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November 2010

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galaxy-dist commit 1ebd342fb4eb: branch merge
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Ross Lazarus <ross.lazarus(a)gmail.com> # Date 1289244516 18000 # Node ID 1ebd342fb4eb29c095b19a960503402f75cbe944 # Parent d344c55b4f81f273d712c397d648fbaf308a9beb # Parent 3ea6ee14a8b71cd7ac48da98a6ecdb50b9067040 branch merge

1 0

galaxy-dist commit 43c1f36a8e4e: merge
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1289249727 18000 # Node ID 43c1f36a8e4e3f9aa62dc9bc144e54b8312364bf # Parent 2f02897723c2f3c1d0d7be8c14f4c664409e1c59 # Parent eee0e1d344d21de7fb079fcccc3df8e251d1e025 merge --- a/test-data/tophat_out1.sam +++ /dev/null @@ -1,179 +0,0 @@ -test_mRNA_103_284_2a 161 test_chromosome 153 255 75M = 360 0 CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_103_284_2a 81 test_chromosome 360 255 41M100N34M = 153 0 TTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_104_274_1c 73 test_chromosome 350 255 51M100N24M * 0 0 CACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_104_278_3e 161 test_chromosome 154 255 75M = 354 0 GACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTTTTTGGCGCGCGGCCCTACGGCTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_104_278_3e 81 test_chromosome 354 255 47M100N28M = 154 0 ATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGAATCGAGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_105_266_13 163 test_chromosome 155 255 75M = 242 0 ACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_105_266_13 83 test_chromosome 242 255 9M100N50M100N16M = 155 0 CGATCCGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_105_276_c 161 test_chromosome 155 255 75M = 352 0 ACTGGACTATTTAGGACGATCGGACTGAGGAAGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_105_276_c 81 test_chromosome 352 255 49M100N26M = 155 0 CTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGGCTTTTTCTACTTGAGACTGGGATCGAGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_106_253_45 137 test_chromosome 156 255 75M * 0 0 CTGGACTATTTAGGTCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_107_286_5 161 test_chromosome 157 255 75M = 362 0 TGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGCATTTGGCGCGCGGCCCTACGGCTGAGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_107_286_5 81 test_chromosome 362 255 39M100N36M = 157 0 ATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_110_267_22 163 test_chromosome 160 255 75M = 243 0 ACTAGTTAGGGCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAGTTGGCGCGCGGCCCTACGACTGAGCGTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:5 NH:i:1 -test_mRNA_110_267_22 83 test_chromosome 243 255 8M100N50M100N17M = 160 0 GATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_110_271_28 147 test_chromosome 247 255 4M100N50M100N21M = 160 0 CGCCACTATTACTTTATTATCTTACTCGGACGAAGACGGATCGGCAACGGGGCTTTTTCTACTTGAGACTGGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_110_271_28 99 test_chromosome 160 255 75M = 247 0 ACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_111_268_d 73 test_chromosome 244 255 7M100N50M100N18M * 0 0 ATACGCCACTATTATTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_111_297_61 161 test_chromosome 161 255 75M = 373 0 CTATTTAGGACGATCGGACTGGGGAGGGCAGTAGGACGCTACGGATTTGGCGCGCGGCCCTACGGCTGAGCGTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_111_297_61 81 test_chromosome 373 255 28M100N47M = 161 0 CGGACGTAGACGGATCCGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_114_277_5b 161 test_chromosome 164 255 75M = 353 0 TTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGCCTGAGCGTCGAGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_114_277_5b 81 test_chromosome 353 255 48M100N27M = 164 0 TATTACTTTATTATCTTACTCGGAGGTAGACGGAACGGCAACGGGACTTTTTCTGCTTGAGACTGGGATCGAGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_116_271_2b 163 test_chromosome 166 255 75M = 247 0 TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_116_271_2b 83 test_chromosome 247 255 4M100N50M100N21M = 166 0 CGCCACTATTACTTTATTATCTTACTCGGACGTAGACAGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_116_295_63 161 test_chromosome 166 255 75M = 371 0 TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_116_295_63 81 test_chromosome 371 255 30M100N45M = 166 0 CTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_118_297_f 161 test_chromosome 168 255 75M = 373 0 GGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_118_297_f 81 test_chromosome 373 255 28M100N47M = 168 0 CGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_11_190_1a 147 test_chromosome 166 255 75M = 61 0 TAGGTCGATGGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGTGGCCCTACGGCTGAGCGTCGAGCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 -test_mRNA_11_190_1a 99 test_chromosome 61 255 75M = 166 0 GACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_122_299_6 161 test_chromosome 172 255 75M = 375 0 GATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_122_299_6 81 test_chromosome 375 255 26M100N49M = 172 0 GACGTAGACGGAGCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_125_280_48 145 test_chromosome 356 255 45M100N30M = 175 0 TACTTTATTATCTTACTCTGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGAGCGAGGCGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_125_280_48 97 test_chromosome 175 255 75M = 356 0 CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGAAACGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_125_293_60 161 test_chromosome 175 255 75M = 369 0 CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCTTCGAGGTTGCGATACGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 -test_mRNA_125_293_60 81 test_chromosome 369 255 32M100N43M = 175 0 TACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_126_282_18 161 test_chromosome 176 255 75M = 358 0 GGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_126_282_18 81 test_chromosome 358 255 43M100N32M = 176 0 CTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_128_252_36 137 test_chromosome 228 255 23M100N52M * 0 0 GAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGGAACGGGACTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_131_260_33 147 test_chromosome 236 255 15M100N50M100N10M = 181 0 AGCTTGTGATACGCCACTATTACTTTATTATCTTACTCGGACGTAAACGGATCGGCCACGGGACTTTTTTTACTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_131_260_33 99 test_chromosome 181 255 70M100N5M = 236 0 GAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_145_300_37 163 test_chromosome 195 255 56M100N19M = 376 0 GACGCTACGTATTTGGCGCGGGGCCCTATGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTAGTATATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:5 XS:A:+ NH:i:1 -test_mRNA_145_300_37 83 test_chromosome 376 255 25M100N50M = 195 0 ACGTAGACGGATCGGAAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_150_290_0 73 test_chromosome 366 255 35M100N40M * 0 0 TCTTACTCGGACGTAGACGGATCGCCAACGGGACTTTTTCTACTTGAGACTGAGACCGAGGCGGACTTTTTAGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_151_286_e 137 test_chromosome 362 255 39M100N36M * 0 0 ATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTATCTACTTGAGACTGGGATCGAGGCGGACTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_151_297_1d 137 test_chromosome 373 255 28M100N47M * 0 0 CGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACATTTTAGGACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_16_194_10 163 test_chromosome 66 255 75M = 170 0 GACTGGATGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACGGACGGACTTAAAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_16_194_10 83 test_chromosome 170 255 75M = 66 0 ACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_172_294_4f 147 test_chromosome 370 255 31M100N44M = 222 0 ACTCGGACGTAGACGGGTCGGCAGCGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACGTTTTAGGACGGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_172_294_4f 99 test_chromosome 222 255 29M100N46M = 370 0 ACGGATGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTCCTCGGACGTAGACGGATCGCCAACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_21_208_24 163 test_chromosome 71 255 75M = 184 0 GAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_21_208_24 83 test_chromosome 184 255 67M100N8M = 71 0 GAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGCCTGAGCGTCGAGCTTGCGATACGCCACTATTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_22_173_62 147 test_chromosome 149 255 75M = 72 0 GCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_22_173_62 99 test_chromosome 72 255 75M = 149 0 AGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_23_186_42 163 test_chromosome 73 255 75M = 162 0 GGCGCTTGTGACTGAGCTAGGACGTGCCACTACGGGGATGAAGACTAGGACTACGGACGGACTTAGAGCGTCAGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_23_186_42 83 test_chromosome 162 255 75M = 73 0 TATTTAGGACGATCGGACGGAGGAGGGCAGAAGGACGCTACGTATTTGGCGCGCGGCCCTACGACTGAGCGTCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 -test_mRNA_26_189_30 163 test_chromosome 76 255 75M = 165 0 GCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_26_189_30 83 test_chromosome 165 255 75M = 76 0 TTAGGACGATCGGACTGAGGAGGGCAGTAGGACGGTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_28_188_11 147 test_chromosome 164 255 75M = 78 0 TTTAGGACGATCGGACTGAGGAAGGCAGTAGGACGCTTCGTATTTGGCGCGAGGCCCTACGGCTGAGCGTCGAGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 -test_mRNA_28_188_11 99 test_chromosome 78 255 75M = 164 0 TTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGAACGGACTTAGAGCGTCAGATGCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_28_206_1f 73 test_chromosome 78 255 75M * 0 0 TTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGACGCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_30_231_3c 161 test_chromosome 80 255 75M = 207 0 GCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_30_231_3c 81 test_chromosome 207 255 44M100N31M = 80 0 TTGGCGCGCGGCCCTACGGCTAAGCGTCGAGCTTGCGATACGCCACTATTACTTTAATATCTTACTCGCACGTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_33_189_4a 73 test_chromosome 165 255 75M * 0 0 TTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACCTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGGGCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_33_223_4e 73 test_chromosome 83 255 75M * 0 0 ACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_36_146_27 163 test_chromosome 86 255 75M = 122 0 GCGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACAGACGGACTTAGAGCGTCAGATGCAGCGACTGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_36_146_27 83 test_chromosome 122 255 75M = 86 0 ACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGTGCAGTAGGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_36_218_12 147 test_chromosome 194 255 57M100N18M = 86 0 GGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_36_218_12 99 test_chromosome 86 255 75M = 194 0 GAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGCCTTAGAGCGTCAGATGCAGCGACTGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_38_199_29 147 test_chromosome 175 255 75M = 88 0 CGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_38_199_29 99 test_chromosome 88 255 75M = 175 0 GCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_39_219_5c 147 test_chromosome 195 255 56M100N19M = 89 0 GACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCCAGCTTGCGATACGCCACTATTACTTTATTATCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_39_219_5c 99 test_chromosome 89 255 75M = 195 0 CTAGGACGTCCCACTATGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGGCTGGACTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_3_187_51 147 test_chromosome 163 255 75M = 53 0 ATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_3_187_51 99 test_chromosome 53 255 75M = 163 0 TACTATTTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_41_236_55 145 test_chromosome 212 255 39M100N36M = 91 0 GCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_41_236_55 97 test_chromosome 91 255 75M = 212 0 AGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGAATATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_42_209_25 147 test_chromosome 185 255 66M100N9M = 92 0 AGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_42_209_25 99 test_chromosome 92 255 75M = 185 0 GGACGTGCCACTACGTGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_44_193_3f 147 test_chromosome 169 255 75M = 94 0 GACGATCGGACTGGGGAGAGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_44_193_3f 99 test_chromosome 94 255 75M = 169 0 ACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGTCTATTTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_44_197_35 147 test_chromosome 173 255 75M = 94 0 ATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGATCGTCGAGCTTGCGATAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_44_197_35 99 test_chromosome 94 255 75M = 173 0 ACGTGCAACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_44_225_1e 163 test_chromosome 94 255 75M = 201 0 ACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCGGGTGCAGCGACTGGACTATTTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_44_225_1e 83 test_chromosome 201 255 50M100N25M = 94 0 ACGTATATGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_46_195_17 137 test_chromosome 96 255 75M * 0 0 GTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_46_232_2f 147 test_chromosome 208 255 43M100N32M = 96 0 TGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_46_232_2f 99 test_chromosome 96 255 75M = 208 0 GTGCCACTACGGGGATGACGACTAGGACTACGGCCGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_48_207_39 73 test_chromosome 98 255 75M * 0 0 GCCCCTACGGGGATGACGACTAGGACTACGGACGGATTTAGACCGTCAGATGCAGCGACTGGACTATTTAGGACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_48_249_20 161 test_chromosome 98 255 75M = 225 0 GCCACTACGGGGATGACGACTAGGACGACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_48_249_20 81 test_chromosome 225 255 26M100N49M = 98 0 GCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTACTATCTTACTCGGACGGAGACGGATCGGCAACGGGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_4_191_5d 163 test_chromosome 54 255 75M = 167 0 ACTATCTGACGAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTACCATTACGCGGATGACGACTAGGACTACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 -test_mRNA_4_191_5d 83 test_chromosome 167 255 75M = 54 0 AGGACGATCGGACTGAGTAGGGCAGTAGGACACTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_50_224_2d 163 test_chromosome 100 255 75M = 200 0 CACTACGAGGATGACGTCTAGGACTACGGACGGACTTAGAGCGTCAGACGCAGCGACTGGACTATTTAGGACGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_50_224_2d 83 test_chromosome 200 255 51M100N24M = 100 0 TACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_51_194_47 163 test_chromosome 101 255 75M = 170 0 ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_51_194_47 83 test_chromosome 170 255 75M = 101 0 ACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_51_194_49 147 test_chromosome 170 255 75M = 101 0 ACGTTCGGACTGAGGAGGGCAGTAGGACGCCACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 -test_mRNA_51_194_49 99 test_chromosome 101 255 75M = 170 0 ACTACGGGGATGACGACTAGGCCTACGGATGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_51_237_a 147 test_chromosome 213 255 38M100N37M = 101 0 CGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_51_237_a 99 test_chromosome 101 255 75M = 213 0 ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_51_248_14 145 test_chromosome 224 255 27M100N48M = 101 0 GGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGAACGGCAACGGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_51_248_14 97 test_chromosome 101 255 75M = 224 0 ACTACGGGGATGACGACGAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGAACTTTTTAGGACGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_52_261_1b 145 test_chromosome 237 255 14M100N50M100N11M = 102 0 GCTTGCGATACGCCACTATTACTTAATTATCTTACTCGGACGTAGAAGGATCGGCAACGGGACTTTTTCTACTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_52_261_1b 97 test_chromosome 102 255 75M = 237 0 CTACGGGAATGACGACTAGGGCTACGGAGGGACTTACAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 -test_mRNA_53_212_19 147 test_chromosome 188 255 63M100N12M = 103 0 GCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTTCTTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_53_212_19 99 test_chromosome 103 255 75M = 188 0 TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGAATATTTAGGACGATCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_53_272_5a 161 test_chromosome 103 255 75M = 248 0 TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_53_272_5a 81 test_chromosome 248 255 3M100N50M100N22M = 103 0 GCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGACACTGGGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_56_183_56 147 test_chromosome 159 255 75M = 106 0 GACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_56_183_56 99 test_chromosome 106 255 75M = 159 0 GGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTGGGACGATCGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_57_231_8 147 test_chromosome 207 255 44M100N31M = 107 0 TTGGCGCGCGGCCCTAGGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_57_231_8 99 test_chromosome 107 255 75M = 207 0 GGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCACCGACTGGACTATTTAGGACGATCGGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_58_218_16 163 test_chromosome 108 255 75M = 194 0 GGATGACGACTAGGACTACGGACGGACTTAGAACGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_58_218_16 83 test_chromosome 194 255 57M100N18M = 108 0 GGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_58_220_3d 163 test_chromosome 108 255 75M = 196 0 GGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_58_220_3d 83 test_chromosome 196 255 55M100N20M = 108 0 ACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGGTTGCGATACGCCACTATTACTTTATTATCTTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_58_234_7 163 test_chromosome 108 255 75M = 210 0 GGATGACGCCTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_58_234_7 83 test_chromosome 210 255 41M100N34M = 108 0 GCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTAGTTTATTATCTGACTCGGACGTAGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_5_197_46 145 test_chromosome 173 255 75M = 55 0 ATCGGACGGAGGAGGGCAGTAGGACGCTACGTATTTGGCGGGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_5_197_46 97 test_chromosome 55 255 75M = 173 0 CTATCTGACTAGACTCGAGGCGCTTGCGTCTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_63_229_4c 163 test_chromosome 113 255 75M = 205 0 ACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGGGACTGGACTATTTAGGACGATCGGACTGAGGAGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_63_229_4c 83 test_chromosome 205 255 46M100N29M = 113 0 ATTTGGCGCGCGGCCCTACGGCTGAGTGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_65_238_2e 147 test_chromosome 214 255 37M100N38M = 115 0 GCGGCCCTACGGCTGCGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_65_238_2e 99 test_chromosome 115 255 75M = 214 0 GACTAGGACTACGGACGGACTTAGAGCGTCAGAAGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_69_229_23 163 test_chromosome 119 255 75M = 205 0 AGGACTACGGACGGACTTATAGGGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_69_229_23 83 test_chromosome 205 255 46M100N29M = 119 0 CTTTGGCGCGCGGCCCTACGGCTGAGCGTCTAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_6_182_59 147 test_chromosome 158 255 75M = 56 0 GGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_6_182_59 99 test_chromosome 56 255 75M = 158 0 TATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAGTACGGGGATGACGACTAGGACTACGGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_72_258_4 163 test_chromosome 122 255 75M = 234 0 ACTACGGACGGACTTAGAGCGTCAGATGCAGCAACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_72_258_4 83 test_chromosome 234 255 17M100N50M100N8M = 122 0 CGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATGGGCAACGGGACTTTTTCTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_73_240_34 147 test_chromosome 216 255 35M100N40M = 123 0 GGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTTCTCGGACGTAGACGGATCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_73_240_34 99 test_chromosome 123 255 75M = 216 0 CTACGGACGGACTTAGAGCGTCAGATGCAGCGAATGGACTATTTAGGACGCTCGGACTGAGGAGGGCAGTAGGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_73_259_5e 147 test_chromosome 235 255 16M100N50M100N9M = 123 0 GAGCTTGCGATACGCCACTATTACTGTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_73_259_5e 99 test_chromosome 123 255 75M = 235 0 CTACGGACGGACTTAGAGCGTCAGATGCTGCGACTGGACTATTTGGGACGATCGGACTGAGGAGGGCAGTAGGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_75_204_54 73 test_chromosome 125 255 75M * 0 0 ACGGACGGACTTCGAGCCTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_75_235_21 73 test_chromosome 125 255 75M * 0 0 ACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGCACGATCGGACTGAGGAGGGCAGTAGAACGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_75_277_3b 145 test_chromosome 353 255 48M100N27M = 125 0 TATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACCTGAGACTGGGATCGAGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_75_277_3b 97 test_chromosome 125 255 75M = 353 0 ACGGACGGACTTAAAGCTTCAGATGCAGCGACAGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_77_256_2c 73 test_chromosome 127 255 75M * 0 0 GGACGGACTTAGAGCATCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_78_276_4b 145 test_chromosome 352 255 49M100N26M = 128 0 CTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTAGGATCGAGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_78_276_4b 97 test_chromosome 128 255 75M = 352 0 GACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGGCGCTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_79_256_31 137 test_chromosome 129 255 75M * 0 0 ACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_81_228_3a 163 test_chromosome 131 255 75M = 204 0 GGACTGAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGTAGTAGGACGCTACGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_81_228_3a 83 test_chromosome 204 255 47M100N28M = 131 0 TATTTGGCGCGCGGCCCTATGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGTAGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_81_245_4d 163 test_chromosome 131 255 75M = 221 0 GGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGATGAGGGCAGTAGGACGCTACGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_81_245_4d 83 test_chromosome 221 255 30M100N45M = 131 0 TACGGCTGAGCGTCGAGGTTGCGATACGCCACTATTACTTTATAATCTTACTCGGACGTAGACGGATCGGCAACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_82_255_2 137 test_chromosome 132 255 75M * 0 0 GACTTAGAGCGTCAGATGCAGCGACTGGACTTTTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_82_271_58 147 test_chromosome 247 255 4M100N50M100N21M = 132 0 CGCCACTATTACTTTATTATCTTACTCGGACGTAGACGCATCGGCAACGGGACTTTTTCTACTTGAGACTGGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_82_271_58 99 test_chromosome 132 255 75M = 247 0 GACTTAGAGCGTCAGTTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_85_268_53 147 test_chromosome 244 255 7M100N50M100N18M = 135 0 ATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGTCAACGGGACTTTTTCTACTTGAGACTGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_85_268_53 99 test_chromosome 135 255 75M = 244 0 TTAGTGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_85_275_38 137 test_chromosome 351 255 50M100N25M * 0 0 ACTCTTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTACTACTTGAGACTGGGATCGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_87_250_57 163 test_chromosome 137 255 75M = 226 0 AGAGCGTCAGATGCAGAGACTGGACTATTTAGGACGATCGGACTGAGGAGTGCAGTAGGACGCTACGTATTTGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_87_250_57 83 test_chromosome 226 255 25M100N50M = 137 0 ATGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_87_279_5f 161 test_chromosome 137 255 75M = 355 0 AGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACCGAGGAGGGCAGTAGGACGCTACGTATTTGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_87_279_5f 81 test_chromosome 355 255 46M100N29M = 137 0 TTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_88_257_50 137 test_chromosome 138 255 75M * 0 0 GAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_89_230_b 163 test_chromosome 139 255 75M = 206 0 AGCGTCAGGTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_89_230_b 83 test_chromosome 206 255 45M100N30M = 139 0 TCTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTAACTCACTCGGACGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_89_245_15 147 test_chromosome 221 255 30M100N45M = 139 0 TACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTTCTCTATTATCTTACTCGGACGTAGACGGATCGGCAACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_89_245_15 99 test_chromosome 139 255 75M = 221 0 AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_89_267_32 163 test_chromosome 139 255 75M = 243 0 AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGAGTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_89_267_32 83 test_chromosome 243 255 8M100N50M100N17M = 139 0 GATACGGCACTATTACTTTATTATCTTTCTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_8_155_9 163 test_chromosome 58 255 75M = 131 0 TGTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_8_155_9 83 test_chromosome 131 255 75M = 58 0 GGACTTCGAGCGTCAGATGCAGCGACTGTACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_8_197_1 147 test_chromosome 173 255 75M = 58 0 ATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_8_197_1 99 test_chromosome 58 255 75M = 173 0 TCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGACACTACGGGGATGGCGACTAGGACTACGGACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_91_256_41 73 test_chromosome 141 255 75M * 0 0 CGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_92_250_44 147 test_chromosome 226 255 25M100N50M = 142 0 CTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGGTACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_92_250_44 99 test_chromosome 142 255 75M = 226 0 GTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_92_266_43 147 test_chromosome 242 255 9M100N50M100N16M = 142 0 CGATACGCCACTATTACTTTCTTATCTTACTCGGACGTAGACGGAGCGGCAACGGGACTTTTTCTACTTGAGACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_92_266_43 99 test_chromosome 142 255 75M = 242 0 GTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTCAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_94_291_40 137 test_chromosome 367 255 34M100N41M * 0 0 CTTCCTGGGACGTAGACGGATCGGCAACGCGACATTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTGGGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:5 XS:A:+ NH:i:1 -test_mRNA_96_238_3 163 test_chromosome 146 255 75M = 214 0 GATGCAGCGACTGGACTATTTAGGACGATCGGACGGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_96_238_3 83 test_chromosome 214 255 37M100N38M = 146 0 GCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCTACTAGTACTTTATTATCTTACGCGGACGTAGACGGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_97_275_26 145 test_chromosome 351 255 50M100N25M = 147 0 ACTATTACTTTATTATCTTAGTCGGACGTAGACGGATCGGAAACGGGACTCTTTCTACTTGAGACTGGGATCGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_97_275_26 97 test_chromosome 147 255 75M = 351 0 ATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_9_179_52 163 test_chromosome 59 255 75M = 155 0 CTGACTAGACTGGAGGCGCTCGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_9_179_52 83 test_chromosome 155 255 75M = 59 0 ACTGGACCATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 --- a/test-data/tophat_out2.wig +++ /dev/null @@ -1,175 +0,0 @@ -track type=bedGraph name="TopHat - read coverage" -test_chromosome 0 52 0 -test_chromosome 52 53 1 -test_chromosome 53 54 2 -test_chromosome 54 55 3 -test_chromosome 55 57 4 -test_chromosome 57 58 6 -test_chromosome 58 60 7 -test_chromosome 60 65 8 -test_chromosome 65 70 9 -test_chromosome 70 71 10 -test_chromosome 71 72 11 -test_chromosome 72 75 12 -test_chromosome 75 77 13 -test_chromosome 77 79 15 -test_chromosome 79 82 16 -test_chromosome 82 85 17 -test_chromosome 85 87 19 -test_chromosome 87 88 20 -test_chromosome 88 90 21 -test_chromosome 90 91 22 -test_chromosome 91 93 23 -test_chromosome 93 95 26 -test_chromosome 95 97 28 -test_chromosome 97 99 30 -test_chromosome 99 100 31 -test_chromosome 100 101 35 -test_chromosome 101 102 36 -test_chromosome 102 105 38 -test_chromosome 105 106 39 -test_chromosome 106 107 40 -test_chromosome 107 112 43 -test_chromosome 112 114 44 -test_chromosome 114 118 45 -test_chromosome 118 121 46 -test_chromosome 121 122 48 -test_chromosome 122 124 50 -test_chromosome 124 126 53 -test_chromosome 126 129 54 -test_chromosome 129 130 53 -test_chromosome 130 131 55 -test_chromosome 131 132 57 -test_chromosome 132 133 55 -test_chromosome 133 134 54 -test_chromosome 134 135 55 -test_chromosome 135 136 54 -test_chromosome 136 137 56 -test_chromosome 137 138 57 -test_chromosome 138 141 60 -test_chromosome 141 147 62 -test_chromosome 147 148 61 -test_chromosome 148 150 62 -test_chromosome 150 152 61 -test_chromosome 152 153 60 -test_chromosome 153 154 61 -test_chromosome 154 155 63 -test_chromosome 155 156 64 -test_chromosome 156 158 65 -test_chromosome 158 159 66 -test_chromosome 159 160 68 -test_chromosome 160 161 67 -test_chromosome 161 163 68 -test_chromosome 163 164 69 -test_chromosome 164 165 71 -test_chromosome 165 167 73 -test_chromosome 167 168 74 -test_chromosome 168 169 72 -test_chromosome 169 170 75 -test_chromosome 170 171 73 -test_chromosome 171 172 74 -test_chromosome 172 174 75 -test_chromosome 174 175 77 -test_chromosome 175 176 74 -test_chromosome 176 177 73 -test_chromosome 177 181 71 -test_chromosome 181 182 70 -test_chromosome 182 183 67 -test_chromosome 183 184 68 -test_chromosome 184 189 69 -test_chromosome 189 193 68 -test_chromosome 193 194 69 -test_chromosome 194 195 71 -test_chromosome 195 196 72 -test_chromosome 196 197 70 -test_chromosome 197 199 68 -test_chromosome 199 200 66 -test_chromosome 200 201 67 -test_chromosome 201 202 66 -test_chromosome 202 204 65 -test_chromosome 204 205 67 -test_chromosome 205 207 65 -test_chromosome 207 211 66 -test_chromosome 211 213 65 -test_chromosome 213 216 64 -test_chromosome 216 220 62 -test_chromosome 220 224 63 -test_chromosome 224 225 64 -test_chromosome 225 228 66 -test_chromosome 228 229 65 -test_chromosome 229 230 62 -test_chromosome 230 231 61 -test_chromosome 231 232 60 -test_chromosome 232 234 59 -test_chromosome 234 237 58 -test_chromosome 237 238 57 -test_chromosome 238 239 55 -test_chromosome 239 240 53 -test_chromosome 240 241 50 -test_chromosome 241 242 51 -test_chromosome 242 243 52 -test_chromosome 243 244 53 -test_chromosome 244 246 50 -test_chromosome 246 247 52 -test_chromosome 247 249 50 -test_chromosome 249 250 47 -test_chromosome 250 349 0 -test_chromosome 349 350 1 -test_chromosome 350 351 49 -test_chromosome 351 352 51 -test_chromosome 352 353 53 -test_chromosome 353 354 54 -test_chromosome 354 357 55 -test_chromosome 357 358 56 -test_chromosome 358 361 55 -test_chromosome 361 362 57 -test_chromosome 362 365 56 -test_chromosome 365 366 57 -test_chromosome 366 368 58 -test_chromosome 368 369 57 -test_chromosome 369 372 56 -test_chromosome 372 375 59 -test_chromosome 375 378 60 -test_chromosome 378 379 59 -test_chromosome 379 380 57 -test_chromosome 380 381 56 -test_chromosome 381 382 54 -test_chromosome 382 384 53 -test_chromosome 384 386 52 -test_chromosome 386 387 51 -test_chromosome 387 388 50 -test_chromosome 388 390 48 -test_chromosome 390 395 47 -test_chromosome 395 396 45 -test_chromosome 396 398 44 -test_chromosome 398 399 43 -test_chromosome 399 400 42 -test_chromosome 400 402 1 -test_chromosome 402 500 0 -test_chromosome 500 508 39 -test_chromosome 508 509 38 -test_chromosome 509 510 37 -test_chromosome 510 511 36 -test_chromosome 511 516 35 -test_chromosome 516 517 33 -test_chromosome 517 518 31 -test_chromosome 518 521 29 -test_chromosome 521 522 26 -test_chromosome 522 524 25 -test_chromosome 524 525 24 -test_chromosome 525 526 22 -test_chromosome 526 527 20 -test_chromosome 527 528 18 -test_chromosome 528 529 17 -test_chromosome 529 530 16 -test_chromosome 530 532 15 -test_chromosome 532 534 14 -test_chromosome 534 536 13 -test_chromosome 536 540 11 -test_chromosome 540 541 10 -test_chromosome 541 543 9 -test_chromosome 543 544 8 -test_chromosome 544 545 7 -test_chromosome 545 547 6 -test_chromosome 547 549 3 -test_chromosome 549 549 2 --- a/test-data/tophat_out3.bed +++ /dev/null @@ -1,3 +0,0 @@ -track name=junctions description="TopHat junctions" -test_chromosome 180 402 JUNC00000001 46 + 180 402 255,0,0 2 70,52 0,170 -test_chromosome 349 550 JUNC00000002 38 + 349 550 255,0,0 2 51,50 0,151

1 0

