): + print(line) +F.close() |