galaxy-dist commit 7ca26b1cc9b6: Added a sample loc file listing all fasta files and a script to generate the file given a base genome directory.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1289194982 18000 # Node ID 7ca26b1cc9b6fd67364a6c6af6005ceecaa3f45b # Parent 535d276c92bcc35e563c4ce5a2351f562f451132 Added a sample loc file listing all fasta files and a script to generate the file given a base genome directory. --- /dev/null +++ b/tool-data/all_fasta.loc.sample @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id><dbkey><display_name><file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# --- /dev/null +++ b/scripts/loc_files/create_all_fasta_loc.py @@ -0,0 +1,300 @@ +import optparse, os, sys +import elementtree.ElementTree as etree + +""" +Generates a loc file containing names of all the fasta files that match the +name of the genome subdirectory they're in. +Assumptions: + - fasta files should be named the same as the genome subdirectory they're + in, with the possible addition of a recognized variant (canon, full, etc.) + - for "variants" (like full, canon[ical], chrM, etc.) the naming needs to be + consistent and specific: + - <genome_name><variant>, like hg19canon, hg19full, or hg19chrM +Normal usage: +create_all_fasta_loc.py -f unmatching_fasta.txt -i seq + +usage: %prog [options] + -d, --data-table-xml=d: The name of the data table configuration file to get format of loc file + -t, --data-table=t: The name of the data table listed in the data table XML file + -g, --genome-dir=g: Genome directory to look in + -e, --exemptions=e: Comma-separated list of genome dir subdirectories to not look in + -i, --inspect-dirs=i: Comma-separated list of subdirectories inside genome dirs to look in (default is all) + -x, --fasta-exts=x: Comma-separated list of all fasta extensions to list + -s, --loc-sample=s: The name of the sample loc file (to copy text into top of output loc file) + -f, --unmatching-fasta=f: Name of file to output non-matching fasta files to, if included + -v, --variants=v: Comma-separated list of recognized variants of fasta file names + -a, --append=a: Append to existing all_fasta.loc file rather than create new + -p, --sample-text=p: Copy over text from all_fasta.loc.sample file (false if set to append) +""" + +DEFAULT_TOOL_DATA_TABLE_CONF = 'tool_data_table_conf.xml' +DEFAULT_ALL_FASTA_LOC_BASE = 'all_fasta' +DEFAULT_BASE_GENOME_DIR = '/afs/bx.psu.edu/depot/data/genome' +EXEMPTIONS = 'bin,tmp,lengths,equCab2_chrM,microbes' +INSPECT_DIR = None +FASTA_EXTS = '.fa,.fasta,.fna' +VARIANTS = 'chrM,chr21,full,canon,female,male,haps,nohaps' + +VARIANT_EXCLUSIONS = ':full' + +DBKEY_DESCRIPTION_MAP = { 'AaegL1': 'Mosquito (Aedes aegypti): AaegL1', + 'AgamP3': 'Mosquito (Anopheles gambiae): AgamP3', + 'anoCar1': 'Lizard (Anolis carolinensis): anoCar1', + 'anoGam1': 'Mosquito (Anopheles gambiae): anoGam1', + 'apiMel1': 'Honeybee (Apis mellifera): apiMel1', + 'apiMel2': 'Honeybee (Apis mellifera): apiMel2', + 'apiMel3': 'Honeybee (Apis mellifera): apiMel3', + 'Arabidopsis_thaliana_TAIR9': '', + 'borEut13': 'Boreoeutherian: borEut13', + 'bosTau2': 'Cow (Bos taurus): bosTau2', + 'bosTau3': 'Cow (Bos taurus): bosTau3', + 'bosTau4': 'Cow (Bos taurus): bosTau4', + 'bosTauMd3': 'Cow (Bos taurus): bosTauMd3', + 'calJac1': 'Marmoset (Callithrix jacchus): calJac1', + 'canFam1': 'Dog (Canis lupus familiaris): canFam1', + 'canFam2': 'Dog (Canis lupus familiaris): canFam2', + 'cavPor3': 'Guinea Pig (Cavia porcellus): cavPor3', + 'ce2': 'Caenorhabditis elegans: ce2', + 'ce4': 'Caenorhabditis elegans: ce4', + 'ce5': 'Caenorhabditis elegans: ce5', + 'ce6': 'Caenorhabditis elegans: ce6', + 'CpipJ1': 'Mosquito (Culex quinquefasciatus): CpipJ1', + 'danRer2': 'Zebrafish (Danio rerio): danRer2', + 'danRer3': 'Zebrafish (Danio rerio): danRer3', + 'danRer4': 'Zebrafish (Danio rerio): danRer4', + 'danRer5': 'Zebrafish (Danio rerio): danRer5', + 'danRer6': 'Zebrafish (Danio rerio): danRer6', + 'dm1': 'Fruit Fly (Drosophila melanogaster): dm1', + 'dm2': 'Fruit Fly (Drosophila melanogaster): dm2', + 'dm3': 'Fruit Fly (Drosophila melanogaster): dm3', + 'dm4': 'Fruit Fly (Drosophila melanogaster): dm', + 'dp3': 'Fruit Fly (Drosophila pseudoobscura): dp3', + 'dp4': 'Fruit Fly (Drosophila pseudoobscura): dp4', + 'droAna1': 'Fruit Fly (Drosophila ananassae): droAna1', + 'droAna2': 'Fruit Fly (Drosophila ananassae): droAna2', + 'droAna3': 'Fruit Fly (Drosophila ananassae): droAna3', + 'droEre1': 'Fruit Fly (Drosophila erecta): droEre1', + 'droEre2': 'Fruit Fly (Drosophila erecta): droEre2', + 'droGri1': 'Fruit Fly (Drosophila grimshawi): droGri1', + 'droGri2': 'Fruit Fly (Drosophila grimshawi): droGri2', + 'droMoj1': 'Fruit Fly (Drosophila mojavensis): droMoj1', + 'droMoj2': 'Fruit Fly (Drosophila mojavensis): droMoj2', + 'droMoj3': 'Fruit Fly (Drosophila mojavensis): droMoj3', + 'droPer1': 'Fruit Fly (Drosophila persimilis): droPer1', + 'droSec1': 'Fruit Fly (Drosophila sechellia): droSec1', + 'droSim1': 'Fruit Fly (Drosophila simulans): droSim1', + 'droVir1': 'Fruit Fly (Drosophila virilis): droVir1', + 'droVir2': 'Fruit Fly (Drosophila virilis): droVir2', + 'droVir3': 'Fruit Fly (Drosophila virilis): droVir3', + 'droYak1': 'Fruit Fly (Drosophila yakuba): droYak1', + 'droYak2': 'Fruit Fly (Drosophila yakuba): droYak2', + 'echTel1': 'Tenrec (Echinops telfairi): echTel1', + 'equCab1': 'Horse (Equus caballus): equCab1', + 'equCab2': 'Horse (Equus caballus): equCab2', + 'eriEur1': 'Hedgehog (Erinaceus europaeus): eriEur1', + 'felCat3': 'Cat (Felis catus): felCat3', + 'fr1': 'Fugu (Takifugu rubripes): fr1', + 'fr2': 'Fugu (Takifugu rubripes): fr2', + 'galGal2': 'Chicken (Gallus gallus): galGal2', + 'galGal3': 'Chicken (Gallus gallus): galGal3', + 'gasAcu1': 'Stickleback (Gasterosteus aculeatus): gasAcu1', + 'hg16': 'Human (Homo sapiens): hg16', + 'hg17': 'Human (Homo sapiens): hg17', + 'hg18': 'Human (Homo sapiens): hg18', + 'hg19': 'Human (Homo sapiens): hg19', + 'IscaW1': 'Deer Tick (Ixodes scapularis): IscaW1', + 'lMaj5': 'Leishmania major: lMaj5', + 'mm5': 'Mouse (Mus musculus): mm5', + 'mm6': 'Mouse (Mus musculus): mm6', + 'mm7': 'Mouse (Mus musculus): mm7', + 'mm8': 'Mouse (Mus musculus): mm8', + 'mm9': 'Mouse (Mus musculus): mm9', + 'monDom4': 'Opossum (Monodelphis domestica): monDom4', + 'monDom5': 'Opossum (Monodelphis domestica): monDom5', + 'ornAna1': 'Platypus (Ornithorhynchus anatinus): ornAna1', + 'oryCun1': 'Rabbit (Oryctolagus cuniculus): oryCun1', + 'oryLat1': 'Medaka (Oryzias latipes): oryLat1', + 'oryLat2': 'Medaka (Oryzias latipes): oryLat2', + 'oryza_sativa_japonica_nipponbare_IRGSP4.0': 'Rice (Oryza sativa L. ssp. japonica var. Nipponbare): IRGSP4.0', + 'otoGar1': 'Bushbaby (Otolemur garnetti): otoGar1', + 'panTro1': 'Chimpanzee (Pan troglodytes): panTro1', + 'panTro2': 'Chimpanzee (Pan troglodytes): panTro2', + 'petMar1': 'Lamprey (Petromyzon marinus): petMar1', + 'phiX': 'phiX174 (AF176034)', + 'PhumU1': 'Head Louse (Pediculus humanus): PhumU1', + 'ponAbe2': 'Orangutan (Pongo pygmaeus abelii): ponAbe2', + 'pUC18': 'pUC18 (L09136)', + 'rheMac2': 'Rhesus Macaque (Macaca mulatta): rheMac2', + 'rn3': 'Rat (Rattus norvegicus): rn3', + 'rn4': 'Rat (Rattus norvegicus): rn4', + 'sacCer1': 'Yeast (Saccharomyces cerevisiae): sacCer1', + 'sacCer2': 'Yeast (Saccharomyces cerevisiae): sacCer2', + 'sorAra1': 'Common Shrew (Sorex araneus): sorAra1', + 'Sscrofa9.58': 'Pig (Sus scrofa): Sscrofa9.58', + 'strPur2': 'Purple Sea Urchin (Strongylocentrotus purpuratus): strPur2', + 'susScr2': 'Pig (Sus scrofa): susScr2', + 'taeGut1': 'Zebra Finch (Taeniopygia guttata): taeGut1', + 'tetNig1': 'Tetraodon (Tetraodon nigroviridis): tetNig1', + 'tetNig2': 'Tetraodon (Tetraodon nigroviridis): tetNig2', + 'tupBel1': 'Tree Shrew (Tupaia belangeri): tupBel1', + 'venter1': 'Human (J. Craig Venter): venter1', + 'xenTro2': 'Frog (Xenopus tropicalis): xenTro2' + } + +VARIANT_MAP = { 'canon': 'Canonical', + 'full': 'Full', + 'female': 'Female', + 'male': 'Male' + } + +# alphabetize ignoring case +def caseless_compare( a, b ): + au = a.upper() + bu = b.upper() + if au > bu: + return 1 + elif au == bu: + return 0 + elif au < bu: + return -1 + +def __main__(): + # command line variables + parser = optparse.OptionParser() + parser.add_option( '-d', '--data-table-xml', dest='data_table_xml', type='string', default=DEFAULT_TOOL_DATA_TABLE_CONF, help='The name of the data table configuration file to get format of loc file' ) + parser.add_option( '-t', '--data-table', dest='data_table_name', type='string', default=DEFAULT_ALL_FASTA_LOC_BASE, help='The name of the data table listed in the data table XML file' ) + parser.add_option( '-g', '--genome_dir', dest='genome_dir', type='string', default=DEFAULT_BASE_GENOME_DIR, help='Genome directory to look in' ) + parser.add_option( '-e', '--exemptions', dest='exemptions', type='string', default=EXEMPTIONS, help='Comma-separated list of subdirectories in genome dir to not look in' ) + parser.add_option( '-i', '--inspect-dir', dest='inspect_dir', type='string', default=INSPECT_DIR, help='Comma-separated list of subdirectories inside genome dirs to look in (default is all)' ) + parser.add_option( '-x', '--fasta_exts', dest='fasta_exts', type='string', default=FASTA_EXTS, help='Comma-separated list of all fasta extensions to list' ) + parser.add_option( '-s', '--loc-sample', dest='loc_sample_name', type='string', help='The name of the sample loc file (to copy text into top of output loc file)' ) + parser.add_option( '-f', '--unmatching-fasta', dest='unmatching_fasta', type='string', default=None, help='Name of file to output non-matching fasta files to' ) + parser.add_option( '-v', '--variants', dest='variants', type='string', default=VARIANTS, help='Comma-separated list of recognized variants of fasta file names' ) + parser.add_option( '-n', '--variant-exclusions', dest='variant_exclusions', type='string', default=VARIANT_EXCLUSIONS, help="List of files to exclude because they're duplicated by a variants; of the format: '<variant_to_keep_1>:<variant_to_remove_1>[,<variant_to_remove_2>[,...]][;<variant_to_keep_2>:<variant_to_remove_1>[,<variant_to_remove_2>[,...]]]'; default ':(full)' (if non-variant version present (like 'hg19'), full version (like 'hg19full') will be thrown out)" ) + parser.add_option( '-a', '--append', dest='append', action='store_true', default=False, help='Append to existing all_fasta.loc file rather than create new' ) + parser.add_option( '-p', '--sample-text', dest='sample_text', action='store_true', default='True', help='Copy over text from all_fasta.loc.sample file (false if set to append)' ) + (options, args) = parser.parse_args() + + exemptions = [ e.strip() for e in options.exemptions.split( ',' ) ] + fasta_exts = [ x.strip() for x in options.fasta_exts.split( ',' ) ] + variants = [ v.strip() for v in options.variants.split( ',' ) ] + variant_exclusions = {} + try: + for ve in options.variant_exclusions.split( ';' ): + v, e = ve.split( ':' ) + variant_exclusions[ v ] = e.split( ',' ) + except: + sys.stderr.write( 'Problem parsing the variant exclusion parameter (-n/--variant-exclusion). Make sure it follows the expected format\n' ) + sys.exit( 1 ) + if options.append: + sample_text = False + else: + sample_text = options.sample_text + + # all paths to look in + if options.inspect_dir: + paths_to_look_in = [ os.path.join( options.genome_dir, '%s', id ) for id in options.inspect_dir.split( ',' ) ] + else: + paths_to_look_in = os.path.join( options.genome_dir, '%s' ) + + # say what we're looking in + print '\nLooking in:\n\t%s' % '\n\t'.join( [ p % '<build_name>' for p in paths_to_look_in ] ) + poss_names = [ '<build_name>%s' % v for v in variants ] + print 'for files that are named %s' % ', '.join( poss_names[:-1] ), + if len( poss_names ) > 1: + print 'or %s' % poss_names[-1], + if len( options.fasta_exts ) == 1: + print 'with the extension %s.' % ', '.join( fasta_exts[:-1] ) + else: + print 'with the extension %s or %s.' % ( ', '.join( fasta_exts[:-1] ), fasta_exts[-1] ) + print '\nSkipping the following:\n\t%s' % '\n\t'.join( exemptions ) + + # get column names + col_values = [] + loc_path = None + tree = etree.parse( options.data_table_xml ) + tables = tree.getroot() + for table in tables.getiterator(): + name = table.attrib.get( 'name' ) + if name == options.data_table_name: + cols = None + for node in table.getiterator(): + if node.tag == 'columns': + cols = node.text + elif node.tag == 'file': + loc_path = node.attrib.get( 'path' ) + if cols: + col_values = [ col.strip() for col in cols.split( ',' ) ] + if not col_values or not loc_path: + stop_err( 'No columns can be found for this data table (%s) in %s' % ( options.data_table, options.data_table_xml ) ) + + # get all fasta paths under genome directory + fasta_locs = {} + unmatching_fasta_paths = [] + genome_subdirs = [ dr for dr in os.listdir( options.genome_dir ) if dr not in exemptions ] + for genome_subdir in genome_subdirs: + possible_names = [ genome_subdir ] + possible_names.extend( [ '%s%s' % ( genome_subdir, v ) for v in variants ] ) + # get paths to all fasta files + for path_to_look_in in paths_to_look_in: + for dirpath, dirnames, filenames in os.walk( path_to_look_in % genome_subdir ): + for fn in filenames: + ext = os.path.splitext( fn )[-1] + fasta_base = os.path.splitext( fn )[0] + if ext in fasta_exts: + if fasta_base in possible_names: + if fasta_base == genome_subdir: + name = DBKEY_DESCRIPTION_MAP[ genome_subdir ] + else: + try: + name = '%s %s' % ( DBKEY_DESCRIPTION_MAP[ genome_subdir ], VARIANT_MAP[ fasta_base.replace( genome_subdir, '' ) ] ) + except KeyError: + name = '%s %s' % ( DBKEY_DESCRIPTION_MAP[ genome_subdir ], fasta_base.replace( genome_subdir, '' ) ) + fasta_locs[ fasta_base ] = { 'value': fasta_base, 'dbkey': genome_subdir, 'name': name, 'path': os.path.join( dirpath, fn ) } + else: + unmatching_fasta_paths.append( os.path.join( dirpath, fn ) ) + # remove redundant fasta files + if variant_exclusions.keys(): + for k in variant_exclusions.keys(): + leave_in = '%s%s' % ( genome_subdir, k ) + if fasta_locs.has_key( leave_in ): + to_remove = [ '%s%s' % ( genome_subdir, k ) for k in variant_exclusions[ k ] ] + for tr in to_remove: + if fasta_locs.has_key( tr ): + del fasta_locs[ tr ] + + # output results + print '\nThere were %s fasta files found that were not included because they did not have the expected file names.' % len( unmatching_fasta_paths ) + print '%s fasta files were found and listed.\n' % len( fasta_locs.keys() ) + + # output unmatching fasta files + if options.unmatching_fasta and unmatching_fasta_paths: + open( options.unmatching_fasta, 'wb' ).write( '%s\n' % '\n'.join( unmatching_fasta_paths ) ) + + # output loc file + if options.append: + all_fasta_loc = open( loc_path, 'ab' ) + else: + all_fasta_loc = open( loc_path, 'wb' ) + # put sample loc file text at top of file if appropriate + if sample_text: + if options.loc_sample_name: + all_fasta_loc.write( '%s\n' % open( options.loc_sample_name, 'rb' ).read().strip() ) + else: + all_fasta_loc.write( '%s\n' % open( '%s.sample' % loc_path, 'rb' ).read().strip() ) + # output list of fasta files in alphabetical order + fasta_bases = fasta_locs.keys() + fasta_bases.sort( caseless_compare ) + for fb in fasta_bases: + out_line = [] + for col in col_values: + try: + out_line.append( fasta_locs[ fb ][ col ] ) + except KeyError: + stop_err( 'Unexpected column (%s) encountered' % col ) + if out_line: + all_fasta_loc.write( '%s\n' % '\t'.join( out_line ) ) + # close up output loc file + all_fasta_loc.close() + +if __name__=='__main__': __main__()

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galaxy-dist commit 629e14c5f561: Fix for failing rg Haploview test - finally tracked down trivial pdfjoin error - new pdfjam version does not want quoted filespec
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Ross Lazarus <ross.lazarus(a)gmail.com> # Date 1289235967 18000 # Node ID 629e14c5f561446c963b05560f245e2ed7041ff0 # Parent 7ca26b1cc9b6fd67364a6c6af6005ceecaa3f45b Fix for failing rg Haploview test - finally tracked down trivial pdfjoin error - new pdfjam version does not want quoted filespec --- a/lib/galaxy/datatypes/genetics.py +++ b/lib/galaxy/datatypes/genetics.py @@ -100,7 +100,6 @@ class GenomeGraphs( Tabular ): s = ''.join(sl) s = urllib.quote_plus(s) redirect_url = s - log.debug('## rg gg ucsc rdurl=%s; s = %s' % (redirect_url,s)) link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url ) ret_val.append( (site_name, link) ) return ret_val --- a/tools/rgenetics/rgHaploView.py +++ b/tools/rgenetics/rgHaploView.py @@ -394,7 +394,7 @@ def ld(): p=subprocess.Popen(vcl,shell=True,cwd=outfpath,stderr=lf,stdout=lf) retval = p.wait() lf.write('## executing %s returned %d\n' % (vcl,retval)) - vcl = '%s "*.pdf" --fitpaper true --outfile alljoin.pdf' % pdfjoin + vcl = '%s *.pdf --fitpaper true --outfile alljoin.pdf' % pdfjoin p=subprocess.Popen(vcl,shell=True,cwd=outfpath,stderr=lf,stdout=lf) retval = p.wait() lf.write('## executing %s returned %d\n' % (vcl,retval))

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galaxy-dist commit d344c55b4f81: another tiny rgHaploView tool test fix - pdfs differ on Main by 20kb.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Ross Lazarus <ross.lazarus(a)gmail.com> # Date 1289244501 18000 # Node ID d344c55b4f81f273d712c397d648fbaf308a9beb # Parent 629e14c5f561446c963b05560f245e2ed7041ff0 another tiny rgHaploView tool test fix - pdfs differ on Main by 20kb. --- a/tools/rgenetics/rgHaploView.xml +++ b/tools/rgenetics/rgHaploView.xml @@ -1,5 +1,4 @@ -<tool id="rgHaploView1" name="LD plots:"> - <code file="rgHaploView_code.py"/> +<tool id="rgHaploView1" name="LD plots:" version="0.2"><description>and comparisons with HapMap data</description> @@ -16,7 +15,7 @@ label="Current history lPed format data" size="80" help="Linkage Ped format data from your current history" /> - <param name="ucsc_region" type="text" label="Optional subset region (blank=ALL)" + <param name="ucsc_region" type="text" label="Optional subset region (blank=ALL. WARNING: doing this will fail if >1 chromosome in input data!)" size="80" optional="true" help="Region eg: chr9:119,506,000-119,518,000 Leave blank for all or to extract the rs list supplied below."/> @@ -53,7 +52,7 @@ <param name="infoTrack" type="select" label="Add Hapmap information track to image" help="Refseq genes and snp density can be added to the plot if desired for orientation" > - <option value="info">Add Information track (DISABLED! Awaiting fix from Haploview authors)</option> + <option value="info">Add Information track (DISABLED! Awaiting bug fix from Haploview authors since reported in October 2009)</option><option value="noinfo" selected="True">No Information track</option></param> @@ -75,8 +74,7 @@ </inputs><outputs> - <data format="html" name="out_file1" /> - + <data format="html" name="out_file1" label="${title}.html" /></outputs><!-- python $TOOLPATH/$TOOL.py "" "rs2283802Xrs2267000Xrs16997606Xrs4820537Xrs3788347Xrs756632Xrs4820539Xrs2283804Xrs2267006Xrs4822363X" \ @@ -101,9 +99,9 @@ <param name='infoTrack' value='noinfo' /><param name='hires' value='lo' /><param name='memsize' value='2048' /> - <output name='out_file1' file='rgtestouts/rgHaploView/rgHaploViewtest1.html' ftype='html' lines_diff="50"> - <extra_files type="file" name='alljoin.pdf' value="rgtestouts/rgHaploView/alljoin.pdf" compare="sim_size" delta="3000"/> - <extra_files type="file" name='allnup.pdf' value="rgtestouts/rgHaploView/allnup.pdf" compare="sim_size" delta="3000" /> + <output name='out_file1' file='rgtestouts/rgHaploView/rgHaploViewtest1.html' ftype='html' lines_diff="60"> + <extra_files type="file" name='alljoin.pdf' value="rgtestouts/rgHaploView/alljoin.pdf" compare="sim_size" delta="50000"/> + <extra_files type="file" name='allnup.pdf' value="rgtestouts/rgHaploView/allnup.pdf" compare="sim_size" delta="50000" /><extra_files type="file" name='Log_rgHaploViewtest1.txt' value="rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt" compare="diff" lines_diff="50"/><extra_files type="file" name='rgHaploViewtest1.ped.TESTS' value="rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS" compare="diff" lines_diff="20"/>

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galaxy-dist commit 535d276c92bc: Converted several tools to data table style of loc file handling (Bowtie, BWA, Lastz, Megablast, PerM, SRMA). Cleaned up several tool XML files, removing unnecessary None parameters.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1289193013 18000 # Node ID 535d276c92bcc35e563c4ce5a2351f562f451132 # Parent 4187ae2fdb9e3f8b7ff5878e7517a24868b8ffca Converted several tools to data table style of loc file handling (Bowtie, BWA, Lastz, Megablast, PerM, SRMA). Cleaned up several tool XML files, removing unnecessary None parameters. --- a/test-data/bwa_wrapper_out1.sam +++ b/test-data/bwa_wrapper_out1.sam @@ -1,30 +1,30 @@ -seq1 16 phiX 322 25 36M * 0 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 -seq10 0 phiX 4149 37 17M1D19M * 0 0 ATTCTTTCTTTTCGTATCAGGGCGTTGAGTTCGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:5G11^G19 -seq11 0 phiX 4072 37 18M1D18M * 0 0 GCATTTCTACTCCTTCTCATCCCCAATGCTTGGCTT II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:12T5^A18 +seq1 16 phiX174 322 25 36M * 0 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 +seq10 0 phiX174 4149 37 17M1D19M * 0 0 ATTCTTTCTTTTCGTATCAGGGCGTTGAGTTCGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:5G11^G19 +seq11 0 phiX174 4072 37 18M1D18M * 0 0 GCATTTCTACTCCTTCTCATCCCCAATGCTTGGCTT II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:12T5^A18 seq12 4 * 0 0 * * 0 0 CGCGCTTCGATAAAAATGGGATTGGCGTTTCCAACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII seq13 4 * 0 0 * * 0 0 ATTTCTACTCTTTCTCATCCCCAATCCTTGCCTTCC IIIIIIIIIIIIIIIIIIIIIAAIIIIIIIIIIIII -seq14 0 phiX 3998 37 21M1D15M * 0 0 CCCTTTTGAATGTCACGCTGATATTTTGACTTTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:5C15^T15 +seq14 0 phiX174 3998 37 21M1D15M * 0 0 CCCTTTTGAATGTCACGCTGATATTTTGACTTTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:5C15^T15 seq15 4 * 0 0 * * 0 0 CCAACTTACCAAGGTGGGTTACGAAACGCGACGCCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII seq16 4 * 0 0 * * 0 0 TCAGGGTATTAAAAGAGATTATTTTTCTCCAGCCAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -seq17 0 phiX 3034 37 19M1D17M * 0 0 GTGATGTGCTTGCTACCGAAACAATACTTTAGGCAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:19^T9G7 +seq17 0 phiX174 3034 37 19M1D17M * 0 0 GTGATGTGCTTGCTACCGAAACAATACTTTAGGCAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:19^T9G7 seq18 4 * 0 0 * * 0 0 TCAATCCCCCATGCTTGGCCGTTCCATAAGCAGATG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII seq19 4 * 0 0 * * 0 0 TTCCTGCGCTTAATGCTTGAGCGTCCTGGTGCTGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -seq2 0 phiX 141 37 36M * 0 0 ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 -seq20 0 phiX 1082 37 36M * 0 0 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 -seq21 0 phiX 1344 37 15M1D21M * 0 0 CTGATACCAATAAAACCCTAAGCATTTGGTTCAGGG II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:15^T13T7 +seq2 0 phiX174 141 37 36M * 0 0 ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq20 0 phiX174 1082 37 36M * 0 0 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq21 0 phiX174 1344 37 15M1D21M * 0 0 CTGATACCAATAAAACCCTAAGCATTTGGTTCAGGG II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:15^T13T7 seq22 4 * 0 0 * * 0 0 AATCAAACTTACCAAGGGGTTACGACGCGACGCCGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII seq23 4 * 0 0 * * 0 0 TGTGCTTCCCCAACTTGATTTAATAACCCTATAGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -seq24 0 phiX 4084 37 17M1I18M * 0 0 TTTCTCAATCCCCAATGCCTTGGCTTCCCTAAGCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:27A7 -seq25 0 phiX 520 37 16M1I19M * 0 0 TTGCTACTGACCGCTCTTCGTGCTCGTTGCTGCGTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:26C8 -seq26 0 phiX 1976 37 36M * 0 0 CCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 -seq27 0 phiX 2598 37 20M1I15M * 0 0 CGCTAATCAAGTTGTTTCTGTTTGGTGCTGATATTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:9G25 +seq24 0 phiX174 4084 37 17M1I18M * 0 0 TTTCTCAATCCCCAATGCCTTGGCTTCCCTAAGCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:27A7 +seq25 0 phiX174 520 37 16M1I19M * 0 0 TTGCTACTGACCGCTCTTCGTGCTCGTTGCTGCGTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:26C8 +seq26 0 phiX174 1976 37 36M * 0 0 CCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq27 0 phiX174 2598 37 20M1I15M * 0 0 CGCTAATCAAGTTGTTTCTGTTTGGTGCTGATATTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:9G25 seq28 4 * 0 0 * * 0 0 AAAGAGATTATTTGTCGGTCCAGCCACTAAAGTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII seq29 4 * 0 0 * * 0 0 CAAATTAATGCGCGCTTCGATAATGATTGGGGTATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -seq3 0 phiX 505 37 36M * 0 0 GTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 -seq30 0 phiX 4091 37 18M1I17M * 0 0 ATCCCCTATGCTTGGCTTACCATAAGCAGATGGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:6A28 +seq3 0 phiX174 505 37 36M * 0 0 GTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq30 0 phiX174 4091 37 18M1I17M * 0 0 ATCCCCTATGCTTGGCTTACCATAAGCAGATGGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:6A28 seq4 4 * 0 0 * * 0 0 AGCCGCTCGTCTTTTATGTAGGTGGTCAACCATTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -seq5 0 phiX 4985 25 36M * 0 0 CAGTTATATGGCTTTTGGTTTCTATGTGGCTTAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:13G17A4 -seq6 0 phiX 925 37 11M1D25M * 0 0 AGGCGCTCGTCTTGGTATGTAGGTGGTCAACAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:0 XO:i:1 XG:i:1 MD:Z:11^T25 -seq7 0 phiX 943 37 13M1I22M * 0 0 TGTAGGTGGTCAACCAATTTTAATTGCAGGGGCTTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:0 XO:i:1 XG:i:1 MD:Z:35 +seq5 0 phiX174 4985 25 36M * 0 0 CAGTTATATGGCTTTTGGTTTCTATGTGGCTTAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:13G17A4 +seq6 0 phiX174 925 37 11M1D25M * 0 0 AGGCGCTCGTCTTGGTATGTAGGTGGTCAACAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:0 XO:i:1 XG:i:1 MD:Z:11^T25 +seq7 0 phiX174 943 37 13M1I22M * 0 0 TGTAGGTGGTCAACCAATTTTAATTGCAGGGGCTTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:0 XO:i:1 XG:i:1 MD:Z:35 seq8 4 * 0 0 * * 0 0 ACACCCGTCCTTTACGTCATGCGCTCTATTCTCTGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -seq9 0 phiX 2596 37 16M1I19M * 0 0 GCCGCTATTCAGGTTGTTTTCTGTTGGTGCTGATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:7A27 +seq9 0 phiX174 2596 37 16M1I19M * 0 0 GCCGCTATTCAGGTTGTTTTCTGTTGGTGCTGATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:7A27 --- a/test-data/perm_in2.fastqsanger +++ b/test-data/perm_in2.fastqsanger @@ -1,76 +1,76 @@ @HWI-EAS91_1_30788AAXX:1:1:1761:343/2 TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG -+/2 ++ IIIIIII""IIIIIII0II?I""IIIIIIIIIIII?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1578:331/2 AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1647:512/2 TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1570:620/2 CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT -+/2 ++ IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1599:330/2 TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIIII<III@II?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1652:270/2 GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1746:351/2 CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIII?I0IIIIHIIIGIIIIIIIIIII @HWI-EAS91_1_30788AAXX:1:1:1582:633/2 TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1598:534/2 TTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCC -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1572:324/2 GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1749:466/2 GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1629:446/2 CAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGA -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1763:587/2 CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1616:363/2 GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGG -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1768:715/2 AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA -+/2 ++ IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1572:270/2 ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1785:1272/2 GACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTC -+/2 ++ III""""""IIIIIIIII""FI"IIII""II+ICI?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1673:514/2 GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1634:330/2 TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTAT -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II?I0IIIIHIIIGIII --- a/tools/sr_mapping/PerM.xml +++ b/tools/sr_mapping/PerM.xml @@ -1,49 +1,55 @@ -<tool id="PerM" name="Map with PerM" version="1.0.0"> +<tool id="PerM" name="Map with PerM" version="1.1.0"><description>for SOLiD and Illumina</description><requirements><requirement type="package">perm</requirement></requirements><command> -PerM -#if $s.sourceOfRef.refSource == "history": - $s.sourceOfRef.ref -#else: - $s.sourceOfRef.index -#end if -#if $s.mate.singleOrPairs == "single": - $s.mate.reads -#else: - -1 $s.mate.reads1 -2 $s.mate.reads2 - -U $s.mate.upperbound - -L $s.mate.lowerbound - $s.mate.excludeAmbiguousPairs -#end if -#if $s.space == "color": - --readFormat "csfastq" -#else: - --readFormat "fastq" -#end if -#if $int($str($valAlign)) >= 0: - -v $valAlign -#end if -#if $align.options == "full": - --seed $align.seed - -$align.alignments - #if $str($align.delimiter) != "None": - --delimiter $align.delimiter - #end if - -T $align.sTrimL - $align.includeReadsWN - $align.statsOnly - $align.ignoreQS -#end if -#if $str($bUnmappedRead) == "true" and $s.space == "color": - -u $unmappedReadOutCS -#elif $str($bUnmappedRead) == "true" and $s.space == "base": - -u $unmappedReadOut -#end if --o $output --outputFormat sam --noSamHeader | tr '\r' '\n' | tr -cd "[:print:]\t\n " | grep "Reads\|Sub0\|Pairs\|single" | sed 's/.*Reads:,//' | sed 's/\/.*dat,_ Sub0/Sub0/' + PerM + #if $s.sourceOfRef.refSource == "history" + $s.sourceOfRef.ref + #else + #if $s.space == "color" + "${ filter( lambda x: str( x[0] ) == str( $s.sourceOfRef.index ), $__app__.tool_data_tables[ 'perm_color_indexes' ].get_fields() )[0][-1] }" + #elif $s.space == "base" + "${ filter( lambda x: str( x[0] ) == str( $s.sourceOfRef.index ), $__app__.tool_data_tables[ 'perm_base_indexes' ].get_fields() )[0][-1] }" + #end if + #end if + #if $s.mate.singleOrPairs == "single": + $s.mate.reads + #else: + -1 $s.mate.reads1 -2 $s.mate.reads2 + -U $s.mate.upperbound + -L $s.mate.lowerbound + $s.mate.excludeAmbiguousPairs + #end if + #if $s.space == "color": + --readFormat "csfastq" + #else: + --readFormat "fastq" + #end if + #if $int($str($valAlign)) >= 0 + -v $valAlign + #end if + #if $align.options == "full": + --seed $align.seed + -$align.alignments + #if $str($align.delimiter) != "None" + --delimiter $align.delimiter + #end if + -T $align.sTrimL + $align.includeReadsWN + $align.statsOnly + $align.ignoreQS + #end if + #if $str($bUnmappedRead) == "true" and $s.space == "color" + -u $unmappedReadOutCS + #elif $str($bUnmappedRead) == "true" and $s.space == "base" + -u $unmappedReadOut + #end if + -o $output + --outputFormat sam + --noSamHeader | tr '\r' '\n' | tr -cd "[:print:]\t\n " | grep "Reads\|Sub0\|Pairs\|single" | sed 's/.*Reads:,//' | sed 's/\/.*dat,_ Sub0/Sub0/' </command><inputs><conditional name="s"> @@ -59,10 +65,7 @@ PerM </param><when value="indexed"><param name="index" type="select" label="Select a reference genome (with seed and read length)" help="if your genome of interest is not listed - contact Galaxy team"> - <options from_file="perm_color_index.loc"> - <column name="value" index="1" /> - <column name="name" index="0" /> - </options> + <options from_data_table="perm_color_indexes"/></param></when><when value="history"> @@ -94,10 +97,7 @@ PerM </param><when value="indexed"><param name="index" type="select" label="Select a reference genome with seed and read length" help="if your genome of interest is not listed - contact Galaxy team"> - <options from_file="perm_base_index.loc"> - <column name="value" index="1" /> - <column name="name" index="0" /> - </options> + <options from_data_table="perm_base_indexes"/></param></when><when value="history"> @@ -148,7 +148,7 @@ PerM </param><param label="Use the first n bases of each read for alignment (-T)" name="sTrimL" type="integer" size="5" value="50" /><param name="includeReadsWN" type="boolean" checked="true" truevalue="--includeReadsWN" falsevalue="" label="Include reads with 'N' or '.' by encoding '.' as 3, 'N' as 'A' (--includeReadsWN)" /> - <param name="statsOnly" type="boolean" checked="false" truevalue="--statsOnly" falsevalue="" label="output mapping stats only. Don't output alignments (--statsOnly)" /> + <param name="statsOnly" type="boolean" checked="false" truevalue="--statsOnly" falsevalue="" label="Output mapping stats only. Don't output alignments (--statsOnly)" /><param name="ignoreQS" type="boolean" checked="false" truevalue="--ignoreQS" falsevalue="" label="Ignore quality scores (--ignoreQS)" /></when></conditional> @@ -170,8 +170,7 @@ PerM <test><param name="space" value="base" /> @@ -186,7 +185,7 @@ PerM <param name="valAlign" value="0" /><param name="options" value="full" /><param name="alignments" value="A" /> - <param name="seed" value="F2" /> + <param name="seed" value="F3" /><param name="delimiter" value="None" /><param name="sTrimL" value="50" /><param name="includeReadsWN" value="true" /> @@ -198,7 +197,7 @@ PerM <test><param name="space" value="base" /> @@ -215,7 +214,7 @@ PerM <test><param name="space" value="color" /> @@ -231,14 +230,12 @@ PerM <test><param name="space" value="color" /><param name="refSource" value="indexed" /> - <param name="index" value="equCab2_chrM_F3_50" /> + <param name="index" value="equCab2_chrM_F2_50" /><param name="singleOrPairs" value="paired" /><param name="reads1" value="perm_in5.fastqcssanger" ftype="fastqcssanger" /><param name="reads2" value="perm_in6.fastqcssanger" ftype="fastqcssanger" /> --- a/test-data/perm_in3.fastqsanger +++ b/test-data/perm_in3.fastqsanger @@ -1,396 +1,396 @@ @HWI-EAS91_1_30788AAXX:1:1:1513:715/1 GTTTTTTGGGCATAGATGTTTAGTTGTGGTAGTCAG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIDI?II-+I @HWI-EAS91_1_30788AAXX:1:1:1698:516/1 GTTGTTAGGGAGAGGAGTTGAACCTCTGAGTGTAAA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIII5IIIII9I @HWI-EAS91_1_30788AAXX:1:1:1491:637/1 GCTAGCAGGATGGATCCGGCAATTGGGGCTTCTACA -+/1 ++ IIIIIII""IIIIIIIIIIIIFIIIIIIIIIIIABD @HWI-EAS91_1_30788AAXX:1:1:1711:249/1 GGAAGTAGGGGCCTGCGTTCAGGCGTTCTGTTTGGT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII @HWI-EAS91_1_30788AAXX:1:1:1634:211/1 GAAGCAGGGGCTTGATACTGACACTTCGTCGACGTA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF @HWI-EAS91_1_30788AAXX:1:1:1218:141/1 GTTAAATATTGGGAGTGGGGGGGGGGGGGAGTTTTGT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIII1IIII+I @HWI-EAS91_1_30788AAXX:1:1:1398:854/1 GTGAAGAGGAGGGGATTTATTAGTACGGGAAGGGTG -+/1 ++ IIIIIII""IIIIIBIIIIIIIIIIIIIIA=IIIII @HWI-EAS91_1_30788AAXX:1:1:1310:991/1 GAATAGTGGTAGTATTATTCCTTCTAGGCATAGGAG -+/1 ++ IIIIIII""IIIIIIIIII4IIIIIIDII:IEI2:I @HWI-EAS91_1_30788AAXX:1:1:1716:413/1 GATCCAAGGCTTTATCAACACCTATTCTGATTCTTC -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII @HWI-EAS91_1_30788AAXX:1:1:1630:59/1 GGAGCGGGGGGTTGGTAAGGTTGGGGTCGAGTATGA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIII;IIHIIF @HWI-EAS91_1_30788AAXX:1:1:1601:805/1 GAAAACAGGAAAACAATCCAGTCACTTACCCTATGC -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIII@III @HWI-EAS91_1_30788AAXX:1:1:1663:724/1 GTTTGCCGGCGCCATCCTACGCTCCATTCCCAACAA -+/1 ++ IIIIIII""IIII8IIIIIIHIIII6IIIII1CI=3 @HWI-EAS91_1_30788AAXX:1:1:1454:975/1 GCTAGGCGGGAGTGGTAAAAGGCTCAGAAGAAGCCA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIEIG;IIIIIII @HWI-EAS91_1_30788AAXX:1:1:1461:255/1 GTACACCGGCGCCTGAGCCCTACTAATAACTCTCAT -+/1 ++ IIIIIII""IIIIII9IIIIIIEI(II9.I4III,I @HWI-EAS91_1_30788AAXX:1:1:1775:764/1 GCATCCCGGTAGATCTAATTTTCTAAATCTGTCAAC -+/1 ++ IIIIIII""III@IIII+IIIIII8H8IIIIIIICI @HWI-EAS91_1_30788AAXX:1:1:1269:520/1 GGAGTATGGAATAAGTGATTTTAGATCGGTTTGTCG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII @HWI-EAS91_1_30788AAXX:1:1:1303:1162/1 GAGCAAGGGCAGGAGGAGGAGTCCTAGGATGTCTTT -+/1 ++ IIIIIII""IIIIFII4*IGIAI(IAII49',3I6I @HWI-EAS91_1_30788AAXX:1:1:1090:409/1 GTTTGTTGGGAATGGAGCGTAGGATGGCGTAGGCAA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIII:IIA8I @HWI-EAS91_1_30788AAXX:1:1:1336:1000/1 GGTAAATGGGAAATATTAAGTTTCTGTTTCTAGATC -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIII9II @HWI-EAS91_1_30788AAXX:1:1:1199:1376/1 GTTTTCTGGAAAACCTTCACCTATTTATGGGGGTTT -+/1 ++ IIIIIII""IIIIIIIIIIIII;III3IIG&:/III @HWI-EAS91_1_30788AAXX:1:1:1598:1148/1 GATCAATGGTTTGGATCAATAAGTGATTATATATTT -+/1 ++ IIIIIII""IIIIIDIIIIII?IIICII=IHIIIII @HWI-EAS91_1_30788AAXX:1:1:1723:1459/1 GAAACCCGGACGTTTGGATGGGCCCGGAGCGAGGAT -+/1 ++ IIIIIII""IIIIIIIIDIIIIIIIII9HII-II=I @HWI-EAS91_1_30788AAXX:1:1:1442:1346/1 TATCAAGGGGCTGCTTCGAATCCGAAGTGGTGGCTG -+/1 ++ IIIIIII""IIIIIDIIIII1I(I4II<?<-II*,& @HWI-EAS91_1_30788AAXX:1:1:850:117/1 GTATGACGGTAAAGAAAATTATTACGAATGCATGGG -+/1 ++ IIIIIII""IIIIIIEIEIIIIIIIIEBIDD9I;:? @HWI-EAS91_1_30788AAXX:1:1:795:325/1 GGGTACTGGGAAGTGGAATGGTGTGAGTCCAAGTTT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIII65IIII @HWI-EAS91_1_30788AAXX:1:1:873:453/1 GAGTAGGGGGATTGCTAGAGTTACTTCGTATGAGAT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIII@IIIIIII=I @HWI-EAS91_1_30788AAXX:1:1:1285:1334/1 GATATGGGGTCTGGAATAGGATTGCGCTGTTATCCC -+/1 ++ IIIIIII""IIIIIBIIGIIIIIIIIII8IIIII8I @HWI-EAS91_1_30788AAXX:1:1:905:406/1 GAAAAGTGGTAGGCTATATGCAACTTCGCAAAGGAC -+/1 ++ IIIIIII""IIIIIIIIBIIIIBIIII=I@96D2*I @HWI-EAS91_1_30788AAXX:1:1:1774:595/1 TTTAGGTGGGATGTGGGGATCATGTAGGAGTCAAAG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIEI @HWI-EAS91_1_30788AAXX:1:1:1694:931/1 TTAAATTGGCATTAGAATTGAGTAGTTTTTAGGTAA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIH,III @HWI-EAS91_1_30788AAXX:1:1:1092:1151/1 GAGAGTTGGCTGATTTAGGCGCCCAGGGATAGCGTC -+/1 ++ IIIIIII""IIIIIIIIIII5III>IIIII6@III5 @HWI-EAS91_1_30788AAXX:1:1:803:557/1 GGTGTGTGGGCGCTTCATGGCCTGATTCAATTAAGC -+/1 ++ IIIIIII""IIIIIIIIIIIIIII<IIII?III406 @HWI-EAS91_1_30788AAXX:1:1:1315:1200/1 TAGTTTTGGGGGGTTTTCTTCAAAACCTTCACCTAT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII;I @HWI-EAS91_1_30788AAXX:1:1:765:358/1 GGTGTTTGGATGAGGACGGCTACGATTACTAGGGCT -+/1 ++ IIIIIII""IIIIIIIIIIIIDIIAII4@I0D='1I @HWI-EAS91_1_30788AAXX:1:1:1425:1167/1 GACCTTAGGTGTAGGACATGGTGTAATTCGGTAGCA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIII(%II+IG @HWI-EAS91_1_30788AAXX:1:1:1775:635/1 AATAGCCGGATAGCTAGAAGTAAGGTTGAGTTAAAG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIBI @HWI-EAS91_1_30788AAXX:1:1:1433:749/1 GACTATGGGTGCTATTATACATGCTAGTCATAGGAA -+/1 ++ IIIIIII""IIIIIIIIIIIFIIIIICIIIIB/I9E @HWI-EAS91_1_30788AAXX:1:1:798:247/1 GGAGATTGGAAAGTAGTATGCTTAGGGTAAGGGTGA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII @HWI-EAS91_1_30788AAXX:1:1:1249:1238/1 TATTGTTGGGGTAGCGAAAGAGGCGAATAGATTTTC -+/1 ++ IIIIIII""IIIIIIIIIIIBIIIICDIII7IIII@ @HWI-EAS91_1_30788AAXX:1:1:1043:1104/1 GGAAGGGGGAATAGGAGGGCAATTTCTAAGTCGAAT -+/1 ++ II&IIII""IIIIIIDIIIII;IFI<I0II.IIIC, @HWI-EAS91_1_30788AAXX:1:1:1655:1058/1 AAAAATCGGCTTTACAATTATATTCGTAGGGGTAAA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIFIII6AIIIGI @HWI-EAS91_1_30788AAXX:1:1:1764:1403/1 TGATGAAGGGTTTGAGGGGGCTGGTAGGTCAATAAA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIBIIIII @HWI-EAS91_1_30788AAXX:1:1:1632:34/1 AGGATAGGGGCTATCCGTTGGTCTTAGGAACCAAAA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIFIIIH:6I @HWI-EAS91_1_30788AAXX:1:1:1367:1208/1 GACACGTGGCACTTCCAATCATACTATCCAGCATCC -+/1 ++ IIIIIII""IIIIIIII:IIII8IIEIIII-IAIII @HWI-EAS91_1_30788AAXX:1:1:1778:108/1 AATACACGGACCATATCAACAGCATTAAACCTTCAT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII@I @HWI-EAS91_1_30788AAXX:1:1:1152:1115/1 GTAGTATGGCGTAGCCTCCTAGTTTTAGTAGAATGG -+/1 ++ 7IIIIII""IIIIIIIIIII.68IIIDII=7IIIA' @HWI-EAS91_1_30788AAXX:1:1:1165:1121/1 ATACTCAGGTCATTCTAGTCCTTTTTGGGTTCATTC -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIII22?IIIIIIA @HWI-EAS91_1_30788AAXX:1:1:1500:55/1 ATAGAGAGGAGTGCAACTAAGAGTGGGAGGGAACCT -+/1 ++ IIIIIII""IIIIIIIIIIFIIIIIIICIII<IIII @HWI-EAS91_1_30788AAXX:1:1:1142:1196/1 TCATTTTGGTACCACTCGCAAGCACCATCGAAAACA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIII@I=I79I6II @HWI-EAS91_1_30788AAXX:1:1:1693:757/1 AAATTATGGGTTAAACCCCTATATACCTCTATGGCC -+/1 ++ IIIIIII""IIIIIIIIIIIIIBIDIIIII0II-IG @HWI-EAS91_1_30788AAXX:1:1:1364:1053/1 TTATTCAGGTGGGTATGAATCCTGATAGTGGGGGGA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIII?.I31G&4=5 @HWI-EAS91_1_30788AAXX:1:1:1450:1443/1 GTAAAAAGGTGCTCCAAGGCCTATTCATCACAATTT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIEIB8III @HWI-EAS91_1_30788AAXX:1:1:1701:1298/1 TAGTAGAGGCCGCGTCCTACGTGAATGAAGAGGCAG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIII8II;IIIGI @HWI-EAS91_1_30788AAXX:1:1:1729:856/1 TCCTATTGGTTCAATACTGAAACCAAGCACTACCCG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIFIIIII@IIIH @HWI-EAS91_1_30788AAXX:1:1:1748:933/1 TGAGCTCGGGGCTTCATCTTCTTATTCACAGTAGGA -+/1 ++ IIIIIII""IIIIIICIIIIIIIIIIIIII@II5@F @HWI-EAS91_1_30788AAXX:1:1:1662:1296/1 TTAGTTAGGAATAGAATTACACATGCAAGTATCCGC -+/1 ++ IIIIIII""IIIIIIIIIIIIIHIIIEI5IIIII4I @HWI-EAS91_1_30788AAXX:1:1:1393:345/1 ATTTACAGGAGAATTGAGTAGTTTTTAGGTAAATTT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIE+IIEIIII @HWI-EAS91_1_30788AAXX:1:1:943:780/1 AGGCGTTGGGTTTGGTTGCCTCAGCGGGTGATGATA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIII;II<IH @HWI-EAS91_1_30788AAXX:1:1:1639:968/1 AGCTCACGGAAAATAGCAGCATCATCCTCCCCACAC -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8I:I @HWI-EAS91_1_30788AAXX:1:1:589:1114/1 GTCATTCGGGATTAGTTGAGGTTAATTCTACTGTAG -+/1 ++ IIIIIII""IIIIIIIIIII1IIIIIIIIIII&II) @HWI-EAS91_1_30788AAXX:1:1:763:408/1 GCCCCACGGCTGGTGTTGACAACATGACTACTGCCA -+/1 ++ IIIIIII""IIIIIIIIIIIIII=I*5II<II'II( @HWI-EAS91_1_30788AAXX:1:1:950:352/1 ACGCATAGGCAACATGAAATACCATCTCATCCATAG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIFIIIIIGI @HWI-EAS91_1_30788AAXX:1:1:1164:103/1 TTAACTAGGACATTCACCAAACCATTAAAGTATAGG -+/1 ++ IIIIIII""IIIIIIIIIIIAII=IIB58I=<I;II @HWI-EAS91_1_30788AAXX:1:1:1078:1202/1 TAGGGCTGGGCATAGTGGGGTATCTAATCCCAGTTT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIEIII @HWI-EAS91_1_30788AAXX:1:1:1617:490/1 AATCCTTGGTAACCGCATCGGGGATATCGGCTTCAT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIII:(D @HWI-EAS91_1_30788AAXX:1:1:843:504/1 ACAACATGGAATACCATCTCATCCATAGGATCTTTT -+/1 ++ IIIIIII""IIIIIIIIAIIIIII>IIHI=IIIIII @HWI-EAS91_1_30788AAXX:1:1:942:318/1 TTCATACGGGCCATGTCCAGCCTAGCTGTCTACTCA -+/1 ++ IIIIIII""IIIIIIIIIIHIIIIIIIIIII<IIIF @HWI-EAS91_1_30788AAXX:1:1:1719:283/1 TTTTGTTGGCCGAGGTCACCCCAACCGAAATTGCTG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIII3=2IGIIII @HWI-EAS91_1_30788AAXX:1:1:1517:961/1 TGTCACTGGTCCATATTAATATCTTCCTAGCATTCA -+/1 ++ IIIIIII""IIIII=III9I@IIIIIIIBIIEIII> @HWI-EAS91_1_30788AAXX:1:1:1482:345/1 AGGATGTGGGTTAATAGCCCTATAGCTAGAAGTAAG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIII?IAHIIAAI @HWI-EAS91_1_30788AAXX:1:1:1697:533/1 ATGAGGTGGATTAGGAGGTGTCCGGCGGTAATGTTA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIII1>IIIII @HWI-EAS91_1_30788AAXX:1:1:1159:1225/1 TTTCTACGGCAAGGGACGCCCATTTTCCTCATCCCC -+/1 ++ IIIIIII""IIIII=I7IIII3IIIIIIII/ID@II @HWI-EAS91_1_30788AAXX:1:1:982:332/1 AAGGATTGGATCCCCTCCTCCTGCGGGGTCGAAGAA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIII?<I7@ @HWI-EAS91_1_30788AAXX:1:1:1073:668/1 AGCATTTGGCAACCCCTACCTGCCAGAACTCTACTC -+/1 ++ IIIIIII""IIIIIIIIIIIIIII>I4@IIIIIIII @HWI-EAS91_1_30788AAXX:1:1:1386:1163/1 AGTTGGCGGAAAAGCAGCCATCAATTAAGAAAGCGT -+/1 ++ IIIIIII""IIIIIIIIIICII=GIIIII@IGIIII @HWI-EAS91_1_30788AAXX:1:1:1196:344/1 ATTGAAGGGAGTTGATTAGGGTATTTAGCTGTTAAC -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII7 @HWI-EAS91_1_30788AAXX:1:1:1551:1269/1 ATTACCAGGATCCTAATAGGAGCCAATATCACCATC -+/1 ++ IIIIIII""IIIIIIIIGIIIIIIIIIIII@II4II @HWI-EAS91_1_30788AAXX:1:1:928:468/1 AGGAGATGGAAATTTTAACTTGGCGCTATAGAGAAA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIC<IHIII @HWI-EAS91_1_30788AAXX:1:1:763:835/1 GCTCAGAGGAAGCCAGAGAAGAAGAAGACTTCTGAG -+/1 ++ IIIIIII""IIIIIIIHIEFIIFI<IIIIIIDII:I @HWI-EAS91_1_30788AAXX:1:1:1363:330/1 TAGCCTCGGAGTTTTAGTAGAATGGCTGCTAGCACT -+/1 ++ IIIIIII""IIIIIIII@IIIIIIIIII5I,5C-75 @HWI-EAS91_1_30788AAXX:1:1:1001:837/1 ATACTATGGCTGTGAGGAATAATCATAACTAGTTCC -+/1 ++ IIIIIII""IIIII2IIIIIIIIIIIFIII:IIIII @HWI-EAS91_1_30788AAXX:1:1:1189:616/1 TTTGATAGGGTAAAACATAGAGGCTCAAACCCTCTT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIICIIIIIIIII @HWI-EAS91_1_30788AAXX:1:1:1212:634/1 ATCAACAGGTATTCTGATTCTTCGGACACCCCGAAG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIAIIIIF(.I @HWI-EAS91_1_30788AAXX:1:1:1271:421/1 ACACGACGGCACCTAATGACCCACCAAACCCACGCT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIII>C:IIIDI<II @HWI-EAS91_1_30788AAXX:1:1:1582:328/1 AGCATTAGGCTTTTAAGTTAAAGATTGAGGGTTCAA -+/1 ++ IIIIIII""IIIIII,IIIB;BI<IIIIII+IIIBI @HWI-EAS91_1_30788AAXX:1:1:1133:687/1 AGAGAGCGGATTAGGAATACGATTATTAGTGTGTGG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIII4III @HWI-EAS91_1_30788AAXX:1:1:1231:662/1 TCACTCTGGAGAACATATAAAACCAACATAACCTCC -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIII?ICCIIIII @HWI-EAS91_1_30788AAXX:1:1:1693:1140/1 ATTGATAGGATGGGGGTTAGGGGGAGGAGTAGGGAG -+/1 ++ IIIIIII""IIIIIIIIIIIIIII:II5II7IIA-I @HWI-EAS91_1_30788AAXX:1:1:867:279/1 AAGCATTGGACTGTAAATCTAAAGACAGGGGTTGGA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII @HWI-EAS91_1_30788AAXX:1:1:1095:605/1 AAGCAAGGGACTGAAAATGCCTAGATGAGTATTCTT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIEIIIIIIIIIII @HWI-EAS91_1_30788AAXX:1:1:1650:1185/1 ACCCCAGGGAACCCTCTCAGCACTCCCCCTCATATT -+/1 ++ IIIIIII""IIIIIIIIIIII6IIIIIIIII5I-II @HWI-EAS91_1_30788AAXX:1:1:799:192/1 AATGTTAGGGGTTAGCCGCACGGCTAGGGCTACAGG -+/1 ++ IIIIIII""IIIIIIIIII8IIIEIIIII<I::%II @HWI-EAS91_1_30788AAXX:1:1:1082:719/1 TCTTGAGGGTCTATGGTGCTGGTATGGGTTAATTTA -+/1 ++ IIIIIII""IIIIIIA8III>I92I3+3IIE0III< @HWI-EAS91_1_30788AAXX:1:1:1746:1180/1 AAAATTAGGGAGAAGTAATCTAGTTTGAAGCTTAGG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIFIIIIIIII @HWI-EAS91_1_30788AAXX:1:1:606:460/1 TTAATTTGGATTATAATAACACTCACAATATTCATA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIII?I6IIIII6 @HWI-EAS91_1_30788AAXX:1:1:1059:362/1 ATCGGTAGGCTCGTAGCTTCAGTATCATTGGTGGCC -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIII2)</II @HWI-EAS91_1_30788AAXX:1:1:1483:1161/1 ATATGTGGGGGGTGGGGATGAGTGCTAGGATCAGGA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIHIAIIFIIIIIH @HWI-EAS91_1_30788AAXX:1:1:1273:600/1 TACTGAGGGGTATCCTGAGGTATGGGTGTCTAATAC -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII @HWI-EAS91_1_30788AAXX:1:1:1190:1283/1 TTTCTGGGGTACAAGACCAGGGTAATGTGCGATATA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIAIIIII-?IIIE --- a/tools/sr_mapping/lastz_wrapper.xml +++ b/tools/sr_mapping/lastz_wrapper.xml @@ -1,25 +1,42 @@ -<tool id="lastz_wrapper_2" name="Lastz" version="1.1.1"> +<tool id="lastz_wrapper_2" name="Lastz" version="1.2.0"><description> map short reads against reference sequence</description><command interpreter="python">lastz_wrapper.py -#if $seq_name.how_to_name=="yes": ---ref_name=$seq_name.ref_name -#else: ---ref_name="None" -#end if ---ref_source=$source.ref_source --source_select=$params.source_select --out_format=$out_format --input2=$input2 -#if $source.ref_source=="history": ---input1=$source.input1 ---ref_sequences=$input1.metadata.sequences -#else: ---input1=$source.input1_2bit ---ref_sequences="None" -#end if -#if $params.source_select=="pre_set": ---pre_set_options=${params.pre_set_options} --strand="None" --seed="None" --gfextend="None" --chain="None" --transition="None" --O="None" --E="None" --X="None" --Y="None" --K="None" --L="None" --entropy="None" -#else: ---pre_set_options="None" --strand=$params.strand --seed=$params.seed --gfextend=$params.gfextend --chain=$params.chain --transition="$params.transition" --O=$params.O --E=$params.E --X=$params.X --Y=$params.Y --K=$params.K --L=$params.L --entropy=$params.entropy -#end if ---identity_min=$min_ident --identity_max=$max_ident --coverage=$min_cvrg --output=$output1 --unmask=$unmask --lastzSeqsFileDir=${GALAXY_DATA_INDEX_DIR} + #if $seq_name.how_to_name=="yes": + --ref_name=$seq_name.ref_name + #end if + --ref_source=$source.ref_source + --source_select=$params.source_select + --out_format=$out_format + --input2=$input2 + #if $source.ref_source=="history": + --input1=$source.input1 + --ref_sequences=$input1.metadata.sequences + #else: + --input1="${ filter( lambda x: str( x[0] ) == str( $source.input1_2bit ), $__app__.tool_data_tables[ 'lastz_seqs' ].get_fields() )[0][-1] }" + --ref_sequences="None" + #end if + #if $params.source_select=="pre_set": + --pre_set_options=${params.pre_set_options} + #else: + --strand=$params.strand + --seed=$params.seed + --gfextend=$params.gfextend + --chain=$params.chain + --transition="$params.transition" + --O=$params.O + --E=$params.E + --X=$params.X + --Y=$params.Y + --K=$params.K + --L=$params.L + --entropy=$params.entropy + #end if + --identity_min=$min_ident + --identity_max=$max_ident + --coverage=$min_cvrg + --output=$output1 + --unmask=$unmask + --lastzSeqsFileDir=${GALAXY_DATA_INDEX_DIR} </command><inputs><param name="input2" format="fasta" type="data" label="Align sequencing reads in" /> @@ -30,10 +47,7 @@ </param><when value="cached"><param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> - <options from_file="lastz_seqs.loc"> - <column name="value" index="1" /> - <column name="name" index="0" /> - </options> + <options from_data_table="lastz_seqs" /></param></when><when value="history"> @@ -127,14 +141,15 @@ <tests><test> - <param name="input2" value="b1.fasta" ftype="fasta" /> + <param name="input2" value="b1.fasta" ftype="fasta" dbkey="phiX" /><param name="ref_source" value="cached" /> - <param name="input1_2bit" value="phiX" /> +  + <param name="input1_2bit" value="/galaxy/data/phiX/seq/phiX.2bit" /><param name="out_format" value="sam" /><param name="source_select" value="full" /><param name="strand" value="both" /> @@ -150,8 +165,8 @@ <param name="L" value="3000" /><param name="entropy" value="noentropy" /><param name="how_to_name" value="yes" /><param name="ref_name" value="Ref" /> @@ -163,10 +178,10 @@ </test><test><param name="input2" value="b1.fasta" ftype="fasta" /><param name="ref_source" value="history" /> @@ -183,17 +198,17 @@ </test><test><param name="input2" value="b1.fasta" ftype="fasta" /><param name="ref_source" value="history" /> --- a/tool-data/blastdb_p.loc.sample +++ b/tool-data/blastdb_p.loc.sample @@ -1,12 +1,27 @@ #This is a sample file distributed with Galaxy that is used to define a -#list of protein BLAST databases, using two columns tab separated: +#list of protein BLAST databases, using three columns tab separated +#(longer whitespace are TAB characters): # -#<database caption><path to base name> +#<unique_id><database_caption><base_name_path> # -#For example: +#The captions typically contain spaces and might end with the build date. +#It is important that the actual database name does not have a space in it, +#and that the first tab that appears in the line is right before the path. # -#NCBI NR (non redundant) /data/blastdb/nr +#So, for example, if your database is NR and the path to your base name +#is /data/blastdb/nr, then the blastdb_p.loc entry would look like this: # -#where /data/blastdb/nr.* are the files making up the NR database. +#nr NCBI NR (non redundant) /data/blastdb/nr # -#See also the blastdb.loc file which is for any nucleotide databases. +#and your /data/blastdb directory would contain all of the files associated +#with the database, /data/blastdb/nr.*. +# +#Your blastdb_p.loc file should include an entry per line for each "base name" +#you have stored. For example: +# +#nr_05Jun2010 NCBI NR (non redundant) 05 Jun 2010 /data/blastdb/05Jun2010/nr +#nr_15Aug2010 NCBI NR (non redundant) 15 Aug 2010 /data/blastdb/15Aug2010/nr +#...etc... +# +#See also blastdb.loc which is for any nucleotide BLAST database. +# --- a/tool-data/perm_base_index.loc.sample +++ b/tool-data/perm_base_index.loc.sample @@ -3,9 +3,9 @@ #to create these data files and then create a perm_base_index.loc file #similar to this one (store it in this directory) that points to #the directories in which those files are stored. The perm_base_index.loc -#file has this format (white space characters are TAB characters): +#file has this format (longer white space characters are TAB characters): # -#<build_seed_readlength><file_base> +#<build_seed_readlength><display_name><file_base> # #Because each PerM index is built with a specific seed and a specific read #length, this needs to be specified so the user can choose the appropriate @@ -13,7 +13,7 @@ #50, and stored in /depot/data/galaxy/phiX/perm_index/, #then the perm_base_index.loc entry would look something like this: # -#phiX_F3_50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index +#phiX_F3_50 phiX: seed=F3, read length=50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index # #and your /depot/data/galaxy/phiX/perm_index/ directory #would contain the file phiX_base_F3_50.index: @@ -21,7 +21,8 @@ #Your perm_base_index.loc file should include an entry per line for each #index set you have stored. For example: # -#phiX_F3_50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index -#phiX_F4_50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index -#hg19_F3_50 /depot/data/galaxy/hg19/perm_index/hg19_base_F3_50.index -#hg19_F4_50 /depot/data/galaxy/hg19/perm_index/hg19_base_F3_50.index +#phiX_F3_50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index +#phiX_F4_50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index +#hg19_F3_50 /depot/data/galaxy/hg19/perm_index/hg19_base_F3_50.index +#hg19_F4_50 /depot/data/galaxy/hg19/perm_index/hg19_base_F3_50.index +# --- a/test-data/lastz_wrapper_out2.sam +++ b/test-data/lastz_wrapper_out2.sam @@ -1,459 +1,459 @@ -HWI-EAS91_1_306UPAAXX 16 PHIX174 4295 255 1H35M * 0 0 CCCCCAACTTGATATTAATAACACTATAGACCACC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3522 255 36M * 0 0 ATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 229 255 36M * 0 0 GATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2071 255 36M * 0 0 GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1067 255 1H35M * 0 0 GGTCAGATTGGTCGTCTTATTACCATTTCAACTAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1788 255 36M * 0 0 GTCGTGTTCAACAGACCTATAAACATTCTGTGCCGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1193 255 36M * 0 0 GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4563 255 36M * 0 0 GGTTGGTTTATCGTTTTTGACACTCTCACGTTGTCT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2668 255 36M * 0 0 GTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4248 255 36M * 0 0 GTTACTGAGAAGTTAATGGATGAATTGGCACAATGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2863 255 36M * 0 0 GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2557 255 36M * 0 0 GGTTTTCTTCATTGCATTCAGATGGATACATCTGTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2511 255 34M2H * 0 0 GTCAACGTTATATTTTGATAGTTTGACGGTTAAT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 5152 255 36M * 0 0 GGATGAAAATGCTCACAATGACAAATCTGTCCACGG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1590 255 36M * 0 0 AAGCTGCTTATGCTAATTTGCATACTGACCAAGAAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4884 255 36M * 0 0 GGTTACAGTATGCCCATCGCAGTTCGCTACACGCAG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 5052 255 36M * 0 0 GCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4909 255 36M * 0 0 GCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2863 255 36M * 0 0 GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4173 255 36M * 0 0 GTTGAGTTCGATAATGGTGATATGTATGTTTACGGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1701 255 36M * 0 0 GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1683 255 36M * 0 0 CTTATGACGCTGACAACCGTCCTTTACTTGTCATGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3126 255 1H35M * 0 0 GAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1665 255 36M * 0 0 CATTTGGAGGTAAAACCTCTTATGACGCTGACAACC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3213 255 36M * 0 0 GTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3420 255 36M * 0 0 GAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 513 255 36M * 0 0 GTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2879 255 36M * 0 0 ATAAGGTTATTAAAGAGATTATTTGTCTCCAGCCAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4471 255 36M * 0 0 GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1229 255 36M * 0 0 GTTTATGGTGAACAGTGGATTAAGTTCATGAAGGAT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 615 255 36M * 0 0 GAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 257 255 36M * 0 0 GCACGTTCGTCAAGGACTGGTTTAGATATGAGTCAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2381 255 36M * 0 0 TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4098 255 36M * 0 0 ATGCTTGGCTTCCATAAGCAGATGGATAACCGCATC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 5099 255 36M * 0 0 GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4254 255 36M * 0 0 GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3408 255 36M * 0 0 GACAATCAGAAAGAGATTGCCGAGATGCAAAATGAG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4043 255 36M * 0 0 GGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4560 255 36M * 0 0 GATGGTTGGTTTATCGTTTTTGACACTCTCACGTTG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1888 255 36M * 0 0 GACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3434 255 1H35M * 0 0 GCAAAATGAGACTCAAAAAGAGATTGCTGGCATTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4539 255 36M * 0 0 GCAATGCGACAGGCTCATGCTGATGGTTGGTTTATC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1828 255 36M * 0 0 CTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3708 255 36M * 0 0 GACTTAGTTCATCAGCAAACGCAGAATCAGCGGTAT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3326 255 36M * 0 0 GCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4176 255 36M * 0 0 GAGTTCGATAATGGTGATATGTATGTTGACGGCCAT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 22 255 36M * 0 0 GCAGAAGTTAACACTTTCGGATATTTCTGATGAGTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2557 255 36M * 0 0 GGTTTTCTTCATTGCATTCAGATGGATACATCTGTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3277 255 36M * 0 0 ATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3592 255 36M * 0 0 AGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 358 255 35M1H * 0 0 GATGCTGTTCAACCACTAATAGGTAAGAAATCATG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1775 255 36M * 0 0 GGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3504 255 36M * 0 0 GTATATGCACAAAATGAGATGCTTGCTTATCAACAG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1554 255 36M * 0 0 CGACTTCTACCACATCTATTGACATTATGGGTCTGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1002 255 36M * 0 0 TGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3626 255 36M * 0 0 GCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3572 255 36M * 0 0 GGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1265 255 36M * 0 0 GGTGTTAATGCCACTCCTCTCCCGACTGTTAACACT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1332 255 36M * 0 0 GCACGATTAACCCTGATACCAATAAAATCCCTAAGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4254 255 36M * 0 0 GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4170 255 36M * 0 0 GGCGTTGAGTTCGATAATGGTGATATGTATGTTGAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2806 255 36M * 0 0 AATAATGTTTATGTTGGTTTCATGGTTTGGTCTAAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3119 255 36M * 0 0 CCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1670 255 36M * 0 0 GGAGGTAAAACCTCTTATGACGCTGACAACCGTCCT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 640 255 36M * 0 0 ATTATGTTCATCCCGTCAACATTCAAACGGCCTGTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2750 255 35M1H * 0 0 GTTATTATACCGTCAAGGACTGTGTGACTATTGAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4606 255 36M * 0 0 GATTAGAGGCGTTTTATGATAATCCCAATGCTTTGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3573 255 36M * 0 0 GAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 5105 255 36M * 0 0 GCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1674 255 36M * 0 0 GTAAAACCTCTTATGACGCTGACAACCGTCCTTTAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4095 255 36M * 0 0 CCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4551 255 36M * 0 0 GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3284 255 36M * 0 0 TGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4005 255 36M * 0 0 GAATGTCACGCTGATTATTTTGACTTTGAGCGTATC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2479 255 36M * 0 0 GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1082 255 36M * 0 0 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3045 255 1H35M * 0 0 GCTACCGATAACAATACTGTAGGCATGGGTGATGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1115 255 36M * 0 0 GGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 636 255 36M * 0 0 GCTTATTATGTTCATCCCGTCAACATTCAAACGTCC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1139 255 34M2H * 0 0 GTTGGCGCTCTCCGTCTTTCTCCATTTCGTCGTG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 852 255 36M * 0 0 CTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 5272 255 36M * 0 0 GATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4330 255 36M * 0 0 GCCCCGAAGGGGACNANAAATGGTTTTTAGAGAACG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4891 255 36M * 0 0 GTATGCCCATCGCAGTTCGCTACACGCAGGACGCTT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4783 255 36M * 0 0 ATTTTATGCGGACACTTCCTACAGGTAGCGTTGACC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3619 255 36M * 0 0 GCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4455 255 36M * 0 0 GGTATTAAGGATGAGTGTTCAAGATTGCTGGATGCC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 632 255 36M * 0 0 CATTGCTTATTATGTTCATCCCGTCAACATTCAAAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2964 255 35M1H * 0 0 GCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2763 255 36M * 0 0 CAAGGACTGTGTGACTATTGACGTCCTTCCCCGTAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2766 255 36M * 0 0 GGACTGTGTGACTATTGACGTCCTTCCCCGTACGCC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1719 255 36M * 0 0 GCTCTAATCTCTGGGCATCTGGCTATGATGTTGATG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3100 255 36M * 0 0 AAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 598 255 35M1H * 0 0 GCTTTCCTGCTCCTGTTGAGTTTATTGCTTCCGTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4126 255 36M * 0 0 ACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4026 255 36M * 0 0 GACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2621 255 36M * 0 0 GTGCTGATATTGCTTTTGATGCCGACCCTAAATTTT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2749 255 36M * 0 0 GGTTATTATACCGTCAAGGACTGTGTGACTATTGAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 379 255 36M * 0 0 GGTAAGAAATCATGAGTCAAGTTACTGAACAATCCG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2160 255 36M * 0 0 GCCACCATGATTATGACCAGTGTTTCCAGTCCGTTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2873 255 36M * 0 0 CGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1508 255 1H35M * 0 0 TGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3863 255 36M * 0 0 TTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 5187 255 36M * 0 0 GAGTGCTTAATCCAACTTACCAAGCTGGGTTACGAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4196 255 36M * 0 0 GTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 635 255 36M * 0 0 TGCTTATTATGTTCATCCCGTCAACATTCAAACGGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1294 255 1H35M * 0 0 TAACACTACTGGTTATATTGACCATGCCGCTTTTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 5157 255 36M * 0 0 AAAATGCTCACAATGACAAATCTGTCCACGGAGTGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 772 255 36M * 0 0 GCGCAGGAAACACTGACGTTCTTACTGACGCAGAAG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1224 255 36M * 0 0 GTCACGTTTATGGTGAACAGTGGATTAAGTTCATGA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1544 255 3H33M * 0 0 CGCCAAATGACGACTTCTACCACATCTATTGAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4840 255 36M * 0 0 GCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 204 255 35M1H * 0 0 GATTCTGTCAAAAACTGACGCGTTGGATGAGGAGA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2481 255 36M * 0 0 ACCTGTTTTAAAGACACCTAAAGCTACATCGTCAAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 332 255 36M * 0 0 AAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3978 255 36M * 0 0 TTTATGGTTCGTTCTTATTACCCTTCTGAATGTCAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4865 255 36M * 0 0 GCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3271 255 36M * 0 0 GAAAGGATACTCGTGATTATCTTGCTGCTGCATTTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4174 255 36M * 0 0 TTGAGTTCGATAATGGTGATATGTATGTTGACGGCC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2738 255 36M * 0 0 GCCATGATGGTGGTTATTATACCGTCAAGGACTGTG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2703 255 1H35M * 0 0 CCCGACTGCCTATGATGTTTATCCTTTGAATGGTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2943 255 36M * 0 0 ATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3861 255 36M * 0 0 AATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3093 255 36M * 0 0 GCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3151 255 36M * 0 0 GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1193 255 36M * 0 0 GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 157 255 36M * 0 0 CGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4792 255 36M * 0 0 GGACACTTCCTACAGGTAGCGTTGACCCTAATTTTG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3849 255 36M * 0 0 GATACTTGGAACAATTTCTGGAAAGACGGTAAAGCT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2743 255 1H35M * 0 0 GATGGTGGTTATTATACCGTCAAGGACTGTGTGAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3015 255 36M * 0 0 GCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1091 255 36M * 0 0 ATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 798 255 1H35M * 0 0 GACGCAGAAGAAAACGTGCGTCAAAAATTACGTGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4866 255 36M * 0 0 CAAAATACGTGGCCTTATGGTTACAGTATGCCCATC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4404 255 36M * 0 0 GAACGCCCTCTTAAGGATATTCGCGATGAGTATAAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1655 255 36M * 0 0 GTTATTTCTTCATTTGGAGGTAAAACCTCTTATGAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 5162 255 36M * 0 0 GCTCACAATGACAAATCTGTCCACGGAGTGCTTAAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1249 255 1H35M * 0 0 TAAGTTCATGAAGGATGGTGTTAATGCCACTCCTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3261 255 36M * 0 0 GCTGATAAAGGAAAGGATACTCGTGATTATCTTGCT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3096 255 36M * 0 0 ATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2811 255 36M * 0 0 TGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3459 255 36M * 0 0 GCTGGCATTCAGTCGGCGACTTCACGCCAGAATACG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 789 255 35M1H * 0 0 GTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3699 255 36M * 0 0 GCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAAT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2641 255 36M * 0 0 GCCGACCCTAAATTTTTTGCCTGTTTGGTTCTCTTT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 305 255 36M * 0 0 GTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3066 255 35M1H * 0 0 GGCATGGGTGATGCTGGTATTAAATCTGCCATTCA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4428 255 36M * 0 0 GATGAGTATAATTACCCCAAAAAGAAAGGTATTAAG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1461 255 36M * 0 0 AAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4000 255 36M * 0 0 CTTCTGAATGTCACGCTGATTATTTTGACTTTGAGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 220 255 36M * 0 0 GACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3194 255 36M * 0 0 GCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTTCT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1266 255 35M1H * 0 0 GTGTTAATGCCACTCCTCTCCCGACTGTTAACTCT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4596 255 36M * 0 0 GCTGACGACCGATTAGAGGCGTTTTATGATAATCCC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1172 255 1H35M * 0 0 GGCCTTGCTATTGACTCTACTGTAGACATTTTTAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 636 255 36M * 0 0 GCTTATTATGTTCATCCCGTCAACATTCAAACGGCC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2873 255 36M * 0 0 CGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1014 255 36M * 0 0 AAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2689 255 36M * 0 0 GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2148 255 36M * 0 0 GCGTACTTATTCGCCACCATGATTATTACCAGTGTT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 5191 255 35M1H * 0 0 GCTTAATCCAACTTACCAAGCTGGGTTACGACGCG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1590 255 36M * 0 0 AAGCTGCTTATGCTAATTTGCATACTGACCAAGAAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 571 255 35M1H * 0 0 GTACGCTGTACTTTGTGGGATACCCTCGCTTTCCT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 242 255 36M * 0 0 GGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 338 255 36M * 0 0 GTGGATTACTATCTGAGTCCGATGCTGTTCAACCAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1112 255 36M * 0 0 GCTGGCGACTCCTTCGAGATGGACGCCGTTTGCGCT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1254 255 2H34M * 0 0 TCATGAAGGATGGTGTTAATGCCACTCCTCTCCC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2970 255 36M * 0 0 GCTGGTGGCGCCATGTCTAAATTTTTTGGAGGCGGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 5151 255 36M * 0 0 GGGATGAAAATGCTCACAATGACAAATCTGTCCACG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 348 255 36M * 0 0 ATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4888 255 1H35M * 0 0 ACAGTATGCCCATCGCAGTTCGCTACACGCAGGAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3972 255 33M3H * 0 0 GGCTTTTTTATGGTTCGTTCTTATTACCCTTCT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 5033 255 36M * 0 0 GTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1552 255 1H35M * 0 0 GACGACTTCTACCACATCTATTGACATTATGGGTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1764 255 36M * 0 0 AAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1529 255 36M * 0 0 GAGACTGAGCTTTCTCGCCAAATGACGACTTCTACC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4950 255 36M * 0 0 CCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4484 255 36M * 0 0 GGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4767 255 1H35M * 0 0 CATTTCCATGCGGTGCATTTTATGCGGACACTTCC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 177 255 36M * 0 0 CTTTGCGACCTTTCGCCATCAACTAACGATTCTGTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2577 255 36M * 0 0 GATGGATACATCTGTCAACGCCGCTAATCAGGTTGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 156 255 36M * 0 0 GCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 227 255 36M * 0 0 TGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 574 255 36M * 0 0 CGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3021 255 36M * 0 0 GGTGGCATTCAAGGTGATGTGCTTGCTACCGATAAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3731 255 36M * 0 0 GAATCAGCGGTATGGCTCTTCTCATATTGGCGCTAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2436 255 36M * 0 0 TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2710 255 36M * 0 0 GCCTATGATGTTTATCCTTTGAATGGTCGCCATGAT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4228 255 35M1H * 0 0 TTCGTGATGAGTTTGTATCTGTTACTGATAAGTTA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4606 255 34M2H * 0 0 GATTAGAGGCGTTTTATGATAATCCCAATGCTTT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2766 255 36M * 0 0 GGACTGTGTGACTATTGACGTCCTTCCCCGTACGCC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 582 255 34M2H * 0 0 TTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1144 255 36M * 0 0 CGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1514 255 36M * 0 0 GCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1657 255 36M * 0 0 TATTTCTTCATTTGGAGGTAAAACCTCTTATGACGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2071 255 36M * 0 0 GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1626 255 36M * 0 0 GTGATTACTTCATGCAGCGTTACCGTGATGTTATTT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3250 255 36M * 0 0 GCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1982 255 36M * 0 0 GAAATTTCTATGAATGATGTTTTCCGTTCTGGTGAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2217 255 36M * 0 0 AGGTTAAATTTAATGTGACCGTTTATCGCAATCTGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3480 255 1H35M * 0 0 TCACGACAGAATACGAAAGACCAGGTATATGCACA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1690 255 36M * 0 0 CGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1082 255 36M * 0 0 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4282 255 36M * 0 0 GCTACAATGTGCTCCCCCAACTTGATATTAATAACA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4136 255 34M2H * 0 0 GCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4414 255 36M * 0 0 TTAAGGATATTCGCGATGAGTATAATTACCCCAAAA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3988 255 36M * 0 0 GTTCTTATTACCCTTCTGAATGTCACGCTGATTATT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4203 255 36M * 0 0 GACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4098 255 36M * 0 0 ATGCTTGGCTTCAATAAGCAGATGGATAACCGCATC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4307 255 35M1H * 0 0 TATTAATAACACTATAGACCACCGCCCCGAAGGGG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1521 255 35M1H * 0 0 TTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 945 255 36M * 0 0 TAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1575 255 36M * 0 0 ACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2689 255 36M * 0 0 GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2099 255 36M * 0 0 GAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 524 255 36M * 0 0 TACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1252 255 36M * 0 0 GTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4916 255 36M * 0 0 GCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGTCC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3828 255 36M * 0 0 GGTATTGATAAAGCTGTTGCCGATACTTGTAACAAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3756 255 36M * 0 0 ATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1116 255 36M * 0 0 GCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3099 255 36M * 0 0 CAAGGCTCTAATGTTCCTAACCCTGATGGGGCCGCC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3082 255 36M * 0 0 GTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 613 255 36M * 0 0 TTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4936 255 36M * 0 0 CTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 289 255 36M * 0 0 TCACATTTTGTTCATGGTAGAGATTCTCTTGTTGAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4690 255 36M * 0 0 GCAAGGCTAATGATTCACACGCCGACTGCTATCAGT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3520 255 36M * 0 0 AGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3858 255 36M * 0 0 AACAATTTCTGGAAAGACGGTAAAGCTGATGGTATT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3344 255 36M * 0 0 TTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4672 255 36M * 0 0 TTCTTGCTGCCGAGGGTCGCAAGGCTATTGTTTCAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1800 255 36M * 0 0 AGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 5077 255 36M * 0 0 GGAACAACTCACTAAAAACCAAGCTGTCGCTACTTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2763 255 1H35M * 0 0 CAAGGACTGTGTGACTATTGACGTCCTTCCCCGTA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4282 255 36M * 0 0 GCTACAATGTGCTCCCCCAACTTGATATTAATAACA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1203 255 36M * 0 0 TTACTTTTTATGTCCCTCATCGTCACGTTTATGTTG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 5107 255 36M * 0 0 TACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 5168 255 1H35M * 0 0 AATGACAAATCTGTCCACGGAGTGCTTAATCCAAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2956 255 36M * 0 0 TTGCTTCTGCTCTTGCTTGTGGCGCCATGTCTAAAT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 624 255 36M * 0 0 GCTGCCGTCATTGCTTATTATGTTCATCCCTTCAAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1877 255 1H35M * 0 0 CCGCCTACTGCGACTAAAGAGATTCAGTACCTTAA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1214 255 36M * 0 0 GTCCCTCATCGTCACGTTTATGGTGAACAGTGGATT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 558 255 36M * 0 0 GCTTGCGTTTATGGTACGCTGGACTTTTTGTGATAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3629 255 36M * 0 0 TACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2254 255 35M1H * 0 0 GACCACTCGCGATTCAATCATGACTTCGTGATAAA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2479 255 36M * 0 0 GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3001 255 36M * 0 0 GCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4667 255 35M1H * 0 0 TATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3464 255 36M * 0 0 CATTCAGTCGGCGACTTCACGCCAGAATACGAAAGA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4911 255 35M1H * 0 0 TACACGCAGGACGCTTTTTCACGTTCTGGTTGGTT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2222 255 36M * 0 0 AAATTTAATGTGAACGTTTATCGCAATCTGCCGACC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 646 255 35M1H * 0 0 TTCATCCCGTCAACATTCAAACGGCCTGTCTCATC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1364 255 36M * 0 0 AAGCATTTGTTTCAGGGTTATTTGAATATCTATAAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1613 255 1H35M * 0 0 ACTGACCAAGAACGTGATTACTTCATGCAGCGTTA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1045 255 35M1H * 0 0 TTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1588 255 36M * 0 0 GCAAGCTGCTTATGCTAATTTGCATACTGACCAAGA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 339 255 36M * 0 0 TGGATTACTATCTGAGTCCGATGCTGTTCAACCACT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4937 255 36M * 0 0 TGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4344 255 2H34M * 0 0 GAAAAATGGTTTTTAGAGAACGAGAAGACGGTTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3674 255 36M * 0 0 CAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4945 255 36M * 0 0 TGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1946 255 36M * 0 0 GGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2662 255 36M * 0 0 TGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCTACT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3313 255 36M * 0 0 TTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 727 255 36M * 0 0 GTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 555 255 36M * 0 0 GAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 485 255 36M * 0 0 TGATTTCGATTTTCTGACGAGTAACAAAGTTTGGAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 318 255 36M * 0 0 TGTTGACATTTTAAAAGAGCGTGGATTACTATCTGA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 910 255 36M * 0 0 TAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4936 255 36M * 0 0 CTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 5005 255 36M * 0 0 TCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1379 255 36M * 0 0 GGTTATTTGAATATCTATAACAACTATTTTAAATCG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3168 255 36M * 0 0 GGTAAAGGACTTCTTGAAGGTACGTTGCAGTCTGGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2738 255 33M3H * 0 0 GCCATGATGGTGGTTATTATACCGTCAAGGACT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4099 255 36M * 0 0 TGCTTGGCTTCCATAAGCAGATGGATAACCGCATCA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2574 255 36M * 0 0 TCAGATGGATACATCTGTCAACGCCGCTAATCAGGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2453 255 36M * 0 0 TCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 5179 255 36M * 0 0 TGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3778 255 34M2H * 0 0 TTTCTAATGTCGTCACTGATGCTGCTTCTGTTGT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1843 255 36M * 0 0 TGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1082 255 36M * 0 0 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1728 255 36M * 0 0 TCTGGGCATCTGGCTATGATGTTGATGGAACTGACC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4637 255 36M * 0 0 TTTGCGTGACTATTTTCGTGATATTGTTCGTATGGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2225 255 36M * 0 0 TTTAATGTGACCGTTTATCGCAATCTGCCGACCACT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3368 255 36M * 0 0 CGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3311 255 36M * 0 0 GCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 5039 255 36M * 0 0 TATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2059 255 36M * 0 0 TTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 388 255 36M * 0 0 TCATGAGTCAAGTTACTGAACAATCCGTACGTTTCC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2754 255 36M * 0 0 TTATACCGTCAAGGACTGTGTGACTATTGACGTCCT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2128 255 36M * 0 0 TTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 154 255 36M * 0 0 TTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3617 255 36M * 0 0 GCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2728 255 36M * 0 0 TTGAATGGTCGCCATGATGGTGGTTATTATACCGTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2775 255 36M * 0 0 GACTATTGACGTCCTTCCCCGTACGCCGGGCAATAA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4217 255 36M * 0 0 TGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4619 255 35M1H * 0 0 TTATGATAATCCCAATGCTTTGCGTGACTATTTTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 411 255 35M1H * 0 0 TCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2730 255 35M1H * 0 0 GAATGGTCGCCATGATGGTGGTTATTATACCGTCA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 521 255 35M1H * 0 0 TGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4260 255 36M * 0 0 TTAATGGATGAATTGGCACAATGCTACAATGTGCTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1662 255 36M * 0 0 CTTCATTTGGAGGTAAAACCTCTTATGACGCTGACA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 533 255 36M * 0 0 CTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 195 255 35M1H * 0 0 TCAACTAACGATTCTGTCAAAAACTGACGCGTTGG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2239 255 36M * 0 0 TTATCGCAATCTGCCGACCACTCGCGATTCAATCAT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1313 255 36M * 0 0 GACCATGCCGCTTTTCTTGGCACGATTAACCCTTAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1545 255 36M * 0 0 GCCAAATGACGACTTCTACCACATCTATTGACATTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 557 255 36M * 0 0 GGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1249 255 36M * 0 0 TAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4174 255 36M * 0 0 TTGAGTTCGATAATGGTGATATGTATGTTGACGTCC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 614 255 35M1H * 0 0 TGAGTTTATTGCTGCCGTCATTGCTTATTATGTTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 206 255 36M * 0 0 TTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4981 255 36M * 0 0 CTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1702 255 36M * 0 0 TCCTTTACTTGTCATGCGCTCTAATCTCTGTGCATC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2321 255 35M1H * 0 0 TAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4088 255 35M1H * 0 0 TCAATCCCCAATGCTTGGCTTCCATAAGCAGATGG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 900 255 36M * 0 0 TGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1155 255 36M * 0 0 TTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3587 255 36M * 0 0 TTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3787 255 36M * 0 0 TCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3834 255 35M1H * 0 0 GATAAAGCTGTTGCCGATACTTGGAACAATTTCTG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 989 255 36M * 0 0 TGAGGATAAATTATGTCTAATATTCAAACTGGCGCC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3712 255 36M * 0 0 TAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1207 255 36M * 0 0 TTTTTATGTCCCTCATCGTCACGTTTATGGTGAACA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2116 255 36M * 0 0 TCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 660 255 36M * 0 0 ATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1536 255 36M * 0 0 AGCTTTCTCGCCAAATGACGACTTCTACCACATCTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2112 255 1H35M * 0 0 TCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2816 255 36M * 0 0 ATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 5176 255 36M * 0 0 ATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3472 255 36M * 0 0 CGGCGACTTCACGCCAGAATACGAAAGACCAGGTAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1948 255 36M * 0 0 CGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2212 255 35M1H * 0 0 TAGTCAGGTTAAATTTAATGTGACCGTTTATCGCA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3817 255 35M1H * 0 0 ATATTTTTCATGGTATTGATAAAGCTGTTGCCGAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3563 255 36M * 0 0 GTCTATTATGGAAAACACCAATCTTTCCAAGCAACA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4198 255 1H35M * 0 0 ATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2907 255 1H35M * 0 0 CCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2843 255 35M1H * 0 0 TTACCGCTACTAAATGCCGCGGATTGGTTTCGCTG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4374 255 36M * 0 0 GTTACGCAGTTTTGCCGCAAGCTGGCTGCTGTACGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1940 255 1H35M * 0 0 ATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 5073 255 36M * 0 0 GAATGGAACAACTCACTAAAAACCAAGCTGTCGCTA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4434 255 36M * 0 0 TATAATTACCCCAAAAAGAAAGGTATTAAGGATGAG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1274 255 1H35M * 0 0 GCCACTCCTCTCCCGACTGTTAACACTACTGGTTA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4440 255 36M * 0 0 TACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3920 255 36M * 0 0 GTCAGGATTGACACCCTCCCAATTGTATGTTTTCAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4587 255 1H35M * 0 0 CTCACGTTGGCTGACGACCGATTAGAGGCGTTTTA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1707 255 36M * 0 0 TACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1582 255 36M * 0 0 GGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1588 255 36M * 0 0 GCAAGCTGCTTATGCTAATTTGCATACTGACCAAGA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1180 255 34M2H * 0 0 TATTGACTCTACTGTAGACATTTTTACTTTTTAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2698 255 36M * 0 0 ACCCTCCCGACTGCCTATGATGTTTATCCTTTGAAT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3167 255 36M * 0 0 TGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2289 255 36M * 0 0 AGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 441 255 36M * 0 0 ATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1012 255 36M * 0 0 TCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 161 255 36M * 0 0 GCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1165 255 1H35M * 0 0 GCGTCGTGGCCTTGCTATTGACTCTACTGTAGACA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 5010 255 36M * 0 0 GTGGATAAATACGTTAACAAAAAGTCAGATATGGAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2286 255 36M * 0 0 AAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 801 255 36M * 0 0 GCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1587 255 36M * 0 0 TGCAAGCTGCTTATGCTAATTTGCATACTGACCAAG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4578 255 36M * 0 0 TTTGACACTCTCACGTTGGCTGACGACCGATTAGAG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3570 255 36M * 0 0 ATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 496 255 36M * 0 0 TTCTGACGAGTAACAAAGTTTGGATTGCTACTGACC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 441 255 36M * 0 0 ATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4754 255 36M * 0 0 TAATGGCCGTCTTCATTTCCATGCGGTGCATTTTAT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4235 255 35M1H * 0 0 TGAGTTTGTATCTGTTACTGAGAAGTTAATGGATG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2293 255 36M * 0 0 TGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1579 255 1H35M * 0 0 TATGGGTCTGCAAGCTGCTTATGCTAATTTGCATA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3332 255 36M * 0 0 TGGTGCTGATGCTTCCTCTGCTGGTATGGTTTACGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4132 255 36M * 0 0 TCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4775 255 36M * 0 0 TGCGGTGCATTTTATGCGGACACTTCCTACAGGTAG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1 255 4H32M * 0 0 GAGTTTTATCGCTTCCATGACGCAGAAGTTAA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 54 255 36M * 0 0 AGTCGAAAAATTATCTTGATAAAGCAGGAATTACTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 680 255 1H35M * 0 0 CATGGAAGGCGCTGAATTTACGGAAAACATTATTA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 231 255 36M * 0 0 TGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4192 255 36M * 0 0 ATATGTATGTTGACGGCCATAAGGCTGCTTCTGACG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1580 255 36M * 0 0 ATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 611 255 36M * 0 0 TGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4532 255 1H35M * 0 0 GATGAATGCAATGCGACAGGCTCATGCTGATGGTT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 638 255 35M1H * 0 0 TTATTATGTTCATCCCGTCAACATTCAAACTGCCT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1957 255 36M * 0 0 TTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2728 255 36M * 0 0 TTGAATGGTCGCCATGATGGTGGTTATTATACCGTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3979 255 36M * 0 0 TTATGGTTCGTTCTTATTACCCTTCTGAATGTCACG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 540 255 1H35M * 0 0 GCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1852 255 36M * 0 0 GTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4684 255 36M * 0 0 AGGGTCGCAAGGCTAATGATTCACACGCCGACTGCT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3690 255 36M * 0 0 AAGGTTAGTGCTGAGGTTGACTTAGTTCATCATCAA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 584 255 36M * 0 0 TGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3852 255 1H35M * 0 0 ACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2857 255 35M1H * 0 0 TGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1728 255 36M * 0 0 TCTGGGCATCTGGCTATGATGTTGATGGAACTGACC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4658 255 35M1H * 0 0 TATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1721 255 36M * 0 0 TCTAATCTCTGGGCATCTGGCTATGATGTTGATGGA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1954 255 36M * 0 0 TGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 962 255 36M * 0 0 TAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2175 255 36M * 0 0 ACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2442 255 36M * 0 0 TAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 5126 255 1H35M * 0 0 CAGAATCAGAATGAGCCGCAACTTCGGGATGAAAA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 5206 255 36M * 0 0 CCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2879 255 36M * 0 0 ATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2004 255 36M * 0 0 TCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2154 255 36M * 0 0 TTATTCGCCACCATGATTATGACCAGTGTTTCCAGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1093 255 35M1H * 0 0 TTCAACTACTCCGGTTATCGCTGGCGACTCCTTCG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3127 255 36M * 0 0 AGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3544 255 36M * 0 0 AGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2508 255 35M1H * 0 0 ATCGTCAACGTTATATTTTGATAGTTTGACGTTTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3600 255 36M * 0 0 CAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1734 255 36M * 0 0 CATCTGGCTATGATGTTGATGGAACTGACCAAACGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2655 255 33M3H * 0 0 TTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2934 255 36M * 0 0 TTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1522 255 36M * 0 0 TCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4063 255 36M * 0 0 AGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3395 255 36M * 0 0 TAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 409 255 36M * 0 0 AATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1867 255 36M * 0 0 TGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3780 255 36M * 0 0 TCTAATGTCGTCACTGATGCTGCTTCTGGTGTGTTT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3982 255 36M * 0 0 TGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2815 255 36M * 0 0 TATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1242 255 36M * 0 0 AGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4659 255 1H35M * 0 0 ATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2436 255 36M * 0 0 TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 527 255 35M1H * 0 0 TGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4817 255 36M * 0 0 CCCTAATTTGGGTCGTCGGGTACGCAATCGCCGCCA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2100 255 36M * 0 0 AAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2762 255 36M * 0 0 TCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4955 255 36M * 0 0 TGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3761 255 36M * 0 0 CGCTACTGCAAAGGATATTTCTAATGTCGTCACTGA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4499 255 36M * 0 0 GAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4039 255 36M * 0 0 TCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4788 255 36M * 0 0 ATGCGGACACTTCCTACAGGTAGCGTTGACCCTAAT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1002 255 36M * 0 0 TGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4381 255 36M * 0 0 AGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4256 255 36M * 0 0 GAAGTTAATGGATGAATTGGCACAATGCTACAATGT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 10 255 1H35M * 0 0 CGCTTCCATGACGCAGAAGTTAACACTTTCGGATA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1579 255 36M * 0 0 TATGGGTCTGCAAGCTGCTTATGCTAATTTGCATAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3862 255 36M * 0 0 ATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3278 255 36M * 0 0 TACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 349 255 36M * 0 0 TCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4608 255 36M * 0 0 TTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3808 255 35M1H * 0 0 GTGTGGTTGATATTTTTCATGGTATTGATAAAGCT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4753 255 36M * 0 0 CTAATGGCCGTCTTCATTTCCATGCGGTGCATTTTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 286 255 36M * 0 0 GAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2850 255 36M * 0 0 TACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 680 255 1H35M * 0 0 CATGGAAGGCGCTGAATTTACGGAAAACATTATTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4740 255 36M * 0 0 GAGTATGGTACAGCTAATGGCCGTCTTCATTTCCAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2467 255 1H35M * 0 0 CCAGCTTCTTCGGCACCTGTTTTACAGACACCTAA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 320 255 34M2H * 0 0 TTGACATTTTAAAAGAGCGTGGATTACTATCTGA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1180 255 34M2H * 0 0 TATTGACTCTACTGTAGACATTTTTACTTTTTAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 521 255 36M * 0 0 TGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 333 255 36M * 0 0 AGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2756 255 36M * 0 0 ATACCGTCAAGGACTGTGTGACTATTGACGTCCTTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4957 255 36M * 0 0 ATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 72 255 36M * 0 0 ATAAAGCAGGAATTACTACTGCTTGTTTACGAATTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4249 255 36M * 0 0 TTACTGAGAAGTTAATGGATGAATTGGCACAATGCT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2592 255 36M * 0 0 CAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1974 255 36M * 0 0 CGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3540 255 36M * 0 0 AAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4130 255 36M * 0 0 CATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 4295 255 1H35M * 0 0 CCCCCAACTTGATATTAATAACACTATAGACCACC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3522 255 36M * 0 0 ATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 229 255 36M * 0 0 GATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2071 255 36M * 0 0 GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT * +HWI-EAS91_1_306UPAAXX 16 phiX174 1067 255 1H35M * 0 0 GGTCAGATTGGTCGTCTTATTACCATTTCAACTAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 1788 255 36M * 0 0 GTCGTGTTCAACAGACCTATAAACATTCTGTGCCGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 1193 255 36M * 0 0 GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4563 255 36M * 0 0 GGTTGGTTTATCGTTTTTGACACTCTCACGTTGTCT * +HWI-EAS91_1_306UPAAXX 0 phiX174 2668 255 36M * 0 0 GTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4248 255 36M * 0 0 GTTACTGAGAAGTTAATGGATGAATTGGCACAATGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2863 255 36M * 0 0 GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT * +HWI-EAS91_1_306UPAAXX 0 phiX174 2557 255 36M * 0 0 GGTTTTCTTCATTGCATTCAGATGGATACATCTGTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2511 255 34M2H * 0 0 GTCAACGTTATATTTTGATAGTTTGACGGTTAAT * +HWI-EAS91_1_306UPAAXX 0 phiX174 5152 255 36M * 0 0 GGATGAAAATGCTCACAATGACAAATCTGTCCACGG * +HWI-EAS91_1_306UPAAXX 16 phiX174 1590 255 36M * 0 0 AAGCTGCTTATGCTAATTTGCATACTGACCAAGAAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4884 255 36M * 0 0 GGTTACAGTATGCCCATCGCAGTTCGCTACACGCAG * +HWI-EAS91_1_306UPAAXX 0 phiX174 5052 255 36M * 0 0 GCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCA * +HWI-EAS91_1_306UPAAXX 0 phiX174 4909 255 36M * 0 0 GCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 2863 255 36M * 0 0 GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT * +HWI-EAS91_1_306UPAAXX 0 phiX174 4173 255 36M * 0 0 GTTGAGTTCGATAATGGTGATATGTATGTTTACGGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 1701 255 36M * 0 0 GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 1683 255 36M * 0 0 CTTATGACGCTGACAACCGTCCTTTACTTGTCATGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3126 255 1H35M * 0 0 GAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1665 255 36M * 0 0 CATTTGGAGGTAAAACCTCTTATGACGCTGACAACC * +HWI-EAS91_1_306UPAAXX 0 phiX174 3213 255 36M * 0 0 GTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 3420 255 36M * 0 0 GAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG * +HWI-EAS91_1_306UPAAXX 0 phiX174 513 255 36M * 0 0 GTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 2879 255 36M * 0 0 ATAAGGTTATTAAAGAGATTATTTGTCTCCAGCCAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4471 255 36M * 0 0 GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 1229 255 36M * 0 0 GTTTATGGTGAACAGTGGATTAAGTTCATGAAGGAT * +HWI-EAS91_1_306UPAAXX 0 phiX174 615 255 36M * 0 0 GAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 257 255 36M * 0 0 GCACGTTCGTCAAGGACTGGTTTAGATATGAGTCAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 2381 255 36M * 0 0 TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4098 255 36M * 0 0 ATGCTTGGCTTCCATAAGCAGATGGATAACCGCATC * +HWI-EAS91_1_306UPAAXX 0 phiX174 5099 255 36M * 0 0 GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAG * +HWI-EAS91_1_306UPAAXX 0 phiX174 4254 255 36M * 0 0 GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT * +HWI-EAS91_1_306UPAAXX 0 phiX174 3408 255 36M * 0 0 GACAATCAGAAAGAGATTGCCGAGATGCAAAATGAG * +HWI-EAS91_1_306UPAAXX 16 phiX174 4043 255 36M * 0 0 GGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4560 255 36M * 0 0 GATGGTTGGTTTATCGTTTTTGACACTCTCACGTTG * +HWI-EAS91_1_306UPAAXX 0 phiX174 1888 255 36M * 0 0 GACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3434 255 1H35M * 0 0 GCAAAATGAGACTCAAAAAGAGATTGCTGGCATTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4539 255 36M * 0 0 GCAATGCGACAGGCTCATGCTGATGGTTGGTTTATC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1828 255 36M * 0 0 CTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 3708 255 36M * 0 0 GACTTAGTTCATCAGCAAACGCAGAATCAGCGGTAT * +HWI-EAS91_1_306UPAAXX 0 phiX174 3326 255 36M * 0 0 GCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 4176 255 36M * 0 0 GAGTTCGATAATGGTGATATGTATGTTGACGGCCAT * +HWI-EAS91_1_306UPAAXX 0 phiX174 22 255 36M * 0 0 GCAGAAGTTAACACTTTCGGATATTTCTGATGAGTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 2557 255 36M * 0 0 GGTTTTCTTCATTGCATTCAGATGGATACATCTGTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3277 255 36M * 0 0 ATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3592 255 36M * 0 0 AGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 358 255 35M1H * 0 0 GATGCTGTTCAACCACTAATAGGTAAGAAATCATG * +HWI-EAS91_1_306UPAAXX 0 phiX174 1775 255 36M * 0 0 GGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAA * +HWI-EAS91_1_306UPAAXX 0 phiX174 3504 255 36M * 0 0 GTATATGCACAAAATGAGATGCTTGCTTATCAACAG * +HWI-EAS91_1_306UPAAXX 16 phiX174 1554 255 36M * 0 0 CGACTTCTACCACATCTATTGACATTATGGGTCTGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1002 255 36M * 0 0 TGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3626 255 36M * 0 0 GCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 3572 255 36M * 0 0 GGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 1265 255 36M * 0 0 GGTGTTAATGCCACTCCTCTCCCGACTGTTAACACT * +HWI-EAS91_1_306UPAAXX 16 phiX174 1332 255 36M * 0 0 GCACGATTAACCCTGATACCAATAAAATCCCTAAGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4254 255 36M * 0 0 GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 4170 255 36M * 0 0 GGCGTTGAGTTCGATAATGGTGATATGTATGTTGAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 2806 255 36M * 0 0 AATAATGTTTATGTTGGTTTCATGGTTTGGTCTAAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3119 255 36M * 0 0 CCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 1670 255 36M * 0 0 GGAGGTAAAACCTCTTATGACGCTGACAACCGTCCT * +HWI-EAS91_1_306UPAAXX 16 phiX174 640 255 36M * 0 0 ATTATGTTCATCCCGTCAACATTCAAACGGCCTGTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2750 255 35M1H * 0 0 GTTATTATACCGTCAAGGACTGTGTGACTATTGAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4606 255 36M * 0 0 GATTAGAGGCGTTTTATGATAATCCCAATGCTTTGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3573 255 36M * 0 0 GAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCC * +HWI-EAS91_1_306UPAAXX 0 phiX174 5105 255 36M * 0 0 GCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAG * +HWI-EAS91_1_306UPAAXX 16 phiX174 1674 255 36M * 0 0 GTAAAACCTCTTATGACGCTGACAACCGTCCTTTAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4095 255 36M * 0 0 CCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4551 255 36M * 0 0 GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACT * +HWI-EAS91_1_306UPAAXX 16 phiX174 3284 255 36M * 0 0 TGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4005 255 36M * 0 0 GAATGTCACGCTGATTATTTTGACTTTGAGCGTATC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2479 255 36M * 0 0 GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA * +HWI-EAS91_1_306UPAAXX 16 phiX174 1082 255 36M * 0 0 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3045 255 1H35M * 0 0 GCTACCGATAACAATACTGTAGGCATGGGTGATGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1115 255 36M * 0 0 GGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 636 255 36M * 0 0 GCTTATTATGTTCATCCCGTCAACATTCAAACGTCC * +HWI-EAS91_1_306UPAAXX 0 phiX174 1139 255 34M2H * 0 0 GTTGGCGCTCTCCGTCTTTCTCCATTTCGTCGTG * +HWI-EAS91_1_306UPAAXX 16 phiX174 852 255 36M * 0 0 CTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 5272 255 36M * 0 0 GATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTT * +HWI-EAS91_1_306UPAAXX 0 phiX174 4330 255 36M * 0 0 GCCCCGAAGGGGACNANAAATGGTTTTTAGAGAACG * +HWI-EAS91_1_306UPAAXX 0 phiX174 4891 255 36M * 0 0 GTATGCCCATCGCAGTTCGCTACACGCAGGACGCTT * +HWI-EAS91_1_306UPAAXX 16 phiX174 4783 255 36M * 0 0 ATTTTATGCGGACACTTCCTACAGGTAGCGTTGACC * +HWI-EAS91_1_306UPAAXX 0 phiX174 3619 255 36M * 0 0 GCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 4455 255 36M * 0 0 GGTATTAAGGATGAGTGTTCAAGATTGCTGGATGCC * +HWI-EAS91_1_306UPAAXX 16 phiX174 632 255 36M * 0 0 CATTGCTTATTATGTTCATCCCGTCAACATTCAAAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2964 255 35M1H * 0 0 GCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGG * +HWI-EAS91_1_306UPAAXX 16 phiX174 2763 255 36M * 0 0 CAAGGACTGTGTGACTATTGACGTCCTTCCCCGTAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 2766 255 36M * 0 0 GGACTGTGTGACTATTGACGTCCTTCCCCGTACGCC * +HWI-EAS91_1_306UPAAXX 0 phiX174 1719 255 36M * 0 0 GCTCTAATCTCTGGGCATCTGGCTATGATGTTGATG * +HWI-EAS91_1_306UPAAXX 16 phiX174 3100 255 36M * 0 0 AAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCC * +HWI-EAS91_1_306UPAAXX 0 phiX174 598 255 35M1H * 0 0 GCTTTCCTGCTCCTGTTGAGTTTATTGCTTCCGTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4126 255 36M * 0 0 ACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4026 255 36M * 0 0 GACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATT * +HWI-EAS91_1_306UPAAXX 0 phiX174 2621 255 36M * 0 0 GTGCTGATATTGCTTTTGATGCCGACCCTAAATTTT * +HWI-EAS91_1_306UPAAXX 0 phiX174 2749 255 36M * 0 0 GGTTATTATACCGTCAAGGACTGTGTGACTATTGAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 379 255 36M * 0 0 GGTAAGAAATCATGAGTCAAGTTACTGAACAATCCG * +HWI-EAS91_1_306UPAAXX 0 phiX174 2160 255 36M * 0 0 GCCACCATGATTATGACCAGTGTTTCCAGTCCGTTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 2873 255 36M * 0 0 CGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1508 255 1H35M * 0 0 TGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3863 255 36M * 0 0 TTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 5187 255 36M * 0 0 GAGTGCTTAATCCAACTTACCAAGCTGGGTTACGAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4196 255 36M * 0 0 GTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCG * +HWI-EAS91_1_306UPAAXX 16 phiX174 635 255 36M * 0 0 TGCTTATTATGTTCATCCCGTCAACATTCAAACGGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1294 255 1H35M * 0 0 TAACACTACTGGTTATATTGACCATGCCGCTTTTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 5157 255 36M * 0 0 AAAATGCTCACAATGACAAATCTGTCCACGGAGTGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 772 255 36M * 0 0 GCGCAGGAAACACTGACGTTCTTACTGACGCAGAAG * +HWI-EAS91_1_306UPAAXX 0 phiX174 1224 255 36M * 0 0 GTCACGTTTATGGTGAACAGTGGATTAAGTTCATGA * +HWI-EAS91_1_306UPAAXX 16 phiX174 1544 255 3H33M * 0 0 CGCCAAATGACGACTTCTACCACATCTATTGAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4840 255 36M * 0 0 GCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 204 255 35M1H * 0 0 GATTCTGTCAAAAACTGACGCGTTGGATGAGGAGA * +HWI-EAS91_1_306UPAAXX 16 phiX174 2481 255 36M * 0 0 ACCTGTTTTAAAGACACCTAAAGCTACATCGTCAAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 332 255 36M * 0 0 AAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3978 255 36M * 0 0 TTTATGGTTCGTTCTTATTACCCTTCTGAATGTCAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4865 255 36M * 0 0 GCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 3271 255 36M * 0 0 GAAAGGATACTCGTGATTATCTTGCTGCTGCATTTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4174 255 36M * 0 0 TTGAGTTCGATAATGGTGATATGTATGTTGACGGCC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2738 255 36M * 0 0 GCCATGATGGTGGTTATTATACCGTCAAGGACTGTG * +HWI-EAS91_1_306UPAAXX 16 phiX174 2703 255 1H35M * 0 0 CCCGACTGCCTATGATGTTTATCCTTTGAATGGTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 2943 255 36M * 0 0 ATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3861 255 36M * 0 0 AATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 3093 255 36M * 0 0 GCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAG * +HWI-EAS91_1_306UPAAXX 0 phiX174 3151 255 36M * 0 0 GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAG * +HWI-EAS91_1_306UPAAXX 0 phiX174 1193 255 36M * 0 0 GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 157 255 36M * 0 0 CGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4792 255 36M * 0 0 GGACACTTCCTACAGGTAGCGTTGACCCTAATTTTG * +HWI-EAS91_1_306UPAAXX 0 phiX174 3849 255 36M * 0 0 GATACTTGGAACAATTTCTGGAAAGACGGTAAAGCT * +HWI-EAS91_1_306UPAAXX 16 phiX174 2743 255 1H35M * 0 0 GATGGTGGTTATTATACCGTCAAGGACTGTGTGAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 3015 255 36M * 0 0 GCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1091 255 36M * 0 0 ATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 798 255 1H35M * 0 0 GACGCAGAAGAAAACGTGCGTCAAAAATTACGTGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4866 255 36M * 0 0 CAAAATACGTGGCCTTATGGTTACAGTATGCCCATC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4404 255 36M * 0 0 GAACGCCCTCTTAAGGATATTCGCGATGAGTATAAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 1655 255 36M * 0 0 GTTATTTCTTCATTTGGAGGTAAAACCTCTTATGAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 5162 255 36M * 0 0 GCTCACAATGACAAATCTGTCCACGGAGTGCTTAAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 1249 255 1H35M * 0 0 TAAGTTCATGAAGGATGGTGTTAATGCCACTCCTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 3261 255 36M * 0 0 GCTGATAAAGGAAAGGATACTCGTGATTATCTTGCT * +HWI-EAS91_1_306UPAAXX 16 phiX174 3096 255 36M * 0 0 ATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCC * +HWI-EAS91_1_306UPAAXX 16 phiX174 2811 255 36M * 0 0 TGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 3459 255 36M * 0 0 GCTGGCATTCAGTCGGCGACTTCACGCCAGAATACG * +HWI-EAS91_1_306UPAAXX 0 phiX174 789 255 35M1H * 0 0 GTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAA * +HWI-EAS91_1_306UPAAXX 0 phiX174 3699 255 36M * 0 0 GCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAAT * +HWI-EAS91_1_306UPAAXX 0 phiX174 2641 255 36M * 0 0 GCCGACCCTAAATTTTTTGCCTGTTTGGTTCTCTTT * +HWI-EAS91_1_306UPAAXX 0 phiX174 305 255 36M * 0 0 GTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTG * +HWI-EAS91_1_306UPAAXX 0 phiX174 3066 255 35M1H * 0 0 GGCATGGGTGATGCTGGTATTAAATCTGCCATTCA * +HWI-EAS91_1_306UPAAXX 0 phiX174 4428 255 36M * 0 0 GATGAGTATAATTACCCCAAAAAGAAAGGTATTAAG * +HWI-EAS91_1_306UPAAXX 16 phiX174 1461 255 36M * 0 0 AAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4000 255 36M * 0 0 CTTCTGAATGTCACGCTGATTATTTTGACTTTGAGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 220 255 36M * 0 0 GACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTT * +HWI-EAS91_1_306UPAAXX 0 phiX174 3194 255 36M * 0 0 GCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTTCT * +HWI-EAS91_1_306UPAAXX 0 phiX174 1266 255 35M1H * 0 0 GTGTTAATGCCACTCCTCTCCCGACTGTTAACTCT * +HWI-EAS91_1_306UPAAXX 16 phiX174 4596 255 36M * 0 0 GCTGACGACCGATTAGAGGCGTTTTATGATAATCCC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1172 255 1H35M * 0 0 GGCCTTGCTATTGACTCTACTGTAGACATTTTTAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 636 255 36M * 0 0 GCTTATTATGTTCATCCCGTCAACATTCAAACGGCC * +HWI-EAS91_1_306UPAAXX 16 phiX174 2873 255 36M * 0 0 CGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1014 255 36M * 0 0 AAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2689 255 36M * 0 0 GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT * +HWI-EAS91_1_306UPAAXX 0 phiX174 2148 255 36M * 0 0 GCGTACTTATTCGCCACCATGATTATTACCAGTGTT * +HWI-EAS91_1_306UPAAXX 0 phiX174 5191 255 35M1H * 0 0 GCTTAATCCAACTTACCAAGCTGGGTTACGACGCG * +HWI-EAS91_1_306UPAAXX 16 phiX174 1590 255 36M * 0 0 AAGCTGCTTATGCTAATTTGCATACTGACCAAGAAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 571 255 35M1H * 0 0 GTACGCTGTACTTTGTGGGATACCCTCGCTTTCCT * +HWI-EAS91_1_306UPAAXX 0 phiX174 242 255 36M * 0 0 GGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 338 255 36M * 0 0 GTGGATTACTATCTGAGTCCGATGCTGTTCAACCAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 1112 255 36M * 0 0 GCTGGCGACTCCTTCGAGATGGACGCCGTTTGCGCT * +HWI-EAS91_1_306UPAAXX 16 phiX174 1254 255 2H34M * 0 0 TCATGAAGGATGGTGTTAATGCCACTCCTCTCCC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2970 255 36M * 0 0 GCTGGTGGCGCCATGTCTAAATTTTTTGGAGGCGGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 5151 255 36M * 0 0 GGGATGAAAATGCTCACAATGACAAATCTGTCCACG * +HWI-EAS91_1_306UPAAXX 16 phiX174 348 255 36M * 0 0 ATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAA * +HWI-EAS91_1_306UPAAXX 16 phiX174 4888 255 1H35M * 0 0 ACAGTATGCCCATCGCAGTTCGCTACACGCAGGAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 3972 255 33M3H * 0 0 GGCTTTTTTATGGTTCGTTCTTATTACCCTTCT * +HWI-EAS91_1_306UPAAXX 0 phiX174 5033 255 36M * 0 0 GTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1552 255 1H35M * 0 0 GACGACTTCTACCACATCTATTGACATTATGGGTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1764 255 36M * 0 0 AAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 1529 255 36M * 0 0 GAGACTGAGCTTTCTCGCCAAATGACGACTTCTACC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4950 255 36M * 0 0 CCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4484 255 36M * 0 0 GGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4767 255 1H35M * 0 0 CATTTCCATGCGGTGCATTTTATGCGGACACTTCC * +HWI-EAS91_1_306UPAAXX 16 phiX174 177 255 36M * 0 0 CTTTGCGACCTTTCGCCATCAACTAACGATTCTGTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2577 255 36M * 0 0 GATGGATACATCTGTCAACGCCGCTAATCAGGTTGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 156 255 36M * 0 0 GCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCG * +HWI-EAS91_1_306UPAAXX 0 phiX174 227 255 36M * 0 0 TGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGT * +HWI-EAS91_1_306UPAAXX 16 phiX174 574 255 36M * 0 0 CGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 3021 255 36M * 0 0 GGTGGCATTCAAGGTGATGTGCTTGCTACCGATAAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3731 255 36M * 0 0 GAATCAGCGGTATGGCTCTTCTCATATTGGCGCTAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2436 255 36M * 0 0 TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2710 255 36M * 0 0 GCCTATGATGTTTATCCTTTGAATGGTCGCCATGAT * +HWI-EAS91_1_306UPAAXX 0 phiX174 4228 255 35M1H * 0 0 TTCGTGATGAGTTTGTATCTGTTACTGATAAGTTA * +HWI-EAS91_1_306UPAAXX 0 phiX174 4606 255 34M2H * 0 0 GATTAGAGGCGTTTTATGATAATCCCAATGCTTT * +HWI-EAS91_1_306UPAAXX 16 phiX174 2766 255 36M * 0 0 GGACTGTGTGACTATTGACGTCCTTCCCCGTACGCC * +HWI-EAS91_1_306UPAAXX 0 phiX174 582 255 34M2H * 0 0 TTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTG * +HWI-EAS91_1_306UPAAXX 16 phiX174 1144 255 36M * 0 0 CGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 1514 255 36M * 0 0 GCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAA * +HWI-EAS91_1_306UPAAXX 16 phiX174 1657 255 36M * 0 0 TATTTCTTCATTTGGAGGTAAAACCTCTTATGACGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2071 255 36M * 0 0 GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT * +HWI-EAS91_1_306UPAAXX 0 phiX174 1626 255 36M * 0 0 GTGATTACTTCATGCAGCGTTACCGTGATGTTATTT * +HWI-EAS91_1_306UPAAXX 0 phiX174 3250 255 36M * 0 0 GCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTG * +HWI-EAS91_1_306UPAAXX 0 phiX174 1982 255 36M * 0 0 GAAATTTCTATGAATGATGTTTTCCGTTCTGGTGAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 2217 255 36M * 0 0 AGGTTAAATTTAATGTGACCGTTTATCGCAATCTGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3480 255 1H35M * 0 0 TCACGACAGAATACGAAAGACCAGGTATATGCACA * +HWI-EAS91_1_306UPAAXX 16 phiX174 1690 255 36M * 0 0 CGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAA * +HWI-EAS91_1_306UPAAXX 16 phiX174 1082 255 36M * 0 0 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4282 255 36M * 0 0 GCTACAATGTGCTCCCCCAACTTGATATTAATAACA * +HWI-EAS91_1_306UPAAXX 0 phiX174 4136 255 34M2H * 0 0 GCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAG * +HWI-EAS91_1_306UPAAXX 0 phiX174 4414 255 36M * 0 0 TTAAGGATATTCGCGATGAGTATAATTACCCCAAAA * +HWI-EAS91_1_306UPAAXX 16 phiX174 3988 255 36M * 0 0 GTTCTTATTACCCTTCTGAATGTCACGCTGATTATT * +HWI-EAS91_1_306UPAAXX 0 phiX174 4203 255 36M * 0 0 GACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAG * +HWI-EAS91_1_306UPAAXX 16 phiX174 4098 255 36M * 0 0 ATGCTTGGCTTCAATAAGCAGATGGATAACCGCATC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4307 255 35M1H * 0 0 TATTAATAACACTATAGACCACCGCCCCGAAGGGG * +HWI-EAS91_1_306UPAAXX 0 phiX174 1521 255 35M1H * 0 0 TTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACG * +HWI-EAS91_1_306UPAAXX 16 phiX174 945 255 36M * 0 0 TAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1575 255 36M * 0 0 ACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2689 255 36M * 0 0 GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT * +HWI-EAS91_1_306UPAAXX 0 phiX174 2099 255 36M * 0 0 GAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGT * +HWI-EAS91_1_306UPAAXX 16 phiX174 524 255 36M * 0 0 TACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 1252 255 36M * 0 0 GTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4916 255 36M * 0 0 GCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGTCC * +HWI-EAS91_1_306UPAAXX 0 phiX174 3828 255 36M * 0 0 GGTATTGATAAAGCTGTTGCCGATACTTGTAACAAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 3756 255 36M * 0 0 ATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1116 255 36M * 0 0 GCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3099 255 36M * 0 0 CAAGGCTCTAATGTTCCTAACCCTGATGGGGCCGCC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3082 255 36M * 0 0 GTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 613 255 36M * 0 0 TTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4936 255 36M * 0 0 CTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 289 255 36M * 0 0 TCACATTTTGTTCATGGTAGAGATTCTCTTGTTGAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4690 255 36M * 0 0 GCAAGGCTAATGATTCACACGCCGACTGCTATCAGT * +HWI-EAS91_1_306UPAAXX 16 phiX174 3520 255 36M * 0 0 AGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3858 255 36M * 0 0 AACAATTTCTGGAAAGACGGTAAAGCTGATGGTATT * +HWI-EAS91_1_306UPAAXX 16 phiX174 3344 255 36M * 0 0 TTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAA * +HWI-EAS91_1_306UPAAXX 0 phiX174 4672 255 36M * 0 0 TTCTTGCTGCCGAGGGTCGCAAGGCTATTGTTTCAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1800 255 36M * 0 0 AGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 5077 255 36M * 0 0 GGAACAACTCACTAAAAACCAAGCTGTCGCTACTTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 2763 255 1H35M * 0 0 CAAGGACTGTGTGACTATTGACGTCCTTCCCCGTA * +HWI-EAS91_1_306UPAAXX 0 phiX174 4282 255 36M * 0 0 GCTACAATGTGCTCCCCCAACTTGATATTAATAACA * +HWI-EAS91_1_306UPAAXX 0 phiX174 1203 255 36M * 0 0 TTACTTTTTATGTCCCTCATCGTCACGTTTATGTTG * +HWI-EAS91_1_306UPAAXX 16 phiX174 5107 255 36M * 0 0 TACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCC * +HWI-EAS91_1_306UPAAXX 16 phiX174 5168 255 1H35M * 0 0 AATGACAAATCTGTCCACGGAGTGCTTAATCCAAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2956 255 36M * 0 0 TTGCTTCTGCTCTTGCTTGTGGCGCCATGTCTAAAT * +HWI-EAS91_1_306UPAAXX 0 phiX174 624 255 36M * 0 0 GCTGCCGTCATTGCTTATTATGTTCATCCCTTCAAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1877 255 1H35M * 0 0 CCGCCTACTGCGACTAAAGAGATTCAGTACCTTAA * +HWI-EAS91_1_306UPAAXX 0 phiX174 1214 255 36M * 0 0 GTCCCTCATCGTCACGTTTATGGTGAACAGTGGATT * +HWI-EAS91_1_306UPAAXX 0 phiX174 558 255 36M * 0 0 GCTTGCGTTTATGGTACGCTGGACTTTTTGTGATAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3629 255 36M * 0 0 TACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAA * +HWI-EAS91_1_306UPAAXX 0 phiX174 2254 255 35M1H * 0 0 GACCACTCGCGATTCAATCATGACTTCGTGATAAA * +HWI-EAS91_1_306UPAAXX 0 phiX174 2479 255 36M * 0 0 GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA * +HWI-EAS91_1_306UPAAXX 0 phiX174 3001 255 36M * 0 0 GCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTG * +HWI-EAS91_1_306UPAAXX 0 phiX174 4667 255 35M1H * 0 0 TATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATG * +HWI-EAS91_1_306UPAAXX 16 phiX174 3464 255 36M * 0 0 CATTCAGTCGGCGACTTCACGCCAGAATACGAAAGA * +HWI-EAS91_1_306UPAAXX 0 phiX174 4911 255 35M1H * 0 0 TACACGCAGGACGCTTTTTCACGTTCTGGTTGGTT * +HWI-EAS91_1_306UPAAXX 16 phiX174 2222 255 36M * 0 0 AAATTTAATGTGAACGTTTATCGCAATCTGCCGACC * +HWI-EAS91_1_306UPAAXX 0 phiX174 646 255 35M1H * 0 0 TTCATCCCGTCAACATTCAAACGGCCTGTCTCATC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1364 255 36M * 0 0 AAGCATTTGTTTCAGGGTTATTTGAATATCTATAAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1613 255 1H35M * 0 0 ACTGACCAAGAACGTGATTACTTCATGCAGCGTTA * +HWI-EAS91_1_306UPAAXX 0 phiX174 1045 255 35M1H * 0 0 TTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 1588 255 36M * 0 0 GCAAGCTGCTTATGCTAATTTGCATACTGACCAAGA * +HWI-EAS91_1_306UPAAXX 0 phiX174 339 255 36M * 0 0 TGGATTACTATCTGAGTCCGATGCTGTTCAACCACT * +HWI-EAS91_1_306UPAAXX 0 phiX174 4937 255 36M * 0 0 TGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4344 255 2H34M * 0 0 GAAAAATGGTTTTTAGAGAACGAGAAGACGGTTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 3674 255 36M * 0 0 CAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGA * +HWI-EAS91_1_306UPAAXX 0 phiX174 4945 255 36M * 0 0 TGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAG * +HWI-EAS91_1_306UPAAXX 0 phiX174 1946 255 36M * 0 0 GGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 2662 255 36M * 0 0 TGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCTACT * +HWI-EAS91_1_306UPAAXX 0 phiX174 3313 255 36M * 0 0 TTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCT * +HWI-EAS91_1_306UPAAXX 0 phiX174 727 255 36M * 0 0 GTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCT * +HWI-EAS91_1_306UPAAXX 16 phiX174 555 255 36M * 0 0 GAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGA * +HWI-EAS91_1_306UPAAXX 0 phiX174 485 255 36M * 0 0 TGATTTCGATTTTCTGACGAGTAACAAAGTTTGGAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 318 255 36M * 0 0 TGTTGACATTTTAAAAGAGCGTGGATTACTATCTGA * +HWI-EAS91_1_306UPAAXX 0 phiX174 910 255 36M * 0 0 TAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGT * +HWI-EAS91_1_306UPAAXX 16 phiX174 4936 255 36M * 0 0 CTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 5005 255 36M * 0 0 TCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA * +HWI-EAS91_1_306UPAAXX 0 phiX174 1379 255 36M * 0 0 GGTTATTTGAATATCTATAACAACTATTTTAAATCG * +HWI-EAS91_1_306UPAAXX 0 phiX174 3168 255 36M * 0 0 GGTAAAGGACTTCTTGAAGGTACGTTGCAGTCTGGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2738 255 33M3H * 0 0 GCCATGATGGTGGTTATTATACCGTCAAGGACT * +HWI-EAS91_1_306UPAAXX 0 phiX174 4099 255 36M * 0 0 TGCTTGGCTTCCATAAGCAGATGGATAACCGCATCA * +HWI-EAS91_1_306UPAAXX 0 phiX174 2574 255 36M * 0 0 TCAGATGGATACATCTGTCAACGCCGCTAATCAGGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 2453 255 36M * 0 0 TCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTT * +HWI-EAS91_1_306UPAAXX 0 phiX174 5179 255 36M * 0 0 TGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGG * +HWI-EAS91_1_306UPAAXX 0 phiX174 3778 255 34M2H * 0 0 TTTCTAATGTCGTCACTGATGCTGCTTCTGTTGT * +HWI-EAS91_1_306UPAAXX 16 phiX174 1843 255 36M * 0 0 TGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1082 255 36M * 0 0 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1728 255 36M * 0 0 TCTGGGCATCTGGCTATGATGTTGATGGAACTGACC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4637 255 36M * 0 0 TTTGCGTGACTATTTTCGTGATATTGTTCGTATGGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 2225 255 36M * 0 0 TTTAATGTGACCGTTTATCGCAATCTGCCGACCACT * +HWI-EAS91_1_306UPAAXX 16 phiX174 3368 255 36M * 0 0 CGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCA * +HWI-EAS91_1_306UPAAXX 0 phiX174 3311 255 36M * 0 0 GCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 5039 255 36M * 0 0 TATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGA * +HWI-EAS91_1_306UPAAXX 0 phiX174 2059 255 36M * 0 0 TTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCT * +HWI-EAS91_1_306UPAAXX 0 phiX174 388 255 36M * 0 0 TCATGAGTCAAGTTACTGAACAATCCGTACGTTTCC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2754 255 36M * 0 0 TTATACCGTCAAGGACTGTGTGACTATTGACGTCCT * +HWI-EAS91_1_306UPAAXX 16 phiX174 2128 255 36M * 0 0 TTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCA * +HWI-EAS91_1_306UPAAXX 0 phiX174 154 255 36M * 0 0 TTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTT * +HWI-EAS91_1_306UPAAXX 16 phiX174 3617 255 36M * 0 0 GCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCA * +HWI-EAS91_1_306UPAAXX 16 phiX174 2728 255 36M * 0 0 TTGAATGGTCGCCATGATGGTGGTTATTATACCGTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 2775 255 36M * 0 0 GACTATTGACGTCCTTCCCCGTACGCCGGGCAATAA * +HWI-EAS91_1_306UPAAXX 0 phiX174 4217 255 36M * 0 0 TGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4619 255 35M1H * 0 0 TTATGATAATCCCAATGCTTTGCGTGACTATTTTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 411 255 35M1H * 0 0 TCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAA * +HWI-EAS91_1_306UPAAXX 0 phiX174 2730 255 35M1H * 0 0 GAATGGTCGCCATGATGGTGGTTATTATACCGTCA * +HWI-EAS91_1_306UPAAXX 0 phiX174 521 255 35M1H * 0 0 TGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTG * +HWI-EAS91_1_306UPAAXX 0 phiX174 4260 255 36M * 0 0 TTAATGGATGAATTGGCACAATGCTACAATGTGCTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1662 255 36M * 0 0 CTTCATTTGGAGGTAAAACCTCTTATGACGCTGACA * +HWI-EAS91_1_306UPAAXX 16 phiX174 533 255 36M * 0 0 CTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTA * +HWI-EAS91_1_306UPAAXX 0 phiX174 195 255 35M1H * 0 0 TCAACTAACGATTCTGTCAAAAACTGACGCGTTGG * +HWI-EAS91_1_306UPAAXX 0 phiX174 2239 255 36M * 0 0 TTATCGCAATCTGCCGACCACTCGCGATTCAATCAT * +HWI-EAS91_1_306UPAAXX 0 phiX174 1313 255 36M * 0 0 GACCATGCCGCTTTTCTTGGCACGATTAACCCTTAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 1545 255 36M * 0 0 GCCAAATGACGACTTCTACCACATCTATTGACATTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 557 255 36M * 0 0 GGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATA * +HWI-EAS91_1_306UPAAXX 0 phiX174 1249 255 36M * 0 0 TAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCT * +HWI-EAS91_1_306UPAAXX 0 phiX174 4174 255 36M * 0 0 TTGAGTTCGATAATGGTGATATGTATGTTGACGTCC * +HWI-EAS91_1_306UPAAXX 0 phiX174 614 255 35M1H * 0 0 TGAGTTTATTGCTGCCGTCATTGCTTATTATGTTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 206 255 36M * 0 0 TTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGT * +HWI-EAS91_1_306UPAAXX 16 phiX174 4981 255 36M * 0 0 CTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTA * +HWI-EAS91_1_306UPAAXX 0 phiX174 1702 255 36M * 0 0 TCCTTTACTTGTCATGCGCTCTAATCTCTGTGCATC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2321 255 35M1H * 0 0 TAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4088 255 35M1H * 0 0 TCAATCCCCAATGCTTGGCTTCCATAAGCAGATGG * +HWI-EAS91_1_306UPAAXX 0 phiX174 900 255 36M * 0 0 TGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1155 255 36M * 0 0 TTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 3587 255 36M * 0 0 TTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCA * +HWI-EAS91_1_306UPAAXX 16 phiX174 3787 255 36M * 0 0 TCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTT * +HWI-EAS91_1_306UPAAXX 0 phiX174 3834 255 35M1H * 0 0 GATAAAGCTGTTGCCGATACTTGGAACAATTTCTG * +HWI-EAS91_1_306UPAAXX 0 phiX174 989 255 36M * 0 0 TGAGGATAAATTATGTCTAATATTCAAACTGGCGCC * +HWI-EAS91_1_306UPAAXX 0 phiX174 3712 255 36M * 0 0 TAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCT * +HWI-EAS91_1_306UPAAXX 0 phiX174 1207 255 36M * 0 0 TTTTTATGTCCCTCATCGTCACGTTTATGGTGAACA * +HWI-EAS91_1_306UPAAXX 0 phiX174 2116 255 36M * 0 0 TCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGT * +HWI-EAS91_1_306UPAAXX 16 phiX174 660 255 36M * 0 0 ATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAA * +HWI-EAS91_1_306UPAAXX 16 phiX174 1536 255 36M * 0 0 AGCTTTCTCGCCAAATGACGACTTCTACCACATCTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 2112 255 1H35M * 0 0 TCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAA * +HWI-EAS91_1_306UPAAXX 16 phiX174 2816 255 36M * 0 0 ATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTA * +HWI-EAS91_1_306UPAAXX 0 phiX174 5176 255 36M * 0 0 ATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3472 255 36M * 0 0 CGGCGACTTCACGCCAGAATACGAAAGACCAGGTAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 1948 255 36M * 0 0 CGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGA * +HWI-EAS91_1_306UPAAXX 0 phiX174 2212 255 35M1H * 0 0 TAGTCAGGTTAAATTTAATGTGACCGTTTATCGCA * +HWI-EAS91_1_306UPAAXX 0 phiX174 3817 255 35M1H * 0 0 ATATTTTTCATGGTATTGATAAAGCTGTTGCCGAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 3563 255 36M * 0 0 GTCTATTATGGAAAACACCAATCTTTCCAAGCAACA * +HWI-EAS91_1_306UPAAXX 16 phiX174 4198 255 1H35M * 0 0 ATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGT * +HWI-EAS91_1_306UPAAXX 16 phiX174 2907 255 1H35M * 0 0 CCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2843 255 35M1H * 0 0 TTACCGCTACTAAATGCCGCGGATTGGTTTCGCTG * +HWI-EAS91_1_306UPAAXX 0 phiX174 4374 255 36M * 0 0 GTTACGCAGTTTTGCCGCAAGCTGGCTGCTGTACGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1940 255 1H35M * 0 0 ATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCC * +HWI-EAS91_1_306UPAAXX 16 phiX174 5073 255 36M * 0 0 GAATGGAACAACTCACTAAAAACCAAGCTGTCGCTA * +HWI-EAS91_1_306UPAAXX 0 phiX174 4434 255 36M * 0 0 TATAATTACCCCAAAAAGAAAGGTATTAAGGATGAG * +HWI-EAS91_1_306UPAAXX 16 phiX174 1274 255 1H35M * 0 0 GCCACTCCTCTCCCGACTGTTAACACTACTGGTTA * +HWI-EAS91_1_306UPAAXX 0 phiX174 4440 255 36M * 0 0 TACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCA * +HWI-EAS91_1_306UPAAXX 0 phiX174 3920 255 36M * 0 0 GTCAGGATTGACACCCTCCCAATTGTATGTTTTCAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 4587 255 1H35M * 0 0 CTCACGTTGGCTGACGACCGATTAGAGGCGTTTTA * +HWI-EAS91_1_306UPAAXX 0 phiX174 1707 255 36M * 0 0 TACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCT * +HWI-EAS91_1_306UPAAXX 16 phiX174 1582 255 36M * 0 0 GGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGA * +HWI-EAS91_1_306UPAAXX 16 phiX174 1588 255 36M * 0 0 GCAAGCTGCTTATGCTAATTTGCATACTGACCAAGA * +HWI-EAS91_1_306UPAAXX 0 phiX174 1180 255 34M2H * 0 0 TATTGACTCTACTGTAGACATTTTTACTTTTTAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 2698 255 36M * 0 0 ACCCTCCCGACTGCCTATGATGTTTATCCTTTGAAT * +HWI-EAS91_1_306UPAAXX 0 phiX174 3167 255 36M * 0 0 TGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGG * +HWI-EAS91_1_306UPAAXX 16 phiX174 2289 255 36M * 0 0 AGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAA * +HWI-EAS91_1_306UPAAXX 16 phiX174 441 255 36M * 0 0 ATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTA * +HWI-EAS91_1_306UPAAXX 0 phiX174 1012 255 36M * 0 0 TCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 161 255 36M * 0 0 GCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1165 255 1H35M * 0 0 GCGTCGTGGCCTTGCTATTGACTCTACTGTAGACA * +HWI-EAS91_1_306UPAAXX 16 phiX174 5010 255 36M * 0 0 GTGGATAAATACGTTAACAAAAAGTCAGATATGGAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 2286 255 36M * 0 0 AAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGT * +HWI-EAS91_1_306UPAAXX 16 phiX174 801 255 36M * 0 0 GCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAA * +HWI-EAS91_1_306UPAAXX 0 phiX174 1587 255 36M * 0 0 TGCAAGCTGCTTATGCTAATTTGCATACTGACCAAG * +HWI-EAS91_1_306UPAAXX 0 phiX174 4578 255 36M * 0 0 TTTGACACTCTCACGTTGGCTGACGACCGATTAGAG * +HWI-EAS91_1_306UPAAXX 16 phiX174 3570 255 36M * 0 0 ATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTT * +HWI-EAS91_1_306UPAAXX 16 phiX174 496 255 36M * 0 0 TTCTGACGAGTAACAAAGTTTGGATTGCTACTGACC * +HWI-EAS91_1_306UPAAXX 0 phiX174 441 255 36M * 0 0 ATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 4754 255 36M * 0 0 TAATGGCCGTCTTCATTTCCATGCGGTGCATTTTAT * +HWI-EAS91_1_306UPAAXX 0 phiX174 4235 255 35M1H * 0 0 TGAGTTTGTATCTGTTACTGAGAAGTTAATGGATG * +HWI-EAS91_1_306UPAAXX 16 phiX174 2293 255 36M * 0 0 TGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATT * +HWI-EAS91_1_306UPAAXX 16 phiX174 1579 255 1H35M * 0 0 TATGGGTCTGCAAGCTGCTTATGCTAATTTGCATA * +HWI-EAS91_1_306UPAAXX 0 phiX174 3332 255 36M * 0 0 TGGTGCTGATGCTTCCTCTGCTGGTATGGTTTACGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4132 255 36M * 0 0 TCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4775 255 36M * 0 0 TGCGGTGCATTTTATGCGGACACTTCCTACAGGTAG * +HWI-EAS91_1_306UPAAXX 16 phiX174 1 255 4H32M * 0 0 GAGTTTTATCGCTTCCATGACGCAGAAGTTAA * +HWI-EAS91_1_306UPAAXX 16 phiX174 54 255 36M * 0 0 AGTCGAAAAATTATCTTGATAAAGCAGGAATTACTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 680 255 1H35M * 0 0 CATGGAAGGCGCTGAATTTACGGAAAACATTATTA * +HWI-EAS91_1_306UPAAXX 0 phiX174 231 255 36M * 0 0 TGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 4192 255 36M * 0 0 ATATGTATGTTGACGGCCATAAGGCTGCTTCTGACG * +HWI-EAS91_1_306UPAAXX 16 phiX174 1580 255 36M * 0 0 ATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACT * +HWI-EAS91_1_306UPAAXX 16 phiX174 611 255 36M * 0 0 TGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGT * +HWI-EAS91_1_306UPAAXX 16 phiX174 4532 255 1H35M * 0 0 GATGAATGCAATGCGACAGGCTCATGCTGATGGTT * +HWI-EAS91_1_306UPAAXX 0 phiX174 638 255 35M1H * 0 0 TTATTATGTTCATCCCGTCAACATTCAAACTGCCT * +HWI-EAS91_1_306UPAAXX 16 phiX174 1957 255 36M * 0 0 TTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 2728 255 36M * 0 0 TTGAATGGTCGCCATGATGGTGGTTATTATACCGTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 3979 255 36M * 0 0 TTATGGTTCGTTCTTATTACCCTTCTGAATGTCACG * +HWI-EAS91_1_306UPAAXX 16 phiX174 540 255 1H35M * 0 0 GCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1852 255 36M * 0 0 GTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4684 255 36M * 0 0 AGGGTCGCAAGGCTAATGATTCACACGCCGACTGCT * +HWI-EAS91_1_306UPAAXX 0 phiX174 3690 255 36M * 0 0 AAGGTTAGTGCTGAGGTTGACTTAGTTCATCATCAA * +HWI-EAS91_1_306UPAAXX 0 phiX174 584 255 36M * 0 0 TGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTT * +HWI-EAS91_1_306UPAAXX 16 phiX174 3852 255 1H35M * 0 0 ACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGA * +HWI-EAS91_1_306UPAAXX 0 phiX174 2857 255 35M1H * 0 0 TGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAA * +HWI-EAS91_1_306UPAAXX 0 phiX174 1728 255 36M * 0 0 TCTGGGCATCTGGCTATGATGTTGATGGAACTGACC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4658 255 35M1H * 0 0 TATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCA * +HWI-EAS91_1_306UPAAXX 16 phiX174 1721 255 36M * 0 0 TCTAATCTCTGGGCATCTGGCTATGATGTTGATGGA * +HWI-EAS91_1_306UPAAXX 0 phiX174 1954 255 36M * 0 0 TGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 962 255 36M * 0 0 TAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAA * +HWI-EAS91_1_306UPAAXX 16 phiX174 2175 255 36M * 0 0 ACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGA * +HWI-EAS91_1_306UPAAXX 0 phiX174 2442 255 36M * 0 0 TAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 5126 255 1H35M * 0 0 CAGAATCAGAATGAGCCGCAACTTCGGGATGAAAA * +HWI-EAS91_1_306UPAAXX 16 phiX174 5206 255 36M * 0 0 CCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGA * +HWI-EAS91_1_306UPAAXX 0 phiX174 2879 255 36M * 0 0 ATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2004 255 36M * 0 0 TCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTG * +HWI-EAS91_1_306UPAAXX 0 phiX174 2154 255 36M * 0 0 TTATTCGCCACCATGATTATGACCAGTGTTTCCAGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 1093 255 35M1H * 0 0 TTCAACTACTCCGGTTATCGCTGGCGACTCCTTCG * +HWI-EAS91_1_306UPAAXX 16 phiX174 3127 255 36M * 0 0 AGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 3544 255 36M * 0 0 AGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACA * +HWI-EAS91_1_306UPAAXX 0 phiX174 2508 255 35M1H * 0 0 ATCGTCAACGTTATATTTTGATAGTTTGACGTTTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 3600 255 36M * 0 0 CAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAA * +HWI-EAS91_1_306UPAAXX 16 phiX174 1734 255 36M * 0 0 CATCTGGCTATGATGTTGATGGAACTGACCAAACGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 2655 255 33M3H * 0 0 TTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 2934 255 36M * 0 0 TTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTT * +HWI-EAS91_1_306UPAAXX 0 phiX174 1522 255 36M * 0 0 TCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4063 255 36M * 0 0 AGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAA * +HWI-EAS91_1_306UPAAXX 0 phiX174 3395 255 36M * 0 0 TAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA * +HWI-EAS91_1_306UPAAXX 0 phiX174 409 255 36M * 0 0 AATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 1867 255 36M * 0 0 TGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCA * +HWI-EAS91_1_306UPAAXX 0 phiX174 3780 255 36M * 0 0 TCTAATGTCGTCACTGATGCTGCTTCTGGTGTGTTT * +HWI-EAS91_1_306UPAAXX 0 phiX174 3982 255 36M * 0 0 TGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTG * +HWI-EAS91_1_306UPAAXX 16 phiX174 2815 255 36M * 0 0 TATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCT * +HWI-EAS91_1_306UPAAXX 16 phiX174 1242 255 36M * 0 0 AGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCA * +HWI-EAS91_1_306UPAAXX 16 phiX174 4659 255 1H35M * 0 0 ATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAA * +HWI-EAS91_1_306UPAAXX 0 phiX174 2436 255 36M * 0 0 TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 527 255 35M1H * 0 0 TGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTT * +HWI-EAS91_1_306UPAAXX 16 phiX174 4817 255 36M * 0 0 CCCTAATTTGGGTCGTCGGGTACGCAATCGCCGCCA * +HWI-EAS91_1_306UPAAXX 0 phiX174 2100 255 36M * 0 0 AAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTG * +HWI-EAS91_1_306UPAAXX 16 phiX174 2762 255 36M * 0 0 TCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTA * +HWI-EAS91_1_306UPAAXX 0 phiX174 4955 255 36M * 0 0 TGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 3761 255 36M * 0 0 CGCTACTGCAAAGGATATTTCTAATGTCGTCACTGA * +HWI-EAS91_1_306UPAAXX 16 phiX174 4499 255 36M * 0 0 GAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 4039 255 36M * 0 0 TCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCA * +HWI-EAS91_1_306UPAAXX 16 phiX174 4788 255 36M * 0 0 ATGCGGACACTTCCTACAGGTAGCGTTGACCCTAAT * +HWI-EAS91_1_306UPAAXX 0 phiX174 1002 255 36M * 0 0 TGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4381 255 36M * 0 0 AGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 4256 255 36M * 0 0 GAAGTTAATGGATGAATTGGCACAATGCTACAATGT * +HWI-EAS91_1_306UPAAXX 16 phiX174 10 255 1H35M * 0 0 CGCTTCCATGACGCAGAAGTTAACACTTTCGGATA * +HWI-EAS91_1_306UPAAXX 16 phiX174 1579 255 36M * 0 0 TATGGGTCTGCAAGCTGCTTATGCTAATTTGCATAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 3862 255 36M * 0 0 ATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCT * +HWI-EAS91_1_306UPAAXX 0 phiX174 3278 255 36M * 0 0 TACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCT * +HWI-EAS91_1_306UPAAXX 0 phiX174 349 255 36M * 0 0 TCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAG * +HWI-EAS91_1_306UPAAXX 0 phiX174 4608 255 36M * 0 0 TTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 3808 255 35M1H * 0 0 GTGTGGTTGATATTTTTCATGGTATTGATAAAGCT * +HWI-EAS91_1_306UPAAXX 16 phiX174 4753 255 36M * 0 0 CTAATGGCCGTCTTCATTTCCATGCGGTGCATTTTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 286 255 36M * 0 0 GAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTT * +HWI-EAS91_1_306UPAAXX 0 phiX174 2850 255 36M * 0 0 TACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGT * +HWI-EAS91_1_306UPAAXX 16 phiX174 680 255 1H35M * 0 0 CATGGAAGGCGCTGAATTTACGGAAAACATTATTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 4740 255 36M * 0 0 GAGTATGGTACAGCTAATGGCCGTCTTCATTTCCAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 2467 255 1H35M * 0 0 CCAGCTTCTTCGGCACCTGTTTTACAGACACCTAA * +HWI-EAS91_1_306UPAAXX 0 phiX174 320 255 34M2H * 0 0 TTGACATTTTAAAAGAGCGTGGATTACTATCTGA * +HWI-EAS91_1_306UPAAXX 0 phiX174 1180 255 34M2H * 0 0 TATTGACTCTACTGTAGACATTTTTACTTTTTAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 521 255 36M * 0 0 TGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGA * +HWI-EAS91_1_306UPAAXX 16 phiX174 333 255 36M * 0 0 AGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCA * +HWI-EAS91_1_306UPAAXX 0 phiX174 2756 255 36M * 0 0 ATACCGTCAAGGACTGTGTGACTATTGACGTCCTTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4957 255 36M * 0 0 ATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATA * +HWI-EAS91_1_306UPAAXX 16 phiX174 72 255 36M * 0 0 ATAAAGCAGGAATTACTACTGCTTGTTTACGAATTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 4249 255 36M * 0 0 TTACTGAGAAGTTAATGGATGAATTGGCACAATGCT * +HWI-EAS91_1_306UPAAXX 16 phiX174 2592 255 36M * 0 0 CAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGA * +HWI-EAS91_1_306UPAAXX 16 phiX174 1974 255 36M * 0 0 CGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTT * +HWI-EAS91_1_306UPAAXX 16 phiX174 3540 255 36M * 0 0 AAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAA * +HWI-EAS91_1_306UPAAXX 16 phiX174 4130 255 36M * 0 0 CATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTAT * --- a/test-data/perm_out4.sam +++ b/test-data/perm_out4.sam @@ -1,53 +1,55 @@ -1831_573_1219 16 phiX 2201 255 35M * 0 0 TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGAC -A@EE>NVA7FQZSC8GRJK<EVGC<==39BP\__ NM:i:0 CS:Z:G1211130300300301021212330201121310 CQ:Z:@@@=4/+)5)408?'665>*/5?<61';<3,:,5- -1831_573_1242 0 phiX 647 255 35M * 0 0 TCATCCCGTCAACATTCAAACGGCCTGTCTCATCA [[WSWNGS]US^_\WQW]WL?CEMUIMSTSJ*1U; NM:i:1 CS:Z:T2132003121011302100130302112221121 CQ:Z:>>>::>17=A5?@@=;7A=;2.60>82<8=74+;; -1831_573_1647 16 phiX 1117 255 35M * 0 0 CGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCC 4NIKVOPIBACPWOQ^^WSZ_\Y][Y]]^_[[_^[ NM:i:0 CS:Z:G0222233301013033120132223202022123 CQ:Z:=?@@<@@???;A==@@;9?@?3=;6.4/;6:=/;4 -1831_573_1684 16 phiX 3695 255 35M * 0 0 TAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGC ?\VWTLTTUZVV[_^\Y[_ZWUW]^_XKR[SQJNT NM:i:0 CS:Z:G3310013212312012302121010221231123 CQ:Z:7>1:8<@39@@??9=;@@<>?@@<;<?7>76?9>? -1831_574_109 0 phiX 3728 255 35M * 0 0 GCAGAATCAGCGGTATGGCTCTTCTCATATTGGCG 07651#4817>@65<2:84716=788<1995.7?6 NM:i:1 CS:Z:G3122332123301331032220222133301033 CQ:Z:07651#4817>@65<2:84716=788<1995.7?6 -1831_574_148 16 phiX 2368 255 35M * 0 0 GTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCA ;NEGQTTTJAMH9B@@PHHSQUJML=LPMUMPJGV NM:i:0 CS:Z:T1200113123030012202302312200010231 CQ:Z:<;->3;;3>//>0;;7=,=4-4/+>029<9<624; -1831_574_575 16 phiX 4005 255 35M * 0 0 GAATGTCACGCTGATTATTTTGACTTTGAGCGTAT <JC>=PXK;2BW[T;CXA"&?U\\__WU]^[Z]^U NM:i:1 CS:Z:A3313322100212102033032123311211302 CQ:Z:7?@>=?@>8@@@=@6*%&<='5@<<',0<=4*5/< -1831_574_592 16 phiX 2949 255 35M * 0 0 GGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCAT 2BBLI?LTSPIFFIMD:?MRLECQ][G7DI9=A?I NM:i:0 CS:Z:A3103330110123102223122023103310330 CQ:Z:73-5)19,,<@>4067<2.-864346;9<1/;212 -1831_574_824 16 phiX 3996 255 35M * 0 0 TACCCTTCTGAATGTCACGCTGATTATTTTGACTT ?VRCD\ZK5?ZWJ7D]WP=AVQRHH[J64CUZ__Z NM:i:0 CS:Z:A0212100033032123311211302122020013 CQ:Z:;@@@;;),+@<-<7;<&89??&29?<$2:A<);8? -1831_574_1194 0 phiX 1135 255 35M * 0 0 CGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTC NRXFJ]WXXX^^PP_\\RO\]]SR^_XLRUKC:A6 NM:i:0 CS:Z:C3303101033322220312200222013013312 CQ:Z::5>;,??9@9@?@1@@=@3=@>@4?@@94?75/,6 -1831_574_1591 16 phiX 5117 255 35M * 0 0 GAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCG 9CB??UTRA!7YIJXQUSUEEZWX[WNV^ZY^\XY NM:i:1 CS:Z:C3202101330322130221230222201123202 CQ:Z:==<A><?@78@<=;@&@6>8:?,><&&<7>8(8+9 -1831_574_1624 16 phiX 4057 255 35M * 0 0 CTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAA )5?C6:LSC5DHJA6@FNI54;D?137CB3-3CQ: NM:i:1 CS:Z:C0122200222132200313011102302210332 CQ:Z:#<6.&(,7-+))7..'/;43.)927.(<85&13-) -1831_574_1903 0 phiX 5208 255 35M * 0 0 AAGCTGGGTTACGACGCGACGCCGTTCAACCAGAC TMJT^]XQV__WQY]UUYXUVVV]QNSGOOJOPI/ NM:i:1 CS:Z:A0232100103132133321330310210101221 CQ:Z:<956?@>;7@@@8:@>8><=9>9>@2=71?1:6;/ -1831_575_54 16 phiX 3586 255 35M * 0 0 TTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGC 8ST4/MPK:7HONA7BTVCHY[^YRSVLMSMU_\Z NM:i:1 CS:Z:G3331330322230200102132110132013200 CQ:Z:>=@@68<2;<8;?@<>+9>7,,6972&57:4&9<8 -1831_575_197 16 phiX 4860 255 35M * 0 0 AGCTTGCAAAATACGTGGCCTTATGGTTACAGTAT ,=.<SADLUZH>67?JXRIFRTTVOQZ`RHIRXF8 NM:i:1 CS:Z:A3312113010133020301131330001310032 CQ:Z:,-:?463@A:88?6?437<=.2&1.;@67.4@%2, -1831_575_444 16 phiX 5097 255 35M * 0 0 AAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAAT >XO0/QUSCCY]]LJWZ^[W\ZVGF[^[JIVZ_QM NM:i:1 CS:Z:A3022120112320220100202132332113320 CQ:Z:<2@@;<.=?@<+=:A<<@?<</>@><(<8>4&5;> -1831_575_622 0 phiX 2484 255 35M * 0 0 TGTTTTACAGACACCTAAAGCTACATCGTCAACGT `XY^\_^Z[^ZY[Z[WNQOLO?DOBJB@M>EQ$!+ NM:i:1 CS:Z:T1100031122111023002323113231210111 CQ:Z:@A8B=@@?<@?<>>=?96<497)<4/<':4+;74+ -1831_575_938 16 phiX 1132 255 35M * 0 0 GGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGC 7N@<NSTMKOQVHAONKTXVTUWZXRTWZ^XY_YT NM:i:0 CS:Z:G3103102220022130222233301013033120 CQ:Z:;:@@:?@;=8;>=;;:=<93<4.;<6:2<9;4)87 -1831_575_970 16 phiX 231 255 35M * 0 0 TGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCG 5PXYYNKY^\[VW[\]XY[VUTRY_[Y]_ZW\\\\ NM:i:0 CS:Z:C3201311301023133303023011202220221 CQ:Z:=@=@=;@@><@@:9<:=?;>@=?9>>?@:2===<5 -1831_575_1138 0 phiX 1912 255 35M * 0 0 CGCTAAAGGTGCTTTGACTTATACCGATATTGCTG XLJ7-IKH@IWNTJJSPUKO]UU[UTNQKDQDCJ1 NM:i:1 CS:Z:C3320002011320012120333103233301321 CQ:Z:<=0;%1936+?96?,?5<:2>@6@<:;4>.7;*:1 -1831_575_1180 0 phiX 4168 255 35M * 0 0 AGGGCGTTGAGTTCGATAATGGTGATATGTATGTT J]_RSE@HENVYKKOINRQOV_]VLPSRLHMBJT7 NM:i:0 CS:Z:A2003310122102323303101123331133110 CQ:Z:/<B>5?':/78?;1;55:997@@>94=7<186->7 -1831_575_1302 16 phiX 5201 255 35M * 0 0 ACTTACCAAGCTGGGTTACGACGCGACGCCGTTCA *57==/2(a)B6+-8?,!,.(.A=+*7>2,841LOB6 NM:i:1 CS:Z:T1201303312333123130200123201013021 CQ:Z:&12>/#2'&-2&%'7+$%*#$/1(&&12/$,2,,* -1831_575_1310 16 phiX 1611 255 35M * 0 0 ATACTGACCAAGAACGTGATTACTTCATGCAGCGT ;QC!!DXV[[Z]UEN_YYPAMSVGGXQWQHKSYWQ NM:i:1 CS:Z:A1332131312021303211310220101211133 CQ:Z:6<<>663?99@(@7=11@:@@/7??<@<;>'3-7; -1831_575_1321 0 phiX 2663 255 35M * 0 0 GTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACT 0;B@?@>=A@<A?>@>?6>@5>'4@9?)7@7?/89 NM:i:1 CS:Z:G1001010233200122122022023000203212 CQ:Z:0;B@?@>=A@<A?>@>?6>@5>'4@9?)7@7?/89 -1831_575_1373 16 phiX 4220 255 35M * 0 0 TTCTGACGTTCGTGATGAGTTTGTATCTGTTACTG <M=?PSE>BHTUGKZZZYY]]VU]^[TUWZ]]__` NM:i:0 CS:Z:C1213011223311001221321132013121220 CQ:Z:A@@@>@;=9<@??7@>@:@;@;17?630/7=4,2< -1831_575_1436 0 phiX 3459 255 35M * 0 0 GCTGGCATTCAGTCGGCGACTTCACGCCAGAATAC ;Q\WMKB<NE=OUWRFO[V?=PUXC6LZN77CHQ< NM:i:0 CS:Z:G3210313021212303321202113301220331 CQ:Z:*2@=;39*3<*4<:>52>>9'7:<='0=>1'136< -1831_575_1442 0 phiX 3316 255 35M * 0 0 ATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCT URLSZUTH;RWB;GTWUNS\^ZJP^SGKFMSB?N> NM:i:0 CS:Z:A3132010022331132101132123132020222 CQ:Z:8>58<?7>+1B6-/9<<:5?>A:1@?539.@4/1> -1831_575_1500 16 phiX 4268 255 35M * 0 0 TGAATTGGCACAATGCTACAATGTGCTCCCCCAAC 9V\UBGWPPNT^YUQQQQUQLPRUQQSV^`_^_^P NM:i:0 CS:Z:G1010000223111301132313011130103021 CQ:Z:2?@@?A@?8<6<:985=99999==B3<5<<,7?>9 -1831_575_1535 16 phiX 1224 255 35M * 0 0 GTCACGTTTATGGTGAACAGTGGATTAAGTTCATG <PRXVWQOTQUST^[\WMT^]Z\_`ZX`a_[[\^a NM:i:0 CS:Z:C1312012030320112110211013300131121 CQ:Z:@B=@<@@B?:A@@=>@?68@=?@5?7;:6<<;>5< -1831_576_86 16 phiX 2980 255 35M * 0 0 CCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCC /@:AJ7;AEH712=EJKF>=LHJP?587CK:9AHN NM:i:0 CS:Z:G0320000121033022010011030032211310 CQ:Z:7811)2:*.++5</:3+43924*))/:,6&29)2/ -1831_576_266 16 phiX 279 255 35M * 0 0 TAGATATGAGTCACATTTTGTTCATGGTAGAGATT 6;*<NGC9=TWH2<P=+#.P]IDV]\SUZVW[^_[ NM:i:1 CS:Z:A0322223101312011300311121221333223 CQ:Z:<@@?=;<?7=@>9,>@1$&&89$/:>7'3178%&6 -1831_576_603 16 phiX 1575 255 35M * 0 0 ACATTATGGGTCTGCAAGCTGCTTATGCTAATTTG 8PMKX]PIR\`ZJO]_[HGZ_XOW\Z]LPb\RIS_ NM:i:0 CS:Z:C1003032313302312320131221001330311 CQ:Z:@@46=@C.??<A79@@;-<@@>29B?>55<B7598 -1831_576_655 16 phiX 3291 255 35M * 0 0 CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGA %06ESGLVW^JATXW73V][JCT_]G?Q[_XYa`\ NM:i:1 CS:Z:T2001023130302322122200313123123102 CQ:Z:=@AA9@@<6*>@@5/<@>9'=;>7+@?9>/9;+,% -1831_576_815 0 phiX 5185 255 35M * 0 0 CGGAGTGCTTAATCCAACTTACCAAGCTGGGTTAC NP]^WV]^`^ZZWX^_]][ZWKFQPA?FSTQPKD. NM:i:0 CS:Z:C3022113203032010120310102321001031 CQ:Z:<3>@?9>@?B=>=;>A???=>:25=4.25?6<57. -1831_576_882 0 phiX 5052 255 35M * 0 0 GCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTC PGTVV^YMQ]]VNT]ZWXQ;7LYVPKIRXTTLNU8 NM:i:0 CS:Z:G3230020122320223230022031020110122 CQ:Z:?26?8?@:4>@>96??<<=5'1<>9846=<9<1>8 -1831_576_898 0 phiX 517 255 35M * 0 0 GGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGC \_bTPa`\ZY]WOMW`YYLL]VNS^]SSLES][J. NM:i:0 CS:Z:G0230132312121033222231132231233213 CQ:Z:=@@C2?C>?<>@886B?;?.??87=B<8<15??=. -1831_576_923 0 phiX 1049 255 35M * 0 0 CATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCT LCBEMWHCNQTTNSXUNLTVUKAKV[TMRRURIJ7 NM:i:0 CS:Z:C1322010320202013210121223010123122 CQ:Z:76.51=;.699<96>;;49<;;11;<@59:9=647 -1831_576_1131 16 phiX 4060 255 35M * 0 0 TTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCC <MJBDSMK>BWZI2FPGKEOI<PWVQ?KNN>>SC@ NM:i:1 CS:Z:G0233122200222132200313011102302210 CQ:Z:104@#@/@,4>9?2+?1571@',>=;(759;*92< -1831_576_1289 16 phiX 1898 255 35M * 0 0 ATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTA 0DBK[ONJ9GWSQ@;@CINYOHKU_VQZ_aRNYTX NM:i:0 CS:Z:T3021210023110200323310302013121203 CQ:Z:@9<>1B@@;7@@663==28,5':8<<,.=2>>.50 -1831_576_1367 0 phiX 1838 255 35M * 0 0 GAGCATGGCACTATGTTTACTCTTGCGCTTGTTCG ]^_[Y]_\\[[[X\]]^]WRXZXZZXSROMXVNN7 NM:i:0 CS:Z:G2231310311233110031222013332011023 CQ:Z:??@@<>@@=@<@<=@>@??9:?<=>=<8;59@787 -1831_576_1416 0 phiX 4521 255 35M * 0 0 ATTCAGCGTTTGATGAATGCAATGCGACAGGCTCA 1AYL;>>I[F4JG@CBSURK<KUQB,AZRJCFPW@ NM:i:0 CS:Z:A3021233100123120313103133211203221 CQ:Z:+';?..1.<@'.=+6.5?7<0-?7;(%=>56.98@ -1831_576_1605 0 phiX 5208 255 35M * 0 0 AAGCTGGGTTACGACGCGACGCCGTTCAACCAGAC Q[bb_]NKZYTVW[_XX^]]WTNQSA>BMPKNMB, NM:i:1 CS:Z:A0232100103132133321330310210101221 CQ:Z:6<@C@@>1;@:;<<@@9@???9<3?5-21=4877, -1831_576_1729 16 phiX 5193 255 35M * 0 0 TTAATCCAACTTACCAAGCTGGGTTACGACGCGAC >ZL:FYXSQV]^ZSW^\TU\\[YKM_^][ZZZ^^^ NM:i:0 CS:Z:G1233312313010012320101302101023030 CQ:Z:@?@?<?<@>A?/==?>?7>?@8<?@>99;><+0=> -1831_576_1982 16 phiX 5023 255 35M * 0 0 TTAACAAAAAGTCAGATATGGACCTTGCTGCTAAA @JFRDK\_\MQUU_UQST^ZX^[\XX[Y^LK^^_K NM:i:0 CS:Z:T0032312310201201333221212000011030 CQ:Z:,@@?@,A><@9@=?@9B=8<6@@6@2<A?>.7<+@ -1831_577_133 16 phiX 1713 255 35M * 0 0 TCATGCGCTCTAATCTCTGGGCATCTGGCTATGAT )&/8<NA=EPP;FEI]YY]_VFO]HDXOM[\[]SB NM:i:1 CS:Z:A3213323012231300122223032223331322 CQ:Z:/4@>>?=1?:+>@07@@><>@*<+1@15)96'2$) -1831_577_281 16 phiX 4576 255 35M * 0 0 TTTTTGACACTCTCACGTTGGCTGACGACCGATTA ?XWE?WXSYURPOYWMJ@I[[RQ]VTXW\WR\[FC NM:i:0 CS:Z:T3032301231212301013112222111210000 CQ:Z:7-:B;8@=;>7@>4?=?+659?;5<7?;9@8(>:? -1831_577_322 16 phiX 457 255 35M * 0 0 CTTCTGCCGTTTTGGATTTAACCGAAGATGATTTC /E?@MNMJTZM79LI;A5:H@IIHIFLPEDHQXWU NM:i:1 CS:Z:G2003213220230103303201000130312202 CQ:Z:9=;>4506;255464-<#7+194&2<?65968)7/ -1831_577_362 0 phiX 2152 255 35M * 0 0 ACTTATTCGCCACCATGATTATGACCAGTGTTTCC GS`XY^^[ZWMLTH>LEDHI?,3EQDAQPB5%(@6 NM:i:1 CS:Z:A1203302330110131230331210121110220 CQ:Z:62B?:@?@<?958=,3:,90:&'-99,6<5.($+6 -1831_577_382 16 phiX 4685 255 35M * 0 0 GGGTCGCAAGGCTAATGATTCACACGCCGACTGCT *>C@NMMI2333IUD=>FNE;1=LSE19JHEKMJB NM:i:0 CS:Z:A2312123033111120321303230201332100 CQ:Z:12957/:1))=76(*24;,3+:<.&.&-=1=2/5* -1831_577_488 16 phiX 4947 255 35M * 0 0 TGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGC @SEJPW]VUWXQLSPSOMXXXTVZQKJJSG59EKM NM:i:0 CS:Z:G3200302330322110200323132101120301 CQ:Z::48.,*>6566<?8=<=<2>6;94>;=9>@8924@ -1831_577_545 0 phiX 1710 255 35M * 0 0 TTGTCATGCGCTCTAATCTCTGGGCATCTGGCTAT [YWTWZY\_\OKHP[[WTY\VLDDFLTMBBMPOD- NM:i:0 CS:Z:T0112131333222303222210031322103233 CQ:Z:>><<9?<>?A<481@<@8==@76/61<95.5988- -1831_577_637 0 phiX 4246 255 35M * 0 0 CTGTTACTGAGAAGTTAATGGATGAATTGGCACAA D8?2<WFB@DQC1-<OMOLMTSRM=6?G>,EYN?, NM:i:1 CS:Z:C2113312122202103031023120301031110 CQ:Z:8-,4#>:-6+:8,&(5;3=0>7=68&1/9&'?;4, -1831_577_692 0 phiX 3904 255 35M * 0 0 TGTCTAGGAAATAACCGTCAGGATTGACACCCTCC aMK^^aIG`_^JJ_]]JI[Z]FCX[[XXTU[UKP< NM:i:0 CS:Z:T1122320200330103121202301211100220 CQ:Z:@B,@?@B(@A?@+@@>@+?=>@'=<@<=<9=?75< +1831_573_1219 16 phiX174 2201 255 35M * 0 0 TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGAC -A@EE>NVA7FQZSC8GRJK<EVGC<==39BP\__ NM:i:0 CS:Z:G1211130300300301021212330201121310 CQ:Z:@@@=4/+)5)408?'665>*/5?<61';<3,:,5- +1831_573_1242 0 phiX174 647 255 35M * 0 0 TCATCCCGTCAACATTCAAACGGCCTGTCTCATCA [[WSWNGS]US^_\WQW]WL?CEMUIMSTSJ*1U; NM:i:1 CS:Z:T2132003121011302100130302112221121 CQ:Z:>>>::>17=A5?@@=;7A=;2.60>82<8=74+;; +1831_573_1647 16 phiX174 1117 255 35M * 0 0 CGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCC 4NIKVOPIBACPWOQ^^WSZ_\Y][Y]]^_[[_^[ NM:i:0 CS:Z:G0222233301013033120132223202022123 CQ:Z:=?@@<@@???;A==@@;9?@?3=;6.4/;6:=/;4 +1831_573_1684 16 phiX174 3695 255 35M * 0 0 TAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGC ?\VWTLTTUZVV[_^\Y[_ZWUW]^_XKR[SQJNT NM:i:0 CS:Z:G3310013212312012302121010221231123 CQ:Z:7>1:8<@39@@??9=;@@<>?@@<;<?7>76?9>? +1831_574_109 0 phiX174 3728 255 35M * 0 0 GCAGAATCAGCGGTATGGCTCTTCTCATATTGGCG 07651#4817>@65<2:84716=788<1995.7?6 NM:i:1 CS:Z:G3122332123301331032220222133301033 CQ:Z:07651#4817>@65<2:84716=788<1995.7?6 +1831_574_148 16 phiX174 2368 255 35M * 0 0 GTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCA ;NEGQTTTJAMH9B@@PHHSQUJML=LPMUMPJGV NM:i:0 CS:Z:T1200113123030012202302312200010231 CQ:Z:<;->3;;3>//>0;;7=,=4-4/+>029<9<624; +1831_574_575 16 phiX174 4005 255 35M * 0 0 GAATGTCACGCTGATTATTTTGACTTTGAGCGTAT <JC>=PXK;2BW[T;CXA"&?U\\__WU]^[Z]^U NM:i:1 CS:Z:A3313322100212102033032123311211302 CQ:Z:7?@>=?@>8@@@=@6*%&<='5@<<',0<=4*5/< +1831_574_592 16 phiX174 2949 255 35M * 0 0 GGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCAT 2BBLI?LTSPIFFIMD:?MRLECQ][G7DI9=A?I NM:i:0 CS:Z:A3103330110123102223122023103310330 CQ:Z:73-5)19,,<@>4067<2.-864346;9<1/;212 +1831_574_824 16 phiX174 3996 255 35M * 0 0 TACCCTTCTGAATGTCACGCTGATTATTTTGACTT ?VRCD\ZK5?ZWJ7D]WP=AVQRHH[J64CUZ__Z NM:i:0 CS:Z:A0212100033032123311211302122020013 CQ:Z:;@@@;;),+@<-<7;<&89??&29?<$2:A<);8? +1831_574_1194 0 phiX174 1135 255 35M * 0 0 CGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTC NRXFJ]WXXX^^PP_\\RO\]]SR^_XLRUKC:A6 NM:i:0 CS:Z:C3303101033322220312200222013013312 CQ:Z::5>;,??9@9@?@1@@=@3=@>@4?@@94?75/,6 +1831_574_1591 16 phiX174 5117 255 35M * 0 0 GAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCG 9CB??UTRA!7YIJXQUSUEEZWX[WNV^ZY^\XY NM:i:1 CS:Z:C3202101330322130221230222201123202 CQ:Z:==<A><?@78@<=;@&@6>8:?,><&&<7>8(8+9 +1831_574_1624 16 phiX174 4057 255 35M * 0 0 CTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAA )5?C6:LSC5DHJA6@FNI54;D?137CB3-3CQ: NM:i:1 CS:Z:C0122200222132200313011102302210332 CQ:Z:#<6.&(,7-+))7..'/;43.)927.(<85&13-) +1831_574_1903 0 phiX174 5208 255 35M * 0 0 AAGCTGGGTTACGACGCGACGCCGTTCAACCAGAC TMJT^]XQV__WQY]UUYXUVVV]QNSGOOJOPI/ NM:i:1 CS:Z:A0232100103132133321330310210101221 CQ:Z:<956?@>;7@@@8:@>8><=9>9>@2=71?1:6;/ +1831_575_54 16 phiX174 3586 255 35M * 0 0 TTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGC 8ST4/MPK:7HONA7BTVCHY[^YRSVLMSMU_\Z NM:i:1 CS:Z:G3331330322230200102132110132013200 CQ:Z:>=@@68<2;<8;?@<>+9>7,,6972&57:4&9<8 +1831_575_197 16 phiX174 4860 255 35M * 0 0 AGCTTGCAAAATACGTGGCCTTATGGTTACAGTAT ,=.<SADLUZH>67?JXRIFRTTVOQZ`RHIRXF8 NM:i:1 CS:Z:A3312113010133020301131330001310032 CQ:Z:,-:?463@A:88?6?437<=.2&1.;@67.4@%2, +1831_575_444 16 phiX174 5097 255 35M * 0 0 AAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAAT >XO0/QUSCCY]]LJWZ^[W\ZVGF[^[JIVZ_QM NM:i:1 CS:Z:A3022120112320220100202132332113320 CQ:Z:<2@@;<.=?@<+=:A<<@?<</>@><(<8>4&5;> +1831_575_622 0 phiX174 2484 255 35M * 0 0 TGTTTTACAGACACCTAAAGCTACATCGTCAACGT `XY^\_^Z[^ZY[Z[WNQOLO?DOBJB@M>EQ$!+ NM:i:1 CS:Z:T1100031122111023002323113231210111 CQ:Z:@A8B=@@?<@?<>>=?96<497)<4/<':4+;74+ +1831_575_938 16 phiX174 1132 255 35M * 0 0 GGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGC 7N@<NSTMKOQVHAONKTXVTUWZXRTWZ^XY_YT NM:i:0 CS:Z:G3103102220022130222233301013033120 CQ:Z:;:@@:?@;=8;>=;;:=<93<4.;<6:2<9;4)87 +1831_575_970 16 phiX174 231 255 35M * 0 0 TGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCG 5PXYYNKY^\[VW[\]XY[VUTRY_[Y]_ZW\\\\ NM:i:0 CS:Z:C3201311301023133303023011202220221 CQ:Z:=@=@=;@@><@@:9<:=?;>@=?9>>?@:2===<5 +1831_575_1138 0 phiX174 1912 255 35M * 0 0 CGCTAAAGGTGCTTTGACTTATACCGATATTGCTG XLJ7-IKH@IWNTJJSPUKO]UU[UTNQKDQDCJ1 NM:i:1 CS:Z:C3320002011320012120333103233301321 CQ:Z:<=0;%1936+?96?,?5<:2>@6@<:;4>.7;*:1 +1831_575_1180 0 phiX174 4168 255 35M * 0 0 AGGGCGTTGAGTTCGATAATGGTGATATGTATGTT J]_RSE@HENVYKKOINRQOV_]VLPSRLHMBJT7 NM:i:0 CS:Z:A2003310122102323303101123331133110 CQ:Z:/<B>5?':/78?;1;55:997@@>94=7<186->7 +1831_575_1302 16 phiX174 5201 255 35M * 0 0 ACTTACCAAGCTGGGTTACGACGCGACGCCGTTCA *57==/2(a)B6+-8?,!,.(.A=+*7>2,841LOB6 NM:i:1 CS:Z:T1201303312333123130200123201013021 CQ:Z:&12>/#2'&-2&%'7+$%*#$/1(&&12/$,2,,* +1831_575_1310 16 phiX174 1611 255 35M * 0 0 ATACTGACCAAGAACGTGATTACTTCATGCAGCGT ;QC!!DXV[[Z]UEN_YYPAMSVGGXQWQHKSYWQ NM:i:1 CS:Z:A1332131312021303211310220101211133 CQ:Z:6<<>663?99@(@7=11@:@@/7??<@<;>'3-7; +1831_575_1321 0 phiX174 2663 255 35M * 0 0 GTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACT 0;B@?@>=A@<A?>@>?6>@5>'4@9?)7@7?/89 NM:i:1 CS:Z:G1001010233200122122022023000203212 CQ:Z:0;B@?@>=A@<A?>@>?6>@5>'4@9?)7@7?/89 +1831_575_1373 16 phiX174 4220 255 35M * 0 0 TTCTGACGTTCGTGATGAGTTTGTATCTGTTACTG <M=?PSE>BHTUGKZZZYY]]VU]^[TUWZ]]__` NM:i:0 CS:Z:C1213011223311001221321132013121220 CQ:Z:A@@@>@;=9<@??7@>@:@;@;17?630/7=4,2< +1831_575_1436 0 phiX174 3459 255 35M * 0 0 GCTGGCATTCAGTCGGCGACTTCACGCCAGAATAC ;Q\WMKB<NE=OUWRFO[V?=PUXC6LZN77CHQ< NM:i:0 CS:Z:G3210313021212303321202113301220331 CQ:Z:*2@=;39*3<*4<:>52>>9'7:<='0=>1'136< +1831_575_1442 0 phiX174 3316 255 35M * 0 0 ATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCT URLSZUTH;RWB;GTWUNS\^ZJP^SGKFMSB?N> NM:i:0 CS:Z:A3132010022331132101132123132020222 CQ:Z:8>58<?7>+1B6-/9<<:5?>A:1@?539.@4/1> +1831_575_1500 16 phiX174 4268 255 35M * 0 0 TGAATTGGCACAATGCTACAATGTGCTCCCCCAAC 9V\UBGWPPNT^YUQQQQUQLPRUQQSV^`_^_^P NM:i:0 CS:Z:G1010000223111301132313011130103021 CQ:Z:2?@@?A@?8<6<:985=99999==B3<5<<,7?>9 +1831_575_1535 16 phiX174 1224 255 35M * 0 0 GTCACGTTTATGGTGAACAGTGGATTAAGTTCATG <PRXVWQOTQUST^[\WMT^]Z\_`ZX`a_[[\^a NM:i:0 CS:Z:C1312012030320112110211013300131121 CQ:Z:@B=@<@@B?:A@@=>@?68@=?@5?7;:6<<;>5< +1831_576_86 16 phiX174 2980 255 35M * 0 0 CCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCC /@:AJ7;AEH712=EJKF>=LHJP?587CK:9AHN NM:i:0 CS:Z:G0320000121033022010011030032211310 CQ:Z:7811)2:*.++5</:3+43924*))/:,6&29)2/ +1831_576_266 16 phiX174 279 255 35M * 0 0 TAGATATGAGTCACATTTTGTTCATGGTAGAGATT 6;*<NGC9=TWH2<P=+#.P]IDV]\SUZVW[^_[ NM:i:1 CS:Z:A0322223101312011300311121221333223 CQ:Z:<@@?=;<?7=@>9,>@1$&&89$/:>7'3178%&6 +1831_576_327 16 phiX174 4516 255 35M * 0 0 TTACTATTCAGCGTTTGATGAATGCAATGCGACAG =RQYVTNGR]_RNXYVYROYZ][Y\^[VZ_UU^^[ NM:i:0 CS:Z:C2112331301313021321001332120332130 CQ:Z:<@?@6@@;<@?><@>==3@:==<3@@>53<9><6= +1831_576_519 16 phiX174 1624 255 35M * 0 0 ACGTGATTACTTCATGCAGCGTTACCGTGATGTTA 7ACFAB?LF;BBIVNHOXTOMLYTD@O]VOTQIPY NM:i:0 CS:Z:T3011321130130133213131202130321131 CQ:Z:==46<97@>2/6?;2<4A881>9121+<1/4.9+7 +1831_576_603 16 phiX174 1575 255 35M * 0 0 ACATTATGGGTCTGCAAGCTGCTTATGCTAATTTG 8PMKX]PIR\`ZJO]_[HGZ_XOW\Z]LPb\RIS_ NM:i:0 CS:Z:C1003032313302312320131221001330311 CQ:Z:@@46=@C.??<A79@@;-<@@>29B?>55<B7598 +1831_576_655 16 phiX174 3291 255 35M * 0 0 CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGA %06ESGLVW^JATXW73V][JCT_]G?Q[_XYa`\ NM:i:1 CS:Z:T2001023130302322122200313123123102 CQ:Z:=@AA9@@<6*>@@5/<@>9'=;>7+@?9>/9;+,% +1831_576_815 0 phiX174 5185 255 35M * 0 0 CGGAGTGCTTAATCCAACTTACCAAGCTGGGTTAC NP]^WV]^`^ZZWX^_]][ZWKFQPA?FSTQPKD. NM:i:0 CS:Z:C3022113203032010120310102321001031 CQ:Z:<3>@?9>@?B=>=;>A???=>:25=4.25?6<57. +1831_576_882 0 phiX174 5052 255 35M * 0 0 GCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTC PGTVV^YMQ]]VNT]ZWXQ;7LYVPKIRXTTLNU8 NM:i:0 CS:Z:G3230020122320223230022031020110122 CQ:Z:?26?8?@:4>@>96??<<=5'1<>9846=<9<1>8 +1831_576_898 0 phiX174 517 255 35M * 0 0 GGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGC \_bTPa`\ZY]WOMW`YYLL]VNS^]SSLES][J. NM:i:0 CS:Z:G0230132312121033222231132231233213 CQ:Z:=@@C2?C>?<>@886B?;?.??87=B<8<15??=. +1831_576_923 0 phiX174 1049 255 35M * 0 0 CATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCT LCBEMWHCNQTTNSXUNLTVUKAKV[TMRRURIJ7 NM:i:0 CS:Z:C1322010320202013210121223010123122 CQ:Z:76.51=;.699<96>;;49<;;11;<@59:9=647 +1831_576_1131 16 phiX174 4060 255 35M * 0 0 TTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCC <MJBDSMK>BWZI2FPGKEOI<PWVQ?KNN>>SC@ NM:i:1 CS:Z:G0233122200222132200313011102302210 CQ:Z:104@#@/@,4>9?2+?1571@',>=;(759;*92< +1831_576_1289 16 phiX174 1898 255 35M * 0 0 ATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTA 0DBK[ONJ9GWSQ@;@CINYOHKU_VQZ_aRNYTX NM:i:0 CS:Z:T3021210023110200323310302013121203 CQ:Z:@9<>1B@@;7@@663==28,5':8<<,.=2>>.50 +1831_576_1367 0 phiX174 1838 255 35M * 0 0 GAGCATGGCACTATGTTTACTCTTGCGCTTGTTCG ]^_[Y]_\\[[[X\]]^]WRXZXZZXSROMXVNN7 NM:i:0 CS:Z:G2231310311233110031222013332011023 CQ:Z:??@@<>@@=@<@<=@>@??9:?<=>=<8;59@787 +1831_576_1416 0 phiX174 4521 255 35M * 0 0 ATTCAGCGTTTGATGAATGCAATGCGACAGGCTCA 1AYL;>>I[F4JG@CBSURK<KUQB,AZRJCFPW@ NM:i:0 CS:Z:A3021233100123120313103133211203221 CQ:Z:+';?..1.<@'.=+6.5?7<0-?7;(%=>56.98@ +1831_576_1605 0 phiX174 5208 255 35M * 0 0 AAGCTGGGTTACGACGCGACGCCGTTCAACCAGAC Q[bb_]NKZYTVW[_XX^]]WTNQSA>BMPKNMB, NM:i:1 CS:Z:A0232100103132133321330310210101221 CQ:Z:6<@C@@>1;@:;<<@@9@???9<3?5-21=4877, +1831_576_1729 16 phiX174 5193 255 35M * 0 0 TTAATCCAACTTACCAAGCTGGGTTACGACGCGAC >ZL:FYXSQV]^ZSW^\TU\\[YKM_^][ZZZ^^^ NM:i:0 CS:Z:G1233312313010012320101302101023030 CQ:Z:@?@?<?<@>A?/==?>?7>?@8<?@>99;><+0=> +1831_576_1982 16 phiX174 5023 255 35M * 0 0 TTAACAAAAAGTCAGATATGGACCTTGCTGCTAAA @JFRDK\_\MQUU_UQST^ZX^[\XX[Y^LK^^_K NM:i:0 CS:Z:T0032312310201201333221212000011030 CQ:Z:,@@?@,A><@9@=?@9B=8<6@@6@2<A?>.7<+@ +1831_577_133 16 phiX174 1713 255 35M * 0 0 TCATGCGCTCTAATCTCTGGGCATCTGGCTATGAT )&/8<NA=EPP;FEI]YY]_VFO]HDXOM[\[]SB NM:i:1 CS:Z:A3213323012231300122223032223331322 CQ:Z:/4@>>?=1?:+>@07@@><>@*<+1@15)96'2$) +1831_577_281 16 phiX174 4576 255 35M * 0 0 TTTTTGACACTCTCACGTTGGCTGACGACCGATTA ?XWE?WXSYURPOYWMJ@I[[RQ]VTXW\WR\[FC NM:i:0 CS:Z:T3032301231212301013112222111210000 CQ:Z:7-:B;8@=;>7@>4?=?+659?;5<7?;9@8(>:? +1831_577_322 16 phiX174 457 255 35M * 0 0 CTTCTGCCGTTTTGGATTTAACCGAAGATGATTTC /E?@MNMJTZM79LI;A5:H@IIHIFLPEDHQXWU NM:i:1 CS:Z:G2003213220230103303201000130312202 CQ:Z:9=;>4506;255464-<#7+194&2<?65968)7/ +1831_577_362 0 phiX174 2152 255 35M * 0 0 ACTTATTCGCCACCATGATTATGACCAGTGTTTCC GS`XY^^[ZWMLTH>LEDHI?,3EQDAQPB5%(@6 NM:i:1 CS:Z:A1203302330110131230331210121110220 CQ:Z:62B?:@?@<?958=,3:,90:&'-99,6<5.($+6 +1831_577_382 16 phiX174 4685 255 35M * 0 0 GGGTCGCAAGGCTAATGATTCACACGCCGACTGCT *>C@NMMI2333IUD=>FNE;1=LSE19JHEKMJB NM:i:0 CS:Z:A2312123033111120321303230201332100 CQ:Z:12957/:1))=76(*24;,3+:<.&.&-=1=2/5* +1831_577_488 16 phiX174 4947 255 35M * 0 0 TGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGC @SEJPW]VUWXQLSPSOMXXXTVZQKJJSG59EKM NM:i:0 CS:Z:G3200302330322110200323132101120301 CQ:Z::48.,*>6566<?8=<=<2>6;94>;=9>@8924@ +1831_577_545 0 phiX174 1710 255 35M * 0 0 TTGTCATGCGCTCTAATCTCTGGGCATCTGGCTAT [YWTWZY\_\OKHP[[WTY\VLDDFLTMBBMPOD- NM:i:0 CS:Z:T0112131333222303222210031322103233 CQ:Z:>><<9?<>?A<481@<@8==@76/61<95.5988- +1831_577_637 0 phiX174 4246 255 35M * 0 0 CTGTTACTGAGAAGTTAATGGATGAATTGGCACAA D8?2<WFB@DQC1-<OMOLMTSRM=6?G>,EYN?, NM:i:1 CS:Z:C2113312122202103031023120301031110 CQ:Z:8-,4#>:-6+:8,&(5;3=0>7=68&1/9&'?;4, +1831_577_692 0 phiX174 3904 255 35M * 0 0 TGTCTAGGAAATAACCGTCAGGATTGACACCCTCC aMK^^aIG`_^JJ_]]JI[Z]FCX[[XXTU[UKP< NM:i:0 CS:Z:T1122320200330103121202301211100220 CQ:Z:@B,@?@B(@A?@+@@>@+?=>@'=<@<=<9=?75< --- a/tool-data/bowtie_indices.loc.sample +++ b/tool-data/bowtie_indices.loc.sample @@ -1,29 +1,37 @@ #This is a sample file distributed with Galaxy that enables tools -#to use a directory of Bowtie indexed sequences data files. You will need -#to create these data files and then create a bowtie_indices.loc file -#similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The bowtie_indices.loc -#file has this format (white space characters are TAB characters): +#to use a directory of Bowtie indexed sequences data files. You will +#need to create these data files and then create a bowtie_indices.loc +#file similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The bowtie_indices.loc +#file has this format (longer white space characters are TAB characters): # -#<build><file_base> +#<unique_build_id><dbkey><display_name><file_base_path> # #So, for example, if you had hg18 indexed stored in #/depot/data2/galaxy/bowtie/hg18/, #then the bowtie_indices.loc entry would look like this: # -#hg18 /depot/data2/galaxy/bowtie/hg18/hg18 +#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18 # #and your /depot/data2/galaxy/bowtie/hg18/ directory #would contain hg18.*.ebwt files: # #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt -#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 gh18.3.ebwt +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt #...etc... # -#Your bowtie_indices.loc file should include an entry per line for -#each index set you have stored. The "file" in the path does not actually -#exist, but it is the prefix for the actual index files. For example: +#Your bowtie_indices.loc file should include an entry per line for each +#index set you have stored. The "file" in the path does not actually +#exist, but it is the prefix for the actual index files. For example: # -#hg18 /depot/data2/galaxy/bowtie/hg18/hg18 -#hg19 /depot/data2/galaxy/bowtie/hg19/hg19 +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon +#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full +#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 +#...etc... +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. That is why the +#hg19 entry above looks odd. New genomes can be better-looking. +# --- a/test-data/bwa_wrapper_out3.sam +++ b/test-data/bwa_wrapper_out3.sam @@ -1,60 +1,60 @@ -seq1 113 phiX 340 37 18M = 322 -18 GGATTACTATCTGAGTCC II9(.+5$IIIIIII#II XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq1 177 phiX 322 25 18M = 340 18 GATATTTTAAAGGAGCGT B&&I13A$G$*%$IIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A6 -seq10 129 phiX 4168 37 18M = 4149 -19 AGGGCGTTGAGTTCGATA IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq10 65 phiX 4149 25 18M = 4168 19 ATTCTTTCTTTTCGTATC IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:5G11G0 -seq11 129 phiX 4091 37 18M = 4072 -19 ATCCCCAATGCTTGGCTT IIIII$%*$G$A31I&&B XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq11 65 phiX 4072 37 18M = 4091 19 GCATTTCTACTCCTTCTC II#IIIIIII$5+.(9II XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:12T5 -seq12 129 phiX 5365 25 18M = 5349 -16 GGATTGGCGTTTCCAACC IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:0T9A7 -seq12 65 phiX 5349 37 18M = 5365 16 CGCGCTTCGATAAAAATG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq13 129 phiX 4093 25 18M = 4074 -19 CCCCAATCCTTGCCTTCC IIIAAIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:7G4G5 -seq13 65 phiX 4074 37 18M = 4093 19 ATTTCTACTCTTTCTCAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:25 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:17A0 -seq14 129 phiX 4016 37 3M1D15M = 3998 -18 TGATATTTTGACTTTGAG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:3^T15 -seq14 65 phiX 3998 37 18M = 4016 18 CCCTTTTGAATGTCACGC IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:5C12 -seq15 129 phiX 5216 37 5M2I11M = 5198 -18 TTACGAAACGCGACGCCG IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:1 XG:i:2 MD:Z:16 -seq15 65 phiX 5198 37 18M = 5216 18 CCAACTTACCAAGGTGGG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:13C4 -seq16 129 phiX 2897 37 18M = 2880 -17 TTATTTTTCTCCAGCCAC IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6G11 -seq16 65 phiX 2880 37 10M1I7M = 2897 17 TCAGGGTATTAAAAGAGA IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:5T11 -seq17 129 phiX 3053 25 18M = 3034 -19 AAACAATACTTTAGGCAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:0T9G7 -seq17 65 phiX 3034 37 18M = 3053 19 GTGATGTGCTTGCTACCG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq18 133 phiX 4088 0 * = 4088 0 CCGTTCCATAAGCAGATG IIIIIIIIIIIIIIIIII -seq18 73 phiX 4088 37 18M = 4088 0 TCAATCCCCCATGCTTGG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:9A8 -seq19 129 phiX 3324 37 18M = 3304 -20 GAGCGTCCTGGTGCTGAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6G11 -seq19 65 phiX 3304 37 18M = 3324 20 TTCCTGCGCTTAATGCTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6A11 -seq2 129 phiX 159 37 18M = 141 -18 CAGCTCGAGAAGCTCTTA IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq2 65 phiX 141 37 18M = 159 18 ATTCGACCTATCCTTGCG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq20 129 phiX 1100 37 18M = 1082 -18 ACTCCGGTTATCGCTGGC IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq20 65 phiX 1082 37 18M = 1100 18 CTTATTACCATTTCAACT IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq21 129 phiX 1363 37 18M = 1344 -19 TAAGCATTTGGTTCAGGG IIIII$%*$G$A31I&&B XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:10T7 -seq21 65 phiX 1344 37 18M = 1363 19 CTGATACCAATAAAACCC II#IIIIIII$5+.(9II XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:15T2 -seq22 137 phiX 5215 37 18M = 5215 0 GTTACGACGCGACGCCGT IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq22 69 phiX 5215 0 * = 5215 0 AATCAAACTTACCAAGGG IIIIIIIIIIIIIIIIII -seq23 129 phiX 4308 25 18M = 4289 -19 TTTAATAACCCTATAGAC IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:0A8A8 -seq23 65 phiX 4289 37 18M = 4308 19 TGTGCTTCCCCAACTTGA IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:25 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6C11 -seq24 129 phiX 4101 37 18M = 4084 -17 CTTGGCTTCCCTAAGCAG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:10A7 -seq24 65 phiX 4084 37 18M = 4101 17 TTTCTCAATCCCCAATGC IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq25 129 phiX 537 37 18M = 520 -17 CGTGCTCGTTGCTGCGTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:9C8 -seq25 65 phiX 520 37 18M = 537 17 TTGCTACTGACCGCTCTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:17C0 -seq26 129 phiX 1994 37 18M = 1976 -18 AAGGATGTTTTCCGTTCT IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq26 65 phiX 1976 37 18M = 1994 18 CCGCGTGAAATTTCTATG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq27 129 phiX 2614 37 3M1D15M = 2598 -16 TGTTTGGTGCTGATATTG IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:1C1^G15 -seq27 65 phiX 2598 37 18M = 2614 16 CGCTAATCAAGTTGTTTC IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:9G8 -seq28 129 phiX 2906 37 18M = 2890 -16 TCCAGCCACTAAAGTGAG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:25 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:10T7 -seq28 65 phiX 2890 25 18M = 2906 16 AAAGAGATTATTTGTCGG IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:16T0C0 -seq29 133 phiX 5339 0 * = 5339 0 GATAATGATTGGGGTATC IIIIIIIIIIIIIIIIII -seq29 73 phiX 5339 37 18M = 5339 0 CAAATTAATGCGCGCTTC IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6T11 -seq3 129 phiX 523 37 18M = 505 -18 CTACTGACCGCTCTCGTG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq3 65 phiX 505 37 18M = 523 18 GTAACAAAGTTTGGATTG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq30 129 phiX 4108 37 18M = 4091 -17 ACCATAAGCAGATGGATA IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:0T17 -seq30 65 phiX 4091 37 18M = 4108 17 ATCCCCTATGCTTGGCTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6A11 -seq4 137 phiX 945 37 18M = 945 0 TAGGTGGTCAACCATTTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:12A5 -seq4 69 phiX 945 0 * = 945 0 AGCCGCTCGTCTTTTATG IIIIIIIIIIIIIIIIII -seq5 129 phiX 5003 37 18M = 4985 -18 TTTCTATGTGGCTTAATA IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:13A4 -seq5 65 phiX 4985 37 18M = 5003 18 CAGTTATATGGCTTTTGG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:13G4 -seq6 129 phiX 944 37 18M = 925 -19 GTAGGTGGTCAACAATTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq6 65 phiX 925 37 11M1D7M = 944 19 AGGCGCTCGTCTTGGTAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:11^T7 -seq7 129 phiX 960 37 18M = 943 -17 TTTAATTGCAGGGGCTTC IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq7 65 phiX 943 25 18M = 960 17 TGTAGGTGGTCAACCAAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:14A1T1 -seq8 137 phiX 1715 37 18M = 1715 0 ATGCGCTCTATTCTCTGG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:10A7 -seq8 69 phiX 1715 0 * = 1715 0 ACACCCGTCCTTTACGTC IIIIIIIIIIIIIIIIII -seq9 129 phiX 2613 37 18M = 2596 -17 TTCTGTTGGTGCTGATAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq9 65 phiX 2596 37 18M = 2613 17 GCCGCTATTCAGGTTGTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:7A10 +seq1 113 phiX174 340 37 18M = 322 -18 GGATTACTATCTGAGTCC II9(.+5$IIIIIII#II XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq1 177 phiX174 322 25 18M = 340 18 GATATTTTAAAGGAGCGT B&&I13A$G$*%$IIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A6 +seq10 129 phiX174 4168 37 18M = 4149 -19 AGGGCGTTGAGTTCGATA IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq10 65 phiX174 4149 25 18M = 4168 19 ATTCTTTCTTTTCGTATC IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:5G11G0 +seq11 129 phiX174 4091 37 18M = 4072 -19 ATCCCCAATGCTTGGCTT IIIII$%*$G$A31I&&B XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq11 65 phiX174 4072 37 18M = 4091 19 GCATTTCTACTCCTTCTC II#IIIIIII$5+.(9II XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:12T5 +seq12 129 phiX174 5365 25 18M = 5349 -16 GGATTGGCGTTTCCAACC IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:0T9A7 +seq12 65 phiX174 5349 37 18M = 5365 16 CGCGCTTCGATAAAAATG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq13 129 phiX174 4093 25 18M = 4074 -19 CCCCAATCCTTGCCTTCC IIIAAIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:7G4G5 +seq13 65 phiX174 4074 37 18M = 4093 19 ATTTCTACTCTTTCTCAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:25 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:17A0 +seq14 129 phiX174 4016 37 3M1D15M = 3998 -18 TGATATTTTGACTTTGAG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:3^T15 +seq14 65 phiX174 3998 37 18M = 4016 18 CCCTTTTGAATGTCACGC IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:5C12 +seq15 129 phiX174 5216 37 5M2I11M = 5198 -18 TTACGAAACGCGACGCCG IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:1 XG:i:2 MD:Z:16 +seq15 65 phiX174 5198 37 18M = 5216 18 CCAACTTACCAAGGTGGG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:13C4 +seq16 129 phiX174 2897 37 18M = 2880 -17 TTATTTTTCTCCAGCCAC IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6G11 +seq16 65 phiX174 2880 37 10M1I7M = 2897 17 TCAGGGTATTAAAAGAGA IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:5T11 +seq17 129 phiX174 3053 25 18M = 3034 -19 AAACAATACTTTAGGCAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:0T9G7 +seq17 65 phiX174 3034 37 18M = 3053 19 GTGATGTGCTTGCTACCG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq18 133 phiX174 4088 0 * = 4088 0 CCGTTCCATAAGCAGATG IIIIIIIIIIIIIIIIII +seq18 73 phiX174 4088 37 18M = 4088 0 TCAATCCCCCATGCTTGG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:9A8 +seq19 129 phiX174 3324 37 18M = 3304 -20 GAGCGTCCTGGTGCTGAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6G11 +seq19 65 phiX174 3304 37 18M = 3324 20 TTCCTGCGCTTAATGCTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6A11 +seq2 129 phiX174 159 37 18M = 141 -18 CAGCTCGAGAAGCTCTTA IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq2 65 phiX174 141 37 18M = 159 18 ATTCGACCTATCCTTGCG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq20 129 phiX174 1100 37 18M = 1082 -18 ACTCCGGTTATCGCTGGC IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq20 65 phiX174 1082 37 18M = 1100 18 CTTATTACCATTTCAACT IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq21 129 phiX174 1363 37 18M = 1344 -19 TAAGCATTTGGTTCAGGG IIIII$%*$G$A31I&&B XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:10T7 +seq21 65 phiX174 1344 37 18M = 1363 19 CTGATACCAATAAAACCC II#IIIIIII$5+.(9II XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:15T2 +seq22 137 phiX174 5215 37 18M = 5215 0 GTTACGACGCGACGCCGT IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq22 69 phiX174 5215 0 * = 5215 0 AATCAAACTTACCAAGGG IIIIIIIIIIIIIIIIII +seq23 129 phiX174 4308 25 18M = 4289 -19 TTTAATAACCCTATAGAC IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:0A8A8 +seq23 65 phiX174 4289 37 18M = 4308 19 TGTGCTTCCCCAACTTGA IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:25 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6C11 +seq24 129 phiX174 4101 37 18M = 4084 -17 CTTGGCTTCCCTAAGCAG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:10A7 +seq24 65 phiX174 4084 37 18M = 4101 17 TTTCTCAATCCCCAATGC IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq25 129 phiX174 537 37 18M = 520 -17 CGTGCTCGTTGCTGCGTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:9C8 +seq25 65 phiX174 520 37 18M = 537 17 TTGCTACTGACCGCTCTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:17C0 +seq26 129 phiX174 1994 37 18M = 1976 -18 AAGGATGTTTTCCGTTCT IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq26 65 phiX174 1976 37 18M = 1994 18 CCGCGTGAAATTTCTATG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq27 129 phiX174 2614 37 3M1D15M = 2598 -16 TGTTTGGTGCTGATATTG IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:1C1^G15 +seq27 65 phiX174 2598 37 18M = 2614 16 CGCTAATCAAGTTGTTTC IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:9G8 +seq28 129 phiX174 2906 37 18M = 2890 -16 TCCAGCCACTAAAGTGAG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:25 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:10T7 +seq28 65 phiX174 2890 25 18M = 2906 16 AAAGAGATTATTTGTCGG IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:16T0C0 +seq29 133 phiX174 5339 0 * = 5339 0 GATAATGATTGGGGTATC IIIIIIIIIIIIIIIIII +seq29 73 phiX174 5339 37 18M = 5339 0 CAAATTAATGCGCGCTTC IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6T11 +seq3 129 phiX174 523 37 18M = 505 -18 CTACTGACCGCTCTCGTG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq3 65 phiX174 505 37 18M = 523 18 GTAACAAAGTTTGGATTG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq30 129 phiX174 4108 37 18M = 4091 -17 ACCATAAGCAGATGGATA IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:0T17 +seq30 65 phiX174 4091 37 18M = 4108 17 ATCCCCTATGCTTGGCTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6A11 +seq4 137 phiX174 945 37 18M = 945 0 TAGGTGGTCAACCATTTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:12A5 +seq4 69 phiX174 945 0 * = 945 0 AGCCGCTCGTCTTTTATG IIIIIIIIIIIIIIIIII +seq5 129 phiX174 5003 37 18M = 4985 -18 TTTCTATGTGGCTTAATA IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:13A4 +seq5 65 phiX174 4985 37 18M = 5003 18 CAGTTATATGGCTTTTGG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:13G4 +seq6 129 phiX174 944 37 18M = 925 -19 GTAGGTGGTCAACAATTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq6 65 phiX174 925 37 11M1D7M = 944 19 AGGCGCTCGTCTTGGTAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:11^T7 +seq7 129 phiX174 960 37 18M = 943 -17 TTTAATTGCAGGGGCTTC IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq7 65 phiX174 943 25 18M = 960 17 TGTAGGTGGTCAACCAAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:14A1T1 +seq8 137 phiX174 1715 37 18M = 1715 0 ATGCGCTCTATTCTCTGG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:10A7 +seq8 69 phiX174 1715 0 * = 1715 0 ACACCCGTCCTTTACGTC IIIIIIIIIIIIIIIIII +seq9 129 phiX174 2613 37 18M = 2596 -17 TTCTGTTGGTGCTGATAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq9 65 phiX174 2596 37 18M = 2613 17 GCCGCTATTCAGGTTGTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:7A10 --- a/tool-data/bwa_index.loc.sample +++ b/tool-data/bwa_index.loc.sample @@ -1,17 +1,17 @@ #This is a sample file distributed with Galaxy that enables tools -#to use a directory of BWA indexed sequences data files. You will need -#to create these data files and then create a bwa_index.loc file -#similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The bwa_index.loc -#file has this format (white space characters are TAB characters): +#to use a directory of BWA indexed sequences data files. You will need +#to create these data files and then create a bwa_index.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The bwa_index.loc +#file has this format (longer white space characters are TAB characters): # -#<build><file_base> +#<unique_build_id><dbkey><display_name><file_path> # #So, for example, if you had phiX indexed stored in #/depot/data2/galaxy/phiX/base/, #then the bwa_index.loc entry would look like this: # -#phiX /depot/data2/galaxy/phiX/base/phiX.fa +#phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa # #and your /depot/data2/galaxy/phiX/base/ directory #would contain phiX.fa.* files: @@ -22,8 +22,17 @@ #...etc... # #Your bwa_index.loc file should include an entry per line for each -#index set you have stored. The "file" in the path does not actually +#index set you have stored. The "file" in the path does not actually #exist, but it is the prefix for the actual index files. For example: # -#phiX /depot/data2/galaxy/phiX/base/phiX.fa -#hg18 /depot/data2/galaxy/hg18/base/hg18.fa +#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa +#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa +#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa +#...etc... +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. That is why the +#hg19 entry above looks odd. New genomes can be better-looking. +# --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.1"> +<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.5"><description>Search translated nucleotide database with protein query sequence(s)</description><command> ## The command is a Cheetah template which allows some Python based syntax. @@ -36,9 +36,10 @@ tblastn </param><when value="db"><param name="database" type="select" label="Nucleotide BLAST database"> + <options from_file="blastdb.loc"> - <column name="name" index="0"/> - <column name="value" index="1"/> + <column name="name" index="2"/> + <column name="value" index="0"/></options></param><param name="subject" type="hidden" value="" /> --- a/tools/sr_mapping/lastz_paired_reads_wrapper.py +++ b/tools/sr_mapping/lastz_paired_reads_wrapper.py @@ -758,7 +758,7 @@ def __main__(): parser.add_option( '', '--lastz_seqs_file_dir', dest='lastz_seqs_file_dir', help='Directory of local lastz_seqs.loc file' ) ( options, args ) = parser.parse_args() - if options.ref_name != 'None': + if options.ref_name: ref_name = '[nickname=%s]' % options.ref_name else: ref_name = '' --- a/tools/sr_mapping/bowtie_wrapper.py +++ b/tools/sr_mapping/bowtie_wrapper.py @@ -137,51 +137,51 @@ def __main__(): indexing_cmds = '%s' % colorspace else: try: - if options.iautoB != 'None' and options.iautoB == 'set': + if options.iautoB and options.iautoB == 'set': iautoB = '--noauto' else: iautoB = '' - if options. ipacked != 'None' and options.ipacked == 'packed': + if options. ipacked and options.ipacked == 'packed': ipacked = '--packed' else: ipacked = '' - if options.ibmax != 'None' and int( options.ibmax ) >= 1: + if options.ibmax and int( options.ibmax ) >= 1: ibmax = '--bmax %s' % options.ibmax else: ibmax = '' - if options.ibmaxdivn != 'None' and int( options.ibmaxdivn ) >= 0: + if options.ibmaxdivn and int( options.ibmaxdivn ) >= 0: ibmaxdivn = '--bmaxdivn %s' % options.ibmaxdivn else: ibmaxdivn = '' - if options.idcv != 'None' and int( options.idcv ) > 0: + if options.idcv and int( options.idcv ) > 0: idcv = '--dcv %s' % options.idcv else: idcv = '' - if options.inodc != 'None' and options.inodc == 'nodc': + if options.inodc and options.inodc == 'nodc': inodc = '--nodc' else: inodc = '' - if options.inoref != 'None' and options.inoref == 'noref': + if options.inoref and options.inoref == 'noref': inoref = '--noref' else: inoref = '' - if options.iftab != 'None' and int( options.iftab ) >= 0: + if options.iftab and int( options.iftab ) >= 0: iftab = '--ftabchars %s' % options.iftab else: iftab = '' - if options.intoa != 'None' and options.intoa == 'yes': + if options.intoa and options.intoa == 'yes': intoa = '--ntoa' else: intoa = '' - if options.iendian != 'None' and options.iendian == 'big': + if options.iendian and options.iendian == 'big': iendian = '--big' else: iendian = '--little' - if options.iseed != 'None' and int( options.iseed ) > 0: + if options.iseed and int( options.iseed ) > 0: iseed = '--seed %s' % options.iseed else: iseed = '' - if options.icutoff != 'None' and int( options.icutoff ) > 0: + if options.icutoff and int( options.icutoff ) > 0: icutoff = '--cutoff %s' % options.icutoff else: icutoff = '' @@ -233,11 +233,11 @@ def __main__(): suppressHeader = '--sam-nohead' else: suppressHeader = '' - if options.maxInsert != 'None' and int( options.maxInsert ) > 0: + if options.maxInsert and int( options.maxInsert ) > 0: maxInsert = '-X %s' % options.maxInsert else: maxInsert = '' - if options.mateOrient != 'None': + if options.mateOrient: mateOrient = '--%s' % options.mateOrient else: mateOrient = '' @@ -246,32 +246,32 @@ def __main__(): ( maxInsert, mateOrient, options.threads, suppressHeader, colorspace ) else: try: - if options.skip != 'None' and int( options.skip ) > 0: + if options.skip and int( options.skip ) > 0: skip = '-s %s' % options.skip else: skip = '' - if options.alignLimit != 'None' and int( options.alignLimit ) >= 0: + if options.alignLimit and int( options.alignLimit ) >= 0: alignLimit = '-u %s' % options.alignLimit else: alignLimit = '' - if options.trimH != 'None' and int( options.trimH ) > 0: + if options.trimH and int( options.trimH ) > 0: trimH = '-5 %s' % options.trimH else: trimH = '' - if options.trimL != 'None' and int( options.trimL ) > 0: + if options.trimL and int( options.trimL ) > 0: trimL = '-3 %s' % options.trimL else: trimL = '' - if options.mismatchSeed != 'None' and (options.mismatchSeed == '0' or options.mismatchSeed == '1' \ + if options.mismatchSeed and (options.mismatchSeed == '0' or options.mismatchSeed == '1' \ or options.mismatchSeed == '2' or options.mismatchSeed == '3'): mismatchSeed = '-n %s' % options.mismatchSeed else: mismatchSeed = '' - if options.mismatchQual != 'None' and int( options.mismatchQual ) >= 0: + if options.mismatchQual and int( options.mismatchQual ) >= 0: mismatchQual = '-e %s' % options.mismatchQual else: mismatchQual = '' - if options.seedLen != 'None' and int( options.seedLen ) >= 5: + if options.seedLen and int( options.seedLen ) >= 5: seedLen = '-l %s' % options.seedLen else: seedLen = '' @@ -283,11 +283,11 @@ def __main__(): maqSoapAlign = '-v %s' % options.maqSoapAlign else: maqSoapAlign = '' - if options.minInsert != 'None' and int( options.minInsert ) > 0: + if options.minInsert and int( options.minInsert ) > 0: minInsert = '-I %s' % options.minInsert else: minInsert = '' - if options.maxAlignAttempt != 'None' and int( options.maxAlignAttempt ) >= 0: + if options.maxAlignAttempt and int( options.maxAlignAttempt ) >= 0: maxAlignAttempt = '--pairtries %s' % options.maxAlignAttempt else: maxAlignAttempt = '' @@ -299,7 +299,7 @@ def __main__(): reverseAlign = '--norc' else: reverseAlign = '' - if options.maxBacktracks != 'None' and int( options.maxBacktracks ) > 0 and \ + if options.maxBacktracks and int( options.maxBacktracks ) > 0 and \ ( options.mismatchSeed == '2' or options.mismatchSeed == '3' ): maxBacktracks = '--maxbts %s' % options.maxBacktracks else: @@ -308,7 +308,7 @@ def __main__(): tryHard = '-y' else: tryHard = '' - if options.valAlign != 'None' and int( options.valAlign ) >= 0: + if options.valAlign and int( options.valAlign ) >= 0: valAlign = '-k %s' % options.valAlign else: valAlign = '' @@ -316,7 +316,7 @@ def __main__(): allValAligns = '-a' else: allValAligns = '' - if options.suppressAlign != 'None' and int( options.suppressAlign ) >= 0: + if options.suppressAlign and int( options.suppressAlign ) >= 0: suppressAlign = '-m %s' % options.suppressAlign else: suppressAlign = '' @@ -328,23 +328,23 @@ def __main__(): strata = '--strata' else: strata = '' - if options.offrate != 'None' and int( options.offrate ) >= 0: + if options.offrate and int( options.offrate ) >= 0: offrate = '-o %s' % options.offrate else: offrate = '' - if options.seed != 'None' and int( options.seed ) >= 0: + if options.seed and int( options.seed ) >= 0: seed = '--seed %s' % options.seed else: seed = '' - if options.snpphred != 'None' and int( options.snpphred ) >= 0: + if options.snpphred and int( options.snpphred ) >= 0: snpphred = '--snpphred %s' % options.snpphred else: snpphred = '' - if options.snpfrac != 'None' and float( options.snpfrac ) >= 0: + if options.snpfrac and float( options.snpfrac ) >= 0: snpfrac = '--snpfrac %s' % options.snpfrac else: snpfrac = '' - if options.keepends != 'None' and options.keepends == 'doKeepends': + if options.keepends and options.keepends == 'doKeepends': keepends = '--col-keepends' else: keepends = '' --- a/test-data/megablast_wrapper_test1.out +++ b/test-data/megablast_wrapper_test1.out @@ -1,20 +1,20 @@ -0_0.666667 PHIX174 100.00 30 0 0 1 30 1 30 1e-13 60.0 -1_0.600000 PHIX174 100.00 30 0 0 1 30 31 60 1e-13 60.0 -2_0.400000 PHIX174 100.00 30 0 0 1 30 76 105 1e-13 60.0 -3_0.566667 PHIX174 100.00 30 0 0 1 30 106 135 1e-13 60.0 -4_0.766667 PHIX174 100.00 30 0 0 1 30 151 180 1e-13 60.0 -5_0.533333 PHIX174 100.00 30 0 0 1 30 181 210 1e-13 60.0 -6_0.533333 PHIX174 100.00 30 0 0 1 30 226 255 1e-13 60.0 -7_0.400000 PHIX174 100.00 30 0 0 1 30 256 285 1e-13 60.0 -8_0.500000 PHIX174 100.00 30 0 0 1 30 301 330 1e-13 60.0 -9_0.400000 PHIX174 100.00 30 0 0 1 30 331 360 1e-13 60.0 -10_0.500000 PHIX174 100.00 30 0 0 1 30 376 405 1e-13 60.0 -11_0.533333 PHIX174 100.00 30 0 0 1 30 406 435 1e-13 60.0 -12_0.700000 PHIX174 100.00 30 0 0 1 30 451 480 1e-13 60.0 -13_0.533333 PHIX174 100.00 30 0 0 1 30 481 510 1e-13 60.0 -14_0.666667 PHIX174 100.00 30 0 0 1 30 526 555 1e-13 60.0 -15_0.666667 PHIX174 100.00 30 0 0 1 30 556 585 1e-13 60.0 -16_0.566667 PHIX174 100.00 30 0 0 1 30 601 630 1e-13 60.0 -17_0.533333 PHIX174 100.00 30 0 0 1 30 631 660 1e-13 60.0 -18_0.566667 PHIX174 100.00 30 0 0 1 30 676 705 1e-13 60.0 -19_0.566667 PHIX174 100.00 30 0 0 1 30 706 735 1e-13 60.0 +0_0.666667 phiX174 5386 100.00 30 0 0 1 30 1 30 1e-13 60.0 +1_0.600000 phiX174 5386 100.00 30 0 0 1 30 31 60 1e-13 60.0 +2_0.400000 phiX174 5386 100.00 30 0 0 1 30 76 105 1e-13 60.0 +3_0.566667 phiX174 5386 100.00 30 0 0 1 30 106 135 1e-13 60.0 +4_0.766667 phiX174 5386 100.00 30 0 0 1 30 151 180 1e-13 60.0 +5_0.533333 phiX174 5386 100.00 30 0 0 1 30 181 210 1e-13 60.0 +6_0.533333 phiX174 5386 100.00 30 0 0 1 30 226 255 1e-13 60.0 +7_0.400000 phiX174 5386 100.00 30 0 0 1 30 256 285 1e-13 60.0 +8_0.500000 phiX174 5386 100.00 30 0 0 1 30 301 330 1e-13 60.0 +9_0.400000 phiX174 5386 100.00 30 0 0 1 30 331 360 1e-13 60.0 +10_0.500000 phiX174 5386 100.00 30 0 0 1 30 376 405 1e-13 60.0 +11_0.533333 phiX174 5386 100.00 30 0 0 1 30 406 435 1e-13 60.0 +12_0.700000 phiX174 5386 100.00 30 0 0 1 30 451 480 1e-13 60.0 +13_0.533333 phiX174 5386 100.00 30 0 0 1 30 481 510 1e-13 60.0 +14_0.666667 phiX174 5386 100.00 30 0 0 1 30 526 555 1e-13 60.0 +15_0.666667 phiX174 5386 100.00 30 0 0 1 30 556 585 1e-13 60.0 +16_0.566667 phiX174 5386 100.00 30 0 0 1 30 601 630 1e-13 60.0 +17_0.533333 phiX174 5386 100.00 30 0 0 1 30 631 660 1e-13 60.0 +18_0.566667 phiX174 5386 100.00 30 0 0 1 30 676 705 1e-13 60.0 +19_0.566667 phiX174 5386 100.00 30 0 0 1 30 706 735 1e-13 60.0 --- a/tools/sr_mapping/srma_wrapper.xml +++ b/tools/sr_mapping/srma_wrapper.xml @@ -1,17 +1,28 @@ -<tool id="srma_wrapper" name="Re-align with SRMA" version="0.1.5"> +<tool id="srma_wrapper" name="Re-align with SRMA" version="0.2.0"><description></description><command interpreter="python">srma_wrapper.py #if $refGenomeSource.refGenomeSource_type == "history": - --ref=$refGenomeSource.ownFile + --ref=$refGenomeSource.ownFile #else: - --refUID=$refGenomeSource.ref - --refLocations=${GALAXY_DATA_INDEX_DIR}/srma_index.loc + --ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.ref ), $__app__.tool_data_tables[ 'srma_indexes' ].get_fields() )[0][-1] }" + --refUID=$refGenomeSource.ref + --refLocations=${GALAXY_DATA_INDEX_DIR}/srma_index.loc #end if - --input=$input --inputIndex=${input.metadata.bam_index} --output=$output - --params=$params.source_select --fileSource=$refGenomeSource.refGenomeSource_type + --input=$input + --inputIndex=${input.metadata.bam_index} + --output=$output + --params=$params.source_select + --fileSource=$refGenomeSource.refGenomeSource_type --jarBin="${GALAXY_DATA_INDEX_DIR}/shared/jars" #if $params.source_select == "full": - --offset=$params.offset --minMappingQuality=$params.minMappingQuality --minAlleleProbability=$params.minAlleleProbability --minAlleleCoverage=$params.minAlleleCoverage --range=$params.range --correctBases=$params.correctBases --useSequenceQualities=$params.useSequenceQualities --maxHeapSize=$params.maxHeapSize + --offset=$params.offset + --minMappingQuality=$params.minMappingQuality + --minAlleleProbability=$params.minAlleleProbability + --minAlleleCoverage=$params.minAlleleCoverage + --range=$params.range + --correctBases=$params.correctBases + --useSequenceQualities=$params.useSequenceQualities + --maxHeapSize=$params.maxHeapSize #end if --jarFile="srma.jar" </command> @@ -23,10 +34,7 @@ </param><when value="built-in"><param name="ref" type="select" label="Select a reference genome"> - <options from_file="srma_index.loc"> - <column name="value" index="0" /> - <column name="name" index="0" /> - </options> + <options from_data_table="srma_indexes" /></param></when><when value="history"> @@ -71,13 +79,13 @@ <tests><test><param name="refGenomeSource_type" value="built-in" /><param name="ref" value="hg18chr21" /> @@ -87,16 +95,16 @@ </test><test><param name="refGenomeSource_type" value="history" /><param name="ownFile" value="srma_in2.fa" /> --- a/tools/sr_mapping/bwa_wrapper.py +++ b/tools/sr_mapping/bwa_wrapper.py @@ -30,8 +30,9 @@ usage: bwa_wrapper.py [options] -T, --outputTopN=T: Output top specified hits -S, --maxInsertSize=S: Maximum insert size for a read pair to be considered mapped good -P, --maxOccurPairing=P: Maximum occurrences of a read for pairings + -H, --suppressHeader=h: Suppress header -D, --dbkey=D: Dbkey for reference genome - -H, --suppressHeader=h: Suppress header + -X, --do_not_build_index: Flag to specify that provided file is already indexed and to just use 'as is' """ import optparse, os, shutil, subprocess, sys, tempfile @@ -68,13 +69,14 @@ def __main__(): parser.add_option( '-S', '--maxInsertSize', dest='maxInsertSize', help='Maximum insert size for a read pair to be considered mapped good' ) parser.add_option( '-P', '--maxOccurPairing', dest='maxOccurPairing', help='Maximum occurrences of a read for pairings' ) parser.add_option( '-D', '--dbkey', dest='dbkey', help='Dbkey for reference genome' ) + parser.add_option( '-X', '--do_not_build_index', dest='do_not_build_index', help="Don't build index" ) parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' ) (options, args) = parser.parse_args() # make temp directory for placement of indices tmp_index_dir = tempfile.mkdtemp() tmp_dir = tempfile.mkdtemp() # index if necessary - if options.fileSource == 'history': + if options.fileSource == 'history' and not options.do_not_build_index: ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir ) ref_file_name = ref_file.name ref_file.close() --- a/tools/sr_mapping/srma_wrapper.py +++ b/tools/sr_mapping/srma_wrapper.py @@ -28,6 +28,15 @@ def stop_err( msg ): sys.stderr.write( '%s\n' % msg ) sys.exit() +def parseRefLoc( refLoc, refUID ): + for line in open( refLoc ): + if not line.startswith( '#' ): + fields = line.strip().split( '\t' ) + if len( fields ) >= 3: + if fields[0] == refUID: + return fields[1] + return None + def __main__(): #Parse Command Line parser = optparse.OptionParser() @@ -125,13 +134,10 @@ def __main__(): stop_err( 'Problem handling SRMA index (dict file) for custom genome file: %s\n' % str( e ) ) # using built-in dict/index files else: - for line in open( options.refLocations ): - if not line.startswith( '#' ): - fields = line.strip().split( '\t' ) - if len( fields ) >= 2: - if fields[0] == options.refUID: - reference_filepath_name = fields[1] - break + if options.ref: + reference_filepath_name = options.ref + else: + reference_filepath_name = parseRefLoc( options.refLocation, options.refUID ) if reference_filepath_name is None: raise ValueError( 'A valid genome reference was not provided.' ) --- a/tool-data/perm_color_index.loc.sample +++ b/tool-data/perm_color_index.loc.sample @@ -5,7 +5,7 @@ #the directories in which those files are stored. The perm_color_index.loc #file has this format (white space characters are TAB characters): # -#<build_seed_readlength><file_base> +#<build_seed_readlength><display_name><file_base> # #Because each PerM index is built with a specific seed and a specific read #length, this needs to be specified so the user can choose the appropriate @@ -13,7 +13,7 @@ #50, and stored in /depot/data/galaxy/phiX/perm_index/, #then the perm_color_index.loc entry would look something like this: # -#phiX_F3_50 /depot/data/galaxy/phiX/perm_index/phiX_color_F3_50.index +#phiX_F3_50 phiX: seed=F3, read length=50 /depot/data/galaxy/phiX/perm_index/phiX_color_F3_50.index # #and your /depot/data/galaxy/phiX/perm_index/ directory #would contain the file phiX_color_F3_50.index: @@ -21,7 +21,8 @@ #Your perm_color_index.loc file should include an entry per line for each #index set you have stored. For example: # -#phiX_F3_50 /depot/data/galaxy/phiX/perm_index/phiX_color_F3_50.index -#phiX_F4_50 /depot/data/galaxy/phiX/perm_index/phiX_color_F3_50.index -#hg19_F3_50 /depot/data/galaxy/hg19/perm_index/hg19_color_F3_50.index -#hg19_F4_50 /depot/data/galaxy/hg19/perm_index/hg19_color_F3_50.index +#phiX_F3_50 /depot/data/galaxy/phiX/perm_index/phiX_color_F3_50.index +#phiX_F4_50 /depot/data/galaxy/phiX/perm_index/phiX_color_F3_50.index +#hg19_F3_50 /depot/data/galaxy/hg19/perm_index/hg19_color_F3_50.index +#hg19_F4_50 /depot/data/galaxy/hg19/perm_index/hg19_color_F3_50.index +# --- a/test-data/perm_out1.sam +++ b/test-data/perm_out1.sam @@ -1,33 +1,33 @@ -HWI-EAS91_1_30788AAXX:1:1:1761:343/1 65 PHIX174 5 255 50M = 69 64 TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1761:343/1 129 PHIX174 69 255 50M = 5 64 TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG IIIIIII""IIIIIII0II?I""IIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1578:331/1 65 PHIX174 209 255 50M = 268 59 TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1578:331/1 129 PHIX174 268 255 50M = 209 59 AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1647:512/1 65 PHIX174 401 255 50M = 451 50 TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1647:512/1 129 PHIX174 451 255 50M = 401 50 TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1570:620/2 0 PHIX174 559 255 50M * 0 0 CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1599:330/1 65 PHIX174 803 255 50M = 868 65 AGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTC IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1599:330/1 129 PHIX174 868 255 50M = 803 65 TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA IIIIIII""IIIIIIIIIIIIIIIIIII<III@II?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1652:270/2 0 PHIX174 973 255 50M * 0 0 GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1746:351/1 0 PHIX174 1218 255 50M * 0 0 CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1582:633/1 0 PHIX174 1517 255 50M * 0 0 CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1598:534/1 65 PHIX174 1717 255 50M = 1772 55 GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1598:534/1 129 PHIX174 1772 255 50M = 1717 55 TTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1572:324/2 0 PHIX174 1972 255 50M * 0 0 GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1749:466/1 65 PHIX174 2201 255 50M = 2251 50 TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1749:466/1 129 PHIX174 2251 255 50M = 2201 50 GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1629:446/1 65 PHIX174 2301 255 50M = 2355 54 AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1629:446/1 129 PHIX174 2355 255 50M = 2301 54 CAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1763:587/1 65 PHIX174 2501 255 50M = 2566 65 AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1763:587/1 129 PHIX174 2566 255 50M = 2501 65 CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1616:363/1 65 PHIX174 2718 255 50M = 2773 55 TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1616:363/1 129 PHIX174 2773 255 50M = 2718 55 GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAATGTTTATGTTGG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1768:715/1 65 PHIX174 3118 255 50M = 3173 55 ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1768:715/1 129 PHIX174 3173 255 50M = 3118 55 AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1572:270/1 65 PHIX174 3518 255 50M = 3577 59 TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1572:270/1 129 PHIX174 3577 255 50M = 3518 59 ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1785:1272/1 65 PHIX174 3818 255 50M = 3873 55 TATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCT III""""""IIIIIIIII""FI"IIII""II+ICI"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1785:1272/1 129 PHIX174 3873 255 50M = 3818 55 GACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTC III""""""IIIIIIIII""FI"IIII""II+ICI?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1673:514/1 65 PHIX174 4018 255 50M = 4072 54 ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1673:514/1 129 PHIX174 4072 255 50M = 4018 54 GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1634:330/1 65 PHIX174 4418 255 50M = 4473 55 GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1634:330/1 129 PHIX174 4473 255 50M = 4418 55 TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTAT IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1761:343/1 65 phiX174 5 255 50M = 69 64 TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1761:343/1 129 phiX174 69 255 50M = 5 64 TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG IIIIIII""IIIIIII0II?I""IIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1578:331/1 65 phiX174 209 255 50M = 268 59 TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1578:331/1 129 phiX174 268 255 50M = 209 59 AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1647:512/1 65 phiX174 401 255 50M = 451 50 TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1647:512/1 129 phiX174 451 255 50M = 401 50 TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1570:620/2 0 phiX174 559 255 50M * 0 0 CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1599:330/1 65 phiX174 803 255 50M = 868 65 AGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTC IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1599:330/1 129 phiX174 868 255 50M = 803 65 TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA IIIIIII""IIIIIIIIIIIIIIIIIII<III@II?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1652:270/2 0 phiX174 973 255 50M * 0 0 GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1746:351/1 0 phiX174 1218 255 50M * 0 0 CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1582:633/1 0 phiX174 1517 255 50M * 0 0 CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1598:534/1 65 phiX174 1717 255 50M = 1772 55 GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1598:534/1 129 phiX174 1772 255 50M = 1717 55 TTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1572:324/2 0 phiX174 1972 255 50M * 0 0 GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1749:466/1 65 phiX174 2201 255 50M = 2251 50 TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1749:466/1 129 phiX174 2251 255 50M = 2201 50 GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1629:446/1 65 phiX174 2301 255 50M = 2355 54 AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1629:446/1 129 phiX174 2355 255 50M = 2301 54 CAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1763:587/1 65 phiX174 2501 255 50M = 2566 65 AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1763:587/1 129 phiX174 2566 255 50M = 2501 65 CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1616:363/1 65 phiX174 2718 255 50M = 2773 55 TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1616:363/1 129 phiX174 2773 255 50M = 2718 55 GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAATGTTTATGTTGG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1768:715/1 65 phiX174 3118 255 50M = 3173 55 ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1768:715/1 129 phiX174 3173 255 50M = 3118 55 AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1572:270/1 65 phiX174 3518 255 50M = 3577 59 TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1572:270/1 129 phiX174 3577 255 50M = 3518 59 ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1785:1272/1 65 phiX174 3818 255 50M = 3873 55 TATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCT III""""""IIIIIIIII""FI"IIII""II+ICI"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1785:1272/1 129 phiX174 3873 255 50M = 3818 55 GACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTC III""""""IIIIIIIII""FI"IIII""II+ICI?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1673:514/1 65 phiX174 4018 255 50M = 4072 54 ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1673:514/1 129 phiX174 4072 255 50M = 4018 54 GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1634:330/1 65 phiX174 4418 255 50M = 4473 55 GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1634:330/1 129 phiX174 4473 255 50M = 4418 55 TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTAT IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II?I0IIIIHIIIGIII NM:i:0 --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.1"> +<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.5"><description>Search nucleotide database with nucleotide query sequence(s)</description><command> ## The command is a Cheetah template which allows some Python based syntax. @@ -36,9 +36,10 @@ blastn </param><when value="db"><param name="database" type="select" label="Nucleotide BLAST database"> + <options from_file="blastdb.loc"> - <column name="name" index="0"/> - <column name="value" index="1"/> + <column name="name" index="2"/> + <column name="value" index="0"/></options></param><param name="subject" type="hidden" value="" /> --- a/tool-data/lastz_seqs.loc.sample +++ b/tool-data/lastz_seqs.loc.sample @@ -1,17 +1,17 @@ #This is a sample file distributed with Galaxy that enables tools -#to use a directory of 2bit genome files for use with Lastz. You will -#need to supply these files and then create a lastz_seqs.loc file -#similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The lastz_seqs.loc +#to use a directory of 2bit genome files for use with Lastz. You will +#need to supply these files and then create a lastz_seqs.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The lastz_seqs.loc #file has this format (white space characters are TAB characters): # -#<build><file_path> +#<unique_build_id><display_name><file_path> # #So, for example, if your lastz_seqs.loc began like this: # -#hg18 /depot/data2/galaxy/twobit/hg18.2bit -#hg19 /depot/data2/galaxy/twobit/hg19.2bit -#mm9 /depot/data2/galaxy/twobit/mm9.2bit +#hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit +#hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit +#mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit # #then your /depot/data2/galaxy/twobit/ directory #would need to contain the following 2bit files: @@ -22,4 +22,9 @@ # #Your lastz_seqs.loc file should include an entry per line for #each file you have stored that you want to be available. Note that -#your files should all have the extension '2bit'. +#your files should all have the extension '2bit'. +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. +# --- a/tools/sr_mapping/bowtie_wrapper.xml +++ b/tools/sr_mapping/bowtie_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.0.6"> +<tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.0"><requirements><requirement type='package'>bowtie</requirement></requirements><description></description><command interpreter="python"> @@ -8,186 +8,100 @@ --output=$output --suppressHeader=$suppressHeader --genomeSource=$refGenomeSource.genomeSource - --snpphred="None" - --snpfrac="None" - --keepends="None" #if $refGenomeSource.genomeSource == "history": - #if $refGenomeSource.ownFile.extension.startswith( 'bowtie_' ): - --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}" - --do_not_build_index - #else: - --ref=$refGenomeSource.ownFile - --indexSettings=$refGenomeSource.indexParams.indexSettings - #if $refGenomeSource.indexParams.indexSettings == "indexFull": - --iautoB=$refGenomeSource.indexParams.autoBehavior.autoB - #if $refGenomeSource.indexParams.autoBehavior.autoB == "set": - --ipacked=$refGenomeSource.indexParams.autoBehavior.packed - --ibmax=$refGenomeSource.indexParams.autoBehavior.bmax - --ibmaxdivn=$refGenomeSource.indexParams.autoBehavior.bmaxdivn - --idcv=$refGenomeSource.indexParams.autoBehavior.dcv + ##index already exists + #if $refGenomeSource.ownFile.extension.startswith( 'bowtie_' ): + ##user previously built + --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}" + --do_not_build_index #else: - --ipacked="None" - --ibmax="None" - --ibmaxdivn="None" - --idcv="None" + ##build index on the fly + --ref=$refGenomeSource.ownFile + --indexSettings=$refGenomeSource.indexParams.indexSettings + #if $refGenomeSource.indexParams.indexSettings == "indexFull": + --iautoB=$refGenomeSource.indexParams.autoBehavior.autoB + #if $refGenomeSource.indexParams.autoBehavior.autoB == "set": + --ipacked=$refGenomeSource.indexParams.autoBehavior.packed + --ibmax=$refGenomeSource.indexParams.autoBehavior.bmax + --ibmaxdivn=$refGenomeSource.indexParams.autoBehavior.bmaxdivn + --idcv=$refGenomeSource.indexParams.autoBehavior.dcv + #end if + --inodc=$refGenomeSource.indexParams.nodc + --inoref=$refGenomeSource.indexParams.noref + --ioffrate=$refGenomeSource.indexParams.offrate + --iftab=$refGenomeSource.indexParams.ftab + --intoa=$refGenomeSource.indexParams.ntoa + --iendian=$refGenomeSource.indexParams.endian + --iseed=$refGenomeSource.indexParams.seed + --icutoff=$refGenomeSource.indexParams.cutoff + #end if #end if - --inodc=$refGenomeSource.indexParams.nodc - --inoref=$refGenomeSource.indexParams.noref - --ioffrate=$refGenomeSource.indexParams.offrate - --iftab=$refGenomeSource.indexParams.ftab - --intoa=$refGenomeSource.indexParams.ntoa - --iendian=$refGenomeSource.indexParams.endian - --iseed=$refGenomeSource.indexParams.seed - --icutoff=$refGenomeSource.indexParams.cutoff - #else: - --iautoB="None" - --ipacked="None" - --ibmax="None" - --ibmaxdivn="None" - --idcv="None" - --inodc="None" - --inoref="None" - --ioffrate="None" - --iftab="None" - --intoa="None" - --iendian="None" - --iseed="None" - --icutoff="None" - #end if - #end if - #else: - --ref=$refGenomeSource.index - --indexSettings="None" - --iautoB="None" - --ipacked="None" - --ibmax="None" - --ibmaxdivn="None" - --idcv="None" - --inodc="None" - --inoref="None" - --ioffrate="None" - --iftab="None" - --intoa="None" - --iendian="None" - --iseed="None" - --icutoff="None" + #else + ##use pre-built index + --ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] }" #end if --paired=$singlePaired.sPaired #if $singlePaired.sPaired == "single": - --input1=$singlePaired.sInput1 - --input2="None" - --params=$singlePaired.sParams.sSettingsType - #if $singlePaired.sParams.sSettingsType == "full": - --skip=$singlePaired.sParams.sSkip - --alignLimit=$singlePaired.sParams.sAlignLimit - --trimH=$singlePaired.sParams.sTrimH - --trimL=$singlePaired.sParams.sTrimL - --mismatchSeed=$singlePaired.sParams.sMismatchSeed - --mismatchQual=$singlePaired.sParams.sMismatchQual - --seedLen=$singlePaired.sParams.sSeedLen - --rounding=$singlePaired.sParams.sRounding - --maqSoapAlign=$singlePaired.sParams.sMaqSoapAlign - --tryHard=$singlePaired.sParams.sTryHard - --valAlign=$singlePaired.sParams.sValAlign - --allValAligns=$singlePaired.sParams.sAllValAligns - --suppressAlign=$singlePaired.sParams.sSuppressAlign - --best=$singlePaired.sParams.sBestOption.sBest - #if $singlePaired.sParams.sBestOption.sBest == "doBest": - --maxBacktracks=$singlePaired.sParams.sBestOption.sdMaxBacktracks - --strata=$singlePaired.sParams.sBestOption.sdStrata - #else: - --maxBacktracks=$singlePaired.sParams.sBestOption.snMaxBacktracks - --strata="None" + --input1=$singlePaired.sInput1 + --params=$singlePaired.sParams.sSettingsType + #if $singlePaired.sParams.sSettingsType == "full": + --skip=$singlePaired.sParams.sSkip + --alignLimit=$singlePaired.sParams.sAlignLimit + --trimH=$singlePaired.sParams.sTrimH + --trimL=$singlePaired.sParams.sTrimL + --mismatchSeed=$singlePaired.sParams.sMismatchSeed + --mismatchQual=$singlePaired.sParams.sMismatchQual + --seedLen=$singlePaired.sParams.sSeedLen + --rounding=$singlePaired.sParams.sRounding + --maqSoapAlign=$singlePaired.sParams.sMaqSoapAlign + --tryHard=$singlePaired.sParams.sTryHard + --valAlign=$singlePaired.sParams.sValAlign + --allValAligns=$singlePaired.sParams.sAllValAligns + --suppressAlign=$singlePaired.sParams.sSuppressAlign + --best=$singlePaired.sParams.sBestOption.sBest + #if $singlePaired.sParams.sBestOption.sBest == "doBest": + --maxBacktracks=$singlePaired.sParams.sBestOption.sdMaxBacktracks + --strata=$singlePaired.sParams.sBestOption.sdStrata + #else: + --maxBacktracks=$singlePaired.sParams.sBestOption.snMaxBacktracks + #end if + --offrate=$singlePaired.sParams.sOffrate + --seed=$singlePaired.sParams.sSeed #end if - --offrate=$singlePaired.sParams.sOffrate - --seed=$singlePaired.sParams.sSeed - #else: - --skip="None" - --alignLimit="None" - --trimH="None" - --trimL="None" - --mismatchSeed="None" - --mismatchQual="None" - --seedLen="None" - --rounding="None" - --maqSoapAlign="None" - --tryHard="None" - --valAlign="None" - --allValAligns="None" - --suppressAlign="None" - --best="None" - --maxBacktracks="None" - --strata="None" - --offrate="None" - --seed="None" - --snpphred="None" - --snpfrac="None" - --keepends="None" - #end if - --minInsert="None" - --maxInsert="None" - --mateOrient="None" - --maxAlignAttempt="None" - --forwardAlign="None" - --reverseAlign="None" #else: - --input1=$singlePaired.pInput1 - --input2=$singlePaired.pInput2 - --maxInsert=$singlePaired.pMaxInsert - --mateOrient=$singlePaired.pMateOrient - --params=$singlePaired.pParams.pSettingsType - #if $singlePaired.pParams.pSettingsType == "full": - --skip=$singlePaired.pParams.pSkip - --alignLimit=$singlePaired.pParams.pAlignLimit - --trimH=$singlePaired.pParams.pTrimH - --trimL=$singlePaired.pParams.pTrimL - --mismatchSeed=$singlePaired.pParams.pMismatchSeed - --mismatchQual=$singlePaired.pParams.pMismatchQual - --seedLen=$singlePaired.pParams.pSeedLen - --rounding=$singlePaired.pParams.pRounding - --maqSoapAlign=$singlePaired.pParams.pMaqSoapAlign - --minInsert=$singlePaired.pParams.pMinInsert - --maxAlignAttempt=$singlePaired.pParams.pMaxAlignAttempt - --forwardAlign=$singlePaired.pParams.pForwardAlign - --reverseAlign=$singlePaired.pParams.pReverseAlign - --tryHard=$singlePaired.pParams.pTryHard - --valAlign=$singlePaired.pParams.pValAlign - --allValAligns=$singlePaired.pParams.pAllValAligns - --suppressAlign=$singlePaired.pParams.pSuppressAlign - --best=$singlePaired.pParams.pBestOption.pBest - #if $singlePaired.pParams.pBestOption.pBest == "doBest": - --maxBacktracks=$singlePaired.pParams.pBestOption.pdMaxBacktracks - --strata=$singlePaired.pParams.pBestOption.pdStrata - #else: - --maxBacktracks=$singlePaired.pParams.pBestOption.pnMaxBacktracks - --strata="None" + --input1=$singlePaired.pInput1 + --input2=$singlePaired.pInput2 + --maxInsert=$singlePaired.pMaxInsert + --mateOrient=$singlePaired.pMateOrient + --params=$singlePaired.pParams.pSettingsType + #if $singlePaired.pParams.pSettingsType == "full": + --skip=$singlePaired.pParams.pSkip + --alignLimit=$singlePaired.pParams.pAlignLimit + --trimH=$singlePaired.pParams.pTrimH + --trimL=$singlePaired.pParams.pTrimL + --mismatchSeed=$singlePaired.pParams.pMismatchSeed + --mismatchQual=$singlePaired.pParams.pMismatchQual + --seedLen=$singlePaired.pParams.pSeedLen + --rounding=$singlePaired.pParams.pRounding + --maqSoapAlign=$singlePaired.pParams.pMaqSoapAlign + --minInsert=$singlePaired.pParams.pMinInsert + --maxAlignAttempt=$singlePaired.pParams.pMaxAlignAttempt + --forwardAlign=$singlePaired.pParams.pForwardAlign + --reverseAlign=$singlePaired.pParams.pReverseAlign + --tryHard=$singlePaired.pParams.pTryHard + --valAlign=$singlePaired.pParams.pValAlign + --allValAligns=$singlePaired.pParams.pAllValAligns + --suppressAlign=$singlePaired.pParams.pSuppressAlign + --best=$singlePaired.pParams.pBestOption.pBest + #if $singlePaired.pParams.pBestOption.pBest == "doBest": + --maxBacktracks=$singlePaired.pParams.pBestOption.pdMaxBacktracks + --strata=$singlePaired.pParams.pBestOption.pdStrata + #else: + --maxBacktracks=$singlePaired.pParams.pBestOption.pnMaxBacktracks + #end if + --offrate=$singlePaired.pParams.pOffrate + --seed=$singlePaired.pParams.pSeed #end if - --offrate=$singlePaired.pParams.pOffrate - --seed=$singlePaired.pParams.pSeed - #else: - --skip="None" - --alignLimit="None" - --trimH="None" - --trimL="None" - --mismatchSeed="None" - --mismatchQual="None" - --seedLen="None" - --rounding="None" - --maqSoapAlign="None" - --tryHard="None" - --valAlign="None" - --allValAligns="None" - --suppressAlign="None" - --best="None" - --maxBacktracks="None" - --strata="None" - --offrate="None" - --seed="None" - --minInsert="None" - --maxAlignAttempt="None" - --forwardAlign="None" - --reverseAlign="None" - #end if #end if </command><inputs> @@ -199,12 +113,6 @@ <when value="indexed"><param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"><options from_data_table="bowtie_indexes"/> - </param></when><when value="history"> @@ -418,7 +326,8 @@ chrM_base needs to be the base location/name of the index files. --><param name="genomeSource" value="indexed" /> - <param name="index" value="equCab2chrM" /> +  + <param name="index" value="/galaxy/data/equCab2_chrM/bowtie_index/chrM" /><param name="sPaired" value="single" /><param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" /><param name="sSettingsType" value="preSet" /> @@ -475,7 +384,8 @@ chrM_base is the index files' location/base name. --><param name="genomeSource" value="indexed" /> - <param name="index" value="equCab2chrM" /> +  + <param name="index" value="/galaxy/data/equCab2_chrM/bowtie_index/chrM" /><param name="sPaired" value="single" /><param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" /><param name="sSettingsType" value="full" /> --- a/tools/metag_tools/megablast_wrapper.xml +++ b/tools/metag_tools/megablast_wrapper.xml @@ -1,31 +1,28 @@ -<tool id="megablast_wrapper" name="Megablast" version="1.0.5"> +<tool id="megablast_wrapper" name="Megablast" version="1.1.0"><description> compare short reads against htgs, nt, and wgs databases</description><command interpreter="python"> - megablast_wrapper.py - --db_build="$source_select" - --input=$input_query - --word_size=$word_size - --identity_cutoff=$iden_cutoff - --eval_cutoff=$evalue_cutoff - --filter_query=$filter_query - --index_dir=${GALAXY_DATA_INDEX_DIR} - --output=$output1 + megablast_wrapper.py + --db_build="${ filter( lambda x: str( x[0] ) == str( $source_select ), $__app__.tool_data_tables[ 'blastdb' ].get_fields() )[0][-1] }" + --input=$input_query + --word_size=$word_size + --identity_cutoff=$iden_cutoff + --eval_cutoff=$evalue_cutoff + --filter_query=$filter_query + --index_dir=${GALAXY_DATA_INDEX_DIR} + --output=$output1 </command><inputs><param name="input_query" type="data" format="fasta" label="Compare these sequences"/><param name="source_select" type="select" display="radio" label="against target database"> - <options from_file="blastdb.loc"> - <column name="name" index="0"/> - <column name="value" index="0"/> - </options> + <options from_data_table="blastdb" /></param> - <param name="word_size" type="select" label="using word size" help="Size of best perfect match"> + <param name="word_size" type="select" label="using word size" help="Size of best perfect match (-W)"><option value="28">28</option><option value="16">16</option></param> - <param name="iden_cutoff" type="float" size="15" value="90.0" label="report hits above this identity" help="no cutoff if 0" /> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> - <param name="filter_query" type="select" label="Filter out low complexity regions?"> + <param name="iden_cutoff" type="float" size="15" value="90.0" label="report hits above this identity (-p)" help="no cutoff if 0" /> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff (-e)" /> + <param name="filter_query" type="select" label="Filter out low complexity regions? (-F)"><option value="T">Yes</option><option value="F">No</option></param> @@ -40,7 +37,7 @@ <test><param name="input_query" value="megablast_wrapper_test1.fa" ftype="fasta"/> - <param name="source_select" value="phiX" /> + <param name="source_select" value="/galaxy/data/blastdb/phiX/phiX" /><param name="word_size" value="28" /><param name="iden_cutoff" value="99.0" /><param name="evalue_cutoff" value="10.0" /> --- a/tool-data/bowtie_indices_color.loc.sample +++ b/tool-data/bowtie_indices_color.loc.sample @@ -1,31 +1,37 @@ #This is a sample file distributed with Galaxy that enables tools -#to use a directory of colorspace Bowtie indexed sequences data files. -#You will need to create these data files and then create a -#bowtie_indices_color.loc file similar to this one (store it in this -#directory) that points to the directories in which those files are -#stored. The bowtie_indices_color.loc file has this format (white -#space characters are TAB characters): +#to use a directory of Bowtie indexed sequences data files. You will +#need to create these data files and then create a bowtie_indices.loc +#file similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The bowtie_indices.loc +#file has this format (longer white space characters are TAB characters): # -#<build><file_base> +#<unique_build_id><dbkey><display_name><file_base_path> # #So, for example, if you had hg18 indexed stored in #/depot/data2/galaxy/bowtie/hg18/, -#then the bowtie_indices_color.loc entry would look like this: +#then the bowtie_indices.loc entry would look like this: # -#hg18 /depot/data2/galaxy/bowtie/hg18/hg18 +#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18 # #and your /depot/data2/galaxy/bowtie/hg18/ directory #would contain hg18.*.ebwt files: # #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt -#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 gh18.3.ebwt +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt #...etc... # -#Your bowtie_indices_color.loc file should include an entry per line -#for each index set you have stored. The "file" in the path does not -#actually exist, but it is the prefix for the actual index files. For -#example: +#Your bowtie_indices.loc file should include an entry per line for each +#index set you have stored. The "file" in the path does not actually +#exist, but it is the prefix for the actual index files. For example: # -#hg18 /depot/data2/galaxy/bowtie/hg18/hg18 -#hg19 /depot/data2/galaxy/bowtie/hg19/hg19 +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon +#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full +#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 +#...etc... +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. That is why the +#hg19 entry above looks odd. New genomes can be better-looking. +# --- a/tools/sr_mapping/bwa_wrapper.xml +++ b/tools/sr_mapping/bwa_wrapper.xml @@ -1,30 +1,44 @@ -<tool id="bwa_wrapper" name="Map with BWA" version="1.0.3"> +<tool id="bwa_wrapper" name="Map with BWA" version="1.1.0"><description></description> - <command interpreter="python">bwa_wrapper.py ---threads="4" -#if $genomeSource.refGenomeSource == "history": ---ref=$genomeSource.ownFile -#else: ---ref=$genomeSource.indices -#end if ---fastq=$paired.input1 -#if $paired.sPaired == "paired": ---rfastq=$paired.input2 -#else: ---rfastq="None" -#end if ---output=$output --genAlignType=$paired.sPaired --params=$params.source_select --fileSource=$genomeSource.refGenomeSource -#if $params.source_select == "pre_set": ---maxEditDist="None" --fracMissingAligns="None" --maxGapOpens="None" --maxGapExtens="None" --disallowLongDel="None" --disallowIndel="None" --seed="None" --maxEditDistSeed="None" --mismatchPenalty="None" --gapOpenPenalty="None" --gapExtensPenalty="None" --suboptAlign="None" --noIterSearch="None" --outputTopN="None" --maxInsertSize="None" --maxOccurPairing="None" -#else: ---maxEditDist=$params.maxEditDist --fracMissingAligns=$params.fracMissingAligns --maxGapOpens=$params.maxGapOpens --maxGapExtens=$params.maxGapExtens --disallowLongDel=$params.disallowLongDel --disallowIndel=$params.disallowIndel --seed=$params.seed --maxEditDistSeed=$params.maxEditDistSeed --mismatchPenalty=$params.mismatchPenalty --gapOpenPenalty=$params.gapOpenPenalty --gapExtensPenalty=$params.gapExtensPenalty --suboptAlign=$params.suboptAlign --noIterSearch=$params.noIterSearch --outputTopN=$params.outputTopN --maxInsertSize=$params.maxInsertSize --maxOccurPairing=$params.maxOccurPairing -#end if -#if $genomeSource.refGenomeSource == "history": ---dbkey=$dbkey -#else: ---dbkey="None" -#end if ---suppressHeader=$suppressHeader + <command interpreter="python"> + bwa_wrapper.py + --threads="4" + #if $genomeSource.refGenomeSource == "history": + ##build index on the fly + --ref="${genomeSource.ownFile}" + --dbkey=$dbkey + #else: + ##use precomputed indexes + --ref="${ filter( lambda x: str( x[0] ) == str( $genomeSource.indices ), $__app__.tool_data_tables[ 'bwa_indexes' ].get_fields() )[0][-1] }" + --do_not_build_index=True + #end if + --fastq=$paired.input1 + #if $paired.sPaired == "paired": + --rfastq=$paired.input2 + #end if + --output=$output + --genAlignType=$paired.sPaired + --params=$params.source_select + --fileSource=$genomeSource.refGenomeSource + #if $params.source_select != "pre_set": + --maxEditDist=$params.maxEditDist + --fracMissingAligns=$params.fracMissingAligns + --maxGapOpens=$params.maxGapOpens + --maxGapExtens=$params.maxGapExtens + --disallowLongDel=$params.disallowLongDel + --disallowIndel=$params.disallowIndel + --seed=$params.seed + --maxEditDistSeed=$params.maxEditDistSeed + --mismatchPenalty=$params.mismatchPenalty + --gapOpenPenalty=$params.gapOpenPenalty + --gapExtensPenalty=$params.gapExtensPenalty + --suboptAlign=$params.suboptAlign + --noIterSearch=$params.noIterSearch + --outputTopN=$params.outputTopN + --maxInsertSize=$params.maxInsertSize + --maxOccurPairing=$params.maxOccurPairing + #end if + --suppressHeader=$suppressHeader </command><requirements><requirement type='package'>bwa</requirement> @@ -38,12 +52,6 @@ <when value="indexed"><param name="indices" type="select" label="Select a reference genome"><options from_data_table="bwa_indexes"/> - </param></when><when value="history"> @@ -62,7 +70,7 @@ <param name="input1" type="data" format="fastqsanger" label="Forward FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/><param name="input2" type="data" format="fastqsanger" label="Reverse FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/></when> - </conditional> + </conditional><conditional name="params"><param name="source_select" type="select" label="BWA settings to use" help="For most mapping needs use Commonly Used settings. If you want full control use Full Parameter List"><option value="pre_set">Commonly Used</option> @@ -110,12 +118,13 @@ <param name="refGenomeSource" value="indexed" /> - <param name="indices" value="phiX" /> +  + <param name="indices" value="/galaxy/data/phiX/bwa_index/phiX.fa" /><param name="sPaired" value="single" /><param name="input1" value="bwa_wrapper_in1.fastq" ftype="fastqsanger" /><param name="source_select" value="pre_set" /> @@ -155,18 +164,19 @@ <param name="maxOccurPairing" value="100000" /><param name="suppressHeader" value="true" /><output name="output" file="bwa_wrapper_out2.sam" ftype="sam" sort="True" /> - </test> + </test><test><param name="refGenomeSource" value="indexed" /> - <param name="indices" value="phiX" /> +  + <param name="indices" value="/galaxy/data/phiX/bwa_index/phiX.fa" /><param name="sPaired" value="paired" /><param name="input1" value="bwa_wrapper_in2.fastq" ftype="fastqsanger" /><param name="input2" value="bwa_wrapper_in3.fastq" ftype="fastqsanger" /> --- a/tools/sr_mapping/bowtie_color_wrapper.xml +++ b/tools/sr_mapping/bowtie_color_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="bowtie_color_wrapper" name="Map with Bowtie for SOLiD" version="1.0.0"> +<tool id="bowtie_color_wrapper" name="Map with Bowtie for SOLiD" version="1.1.0"><requirements><requirement type='package'>bowtie</requirement></requirements><description></description><command interpreter="python"> @@ -9,191 +9,105 @@ --suppressHeader=$suppressHeader --genomeSource=$refGenomeSource.genomeSource #if $refGenomeSource.genomeSource == "history": - #if $refGenomeSource.ownFile.extension.startswith( 'bowtie_' ): - --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}" - --do_not_build_index - #else: - --ref=$refGenomeSource.ownFile - --indexSettings=$refGenomeSource.indexParams.indexSettings - #if $refGenomeSource.indexParams.indexSettings == "indexFull": - --iautoB=$refGenomeSource.indexParams.autoBehavior.autoB - #if $refGenomeSource.indexParams.autoBehavior.autoB == "set": - --ipacked=$refGenomeSource.indexParams.autoBehavior.packed - --ibmax=$refGenomeSource.indexParams.autoBehavior.bmax - --ibmaxdivn=$refGenomeSource.indexParams.autoBehavior.bmaxdivn - --idcv=$refGenomeSource.indexParams.autoBehavior.dcv + ##index already exists + #if $refGenomeSource.ownFile.extension.startswith( 'bowtie_' ): + ##user previously built + --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}" + --do_not_build_index #else: - --ipacked="None" - --ibmax="None" - --ibmaxdivn="None" - --idcv="None" + ##build index on the fly + --ref=$refGenomeSource.ownFile + --indexSettings=$refGenomeSource.indexParams.indexSettings + #if $refGenomeSource.indexParams.indexSettings == "indexFull": + --iautoB=$refGenomeSource.indexParams.autoBehavior.autoB + #if $refGenomeSource.indexParams.autoBehavior.autoB == "set": + --ipacked=$refGenomeSource.indexParams.autoBehavior.packed + --ibmax=$refGenomeSource.indexParams.autoBehavior.bmax + --ibmaxdivn=$refGenomeSource.indexParams.autoBehavior.bmaxdivn + --idcv=$refGenomeSource.indexParams.autoBehavior.dcv + #end if + --inodc=$refGenomeSource.indexParams.nodc + --inoref=$refGenomeSource.indexParams.noref + --ioffrate=$refGenomeSource.indexParams.offrate + --iftab=$refGenomeSource.indexParams.ftab + --intoa=$refGenomeSource.indexParams.ntoa + --iendian=$refGenomeSource.indexParams.endian + --iseed=$refGenomeSource.indexParams.seed + --icutoff=$refGenomeSource.indexParams.cutoff + #end if #end if - --inodc=$refGenomeSource.indexParams.nodc - --inoref=$refGenomeSource.indexParams.noref - --ioffrate=$refGenomeSource.indexParams.offrate - --iftab=$refGenomeSource.indexParams.ftab - --intoa=$refGenomeSource.indexParams.ntoa - --iendian=$refGenomeSource.indexParams.endian - --iseed=$refGenomeSource.indexParams.seed - --icutoff=$refGenomeSource.indexParams.cutoff - #else: - --iautoB="None" - --ipacked="None" - --ibmax="None" - --ibmaxdivn="None" - --idcv="None" - --inodc="None" - --inoref="None" - --ioffrate="None" - --iftab="None" - --intoa="None" - --iendian="None" - --iseed="None" - --icutoff="None" - #end if - #end if - #else: - --ref=$refGenomeSource.index - --indexSettings="None" - --iautoB="None" - --ipacked="None" - --ibmax="None" - --ibmaxdivn="None" - --idcv="None" - --inodc="None" - --inoref="None" - --ioffrate="None" - --iftab="None" - --intoa="None" - --iendian="None" - --iseed="None" - --icutoff="None" + #else + ##use pre-built index + --ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'bowtie_indexes_color' ].get_fields() )[0][-1] }" #end if --paired=$singlePaired.sPaired #if $singlePaired.sPaired == "single": - --input1=$singlePaired.sInput1 - --input2="None" - --params=$singlePaired.sParams.sSettingsType - #if $singlePaired.sParams.sSettingsType == "full": - --skip=$singlePaired.sParams.sSkip - --alignLimit=$singlePaired.sParams.sAlignLimit - --trimH=$singlePaired.sParams.sTrimH - --trimL=$singlePaired.sParams.sTrimL - --mismatchSeed=$singlePaired.sParams.sMismatchSeed - --mismatchQual=$singlePaired.sParams.sMismatchQual - --seedLen=$singlePaired.sParams.sSeedLen - --rounding=$singlePaired.sParams.sRounding - --maqSoapAlign=$singlePaired.sParams.sMaqSoapAlign - --tryHard=$singlePaired.sParams.sTryHard - --valAlign=$singlePaired.sParams.sValAlign - --allValAligns=$singlePaired.sParams.sAllValAligns - --suppressAlign=$singlePaired.sParams.sSuppressAlign - --best=$singlePaired.sParams.sBestOption.sBest - #if $singlePaired.sParams.sBestOption.sBest == "doBest": - --maxBacktracks=$singlePaired.sParams.sBestOption.sdMaxBacktracks - --strata=$singlePaired.sParams.sBestOption.sdStrata - #else: - --maxBacktracks=$singlePaired.sParams.sBestOption.snMaxBacktracks - --strata="None" + --input1=$singlePaired.sInput1 + --params=$singlePaired.sParams.sSettingsType + #if $singlePaired.sParams.sSettingsType == "full": + --skip=$singlePaired.sParams.sSkip + --alignLimit=$singlePaired.sParams.sAlignLimit + --trimH=$singlePaired.sParams.sTrimH + --trimL=$singlePaired.sParams.sTrimL + --mismatchSeed=$singlePaired.sParams.sMismatchSeed + --mismatchQual=$singlePaired.sParams.sMismatchQual + --seedLen=$singlePaired.sParams.sSeedLen + --rounding=$singlePaired.sParams.sRounding + --maqSoapAlign=$singlePaired.sParams.sMaqSoapAlign + --tryHard=$singlePaired.sParams.sTryHard + --valAlign=$singlePaired.sParams.sValAlign + --allValAligns=$singlePaired.sParams.sAllValAligns + --suppressAlign=$singlePaired.sParams.sSuppressAlign + --best=$singlePaired.sParams.sBestOption.sBest + #if $singlePaired.sParams.sBestOption.sBest == "doBest": + --maxBacktracks=$singlePaired.sParams.sBestOption.sdMaxBacktracks + --strata=$singlePaired.sParams.sBestOption.sdStrata + #else: + --maxBacktracks=$singlePaired.sParams.sBestOption.snMaxBacktracks + #end if + --offrate=$singlePaired.sParams.sOffrate + --seed=$singlePaired.sParams.sSeed + --snpphred=$singlePaired.sParams.sSnpphred + --snpfrac=$singlePaired.sParams.sSnpfrac + --keepends=$singlePaired.sParams.sKeepends #end if - --offrate=$singlePaired.sParams.sOffrate - --seed=$singlePaired.sParams.sSeed - --snpphred=$singlePaired.sParams.sSnpphred - --snpfrac=$singlePaired.sParams.sSnpfrac - --keepends=$singlePaired.sParams.sKeepends - #else: - --skip="None" - --alignLimit="None" - --trimH="None" - --trimL="None" - --mismatchSeed="None" - --mismatchQual="None" - --seedLen="None" - --rounding="None" - --maqSoapAlign="None" - --tryHard="None" - --valAlign="None" - --allValAligns="None" - --suppressAlign="None" - --best="None" - --maxBacktracks="None" - --strata="None" - --offrate="None" - --seed="None" - --snpphred="None" - --snpfrac="None" - --keepends="None" - #end if - --minInsert="None" - --maxInsert="None" - --mateOrient="None" - --maxAlignAttempt="None" - --forwardAlign="None" - --reverseAlign="None" #else: - --input1=$singlePaired.pInput1 - --input2=$singlePaired.pInput2 - --maxInsert=$singlePaired.pMaxInsert - --mateOrient=$singlePaired.pMateOrient - --params=$singlePaired.pParams.pSettingsType - #if $singlePaired.pParams.pSettingsType == "full": - --skip=$singlePaired.pParams.pSkip - --alignLimit=$singlePaired.pParams.pAlignLimit - --trimH=$singlePaired.pParams.pTrimH - --trimL=$singlePaired.pParams.pTrimL - --mismatchSeed=$singlePaired.pParams.pMismatchSeed - --mismatchQual=$singlePaired.pParams.pMismatchQual - --seedLen=$singlePaired.pParams.pSeedLen - --rounding=$singlePaired.pParams.pRounding - --maqSoapAlign=$singlePaired.pParams.pMaqSoapAlign - --minInsert=$singlePaired.pParams.pMinInsert - --maxAlignAttempt=$singlePaired.pParams.pMaxAlignAttempt - --forwardAlign=$singlePaired.pParams.pForwardAlign - --reverseAlign=$singlePaired.pParams.pReverseAlign - --tryHard=$singlePaired.pParams.pTryHard - --valAlign=$singlePaired.pParams.pValAlign - --allValAligns=$singlePaired.pParams.pAllValAligns - --suppressAlign=$singlePaired.pParams.pSuppressAlign - --best=$singlePaired.pParams.pBestOption.pBest - #if $singlePaired.pParams.pBestOption.pBest == "doBest": - --maxBacktracks=$singlePaired.pParams.pBestOption.pdMaxBacktracks - --strata=$singlePaired.pParams.pBestOption.pdStrata - #else: - --maxBacktracks=$singlePaired.pParams.pBestOption.pnMaxBacktracks - --strata="None" + --input1=$singlePaired.pInput1 + --input2=$singlePaired.pInput2 + --maxInsert=$singlePaired.pMaxInsert + --mateOrient=$singlePaired.pMateOrient + --params=$singlePaired.pParams.pSettingsType + #if $singlePaired.pParams.pSettingsType == "full": + --skip=$singlePaired.pParams.pSkip + --alignLimit=$singlePaired.pParams.pAlignLimit + --trimH=$singlePaired.pParams.pTrimH + --trimL=$singlePaired.pParams.pTrimL + --mismatchSeed=$singlePaired.pParams.pMismatchSeed + --mismatchQual=$singlePaired.pParams.pMismatchQual + --seedLen=$singlePaired.pParams.pSeedLen + --rounding=$singlePaired.pParams.pRounding + --maqSoapAlign=$singlePaired.pParams.pMaqSoapAlign + --minInsert=$singlePaired.pParams.pMinInsert + --maxAlignAttempt=$singlePaired.pParams.pMaxAlignAttempt + --forwardAlign=$singlePaired.pParams.pForwardAlign + --reverseAlign=$singlePaired.pParams.pReverseAlign + --tryHard=$singlePaired.pParams.pTryHard + --valAlign=$singlePaired.pParams.pValAlign + --allValAligns=$singlePaired.pParams.pAllValAligns + --suppressAlign=$singlePaired.pParams.pSuppressAlign + --best=$singlePaired.pParams.pBestOption.pBest + #if $singlePaired.pParams.pBestOption.pBest == "doBest": + --maxBacktracks=$singlePaired.pParams.pBestOption.pdMaxBacktracks + --strata=$singlePaired.pParams.pBestOption.pdStrata + #else: + --maxBacktracks=$singlePaired.pParams.pBestOption.pnMaxBacktracks + #end if + --offrate=$singlePaired.pParams.pOffrate + --seed=$singlePaired.pParams.pSeed + --snpphred=$singlePaired.pParams.pSnpphred + --snpfrac=$singlePaired.pParams.pSnpfrac + --keepends=$singlePaired.pParams.pKeepends #end if - --offrate=$singlePaired.pParams.pOffrate - --seed=$singlePaired.pParams.pSeed - --snpphred=$singlePaired.pParams.pSnpphred - --snpfrac=$singlePaired.pParams.pSnpfrac - --keepends=$singlePaired.pParams.pKeepends - #else: - --skip="None" - --alignLimit="None" - --trimH="None" - --trimL="None" - --mismatchSeed="None" - --mismatchQual="None" - --seedLen="None" - --rounding="None" - --maqSoapAlign="None" - --minInsert="None" - --maxAlignAttempt="None" - --forwardAlign="None" - --reverseAlign="None" - --tryHard="None" - --valAlign="None" - --allValAligns="None" - --suppressAlign="None" - --best="None" - --maxBacktracks="None" - --strata="None" - --offrate="None" - --seed="None" - --snpphred="None" - --snpfrac="None" - --keepends="None" - #end if #end if </command><inputs> @@ -204,10 +118,7 @@ </param><when value="indexed"><param name="index" type="select" label="Select the reference genome" help="if your genome of interest is not listed - contact Galaxy team"> - <options from_file="bowtie_indices_color.loc"> - <column name="value" index="1" /> - <column name="name" index="0" /> - </options> + <options from_data_table="bowtie_indexes_color"/></param></when><when value="history"> @@ -433,7 +344,8 @@ chrM_color needs to be the base location/name of the index files. --><param name="genomeSource" value="indexed" /> - <param name="index" value="equCab2chrM" /> +  + <param name="index" value="/galaxy/data/equCab2_chrM/bowtie_index/cs/chrM" /><param name="sPaired" value="single" /><param name="sInput1" ftype="fastqcssanger" value="bowtie_in1.fastqcssanger" /><param name="sSettingsType" value="preSet" /> @@ -492,7 +404,8 @@ chrM_base is the index files' location/base name. --><param name="genomeSource" value="indexed" /> - <param name="index" value="equCab2chrM" /> +  + <param name="index" value="/galaxy/data/equCab2_chrM/bowtie_index/cs/chrM" /><param name="sPaired" value="single" /><param name="sInput1" ftype="fastqcssanger" value="bowtie_in1.fastqcssanger" /><param name="sSettingsType" value="full" /> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.1"> +<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.5"><description>Search protein database with protein query sequence(s)</description><command> ## The command is a Cheetah template which allows some Python based syntax. @@ -37,9 +37,10 @@ blastp </param><when value="db"><param name="database" type="select" label="Protein BLAST database"> + <options from_file="blastdb_p.loc"> - <column name="name" index="0"/> - <column name="value" index="1"/> + <column name="name" index="2"/> + <column name="value" index="0"/></options></param><param name="subject" type="hidden" value="" /> --- a/tool-data/blastdb.loc.sample +++ b/tool-data/blastdb.loc.sample @@ -1,7 +1,8 @@ #This is a sample file distributed with Galaxy that is used to define a -#list of nucelotide BLAST databases, using two columns tab separated: +#list of nucleotide BLAST databases, using three columns tab separated +#(longer whitespace are TAB characters): # -#<database caption><path to base name> +#<unique_id><database_caption><base_name_path> # #The captions typically contain spaces and might end with the build date. #It is important that the actual database name does not have a space in it, @@ -11,7 +12,7 @@ #is /depot/data2/galaxy/blastdb/nt/nt.chunk, then the blastdb.loc entry #would look like this: # -#nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk +#nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk # #and your /depot/data2/galaxy/blastdb/nt directory would contain all of #your "base names" (e.g.): @@ -24,9 +25,14 @@ #Your blastdb.loc file should include an entry per line for each "base name" #you have stored. For example: # -#nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk -#wgs 30 Nov 2009 /depot/data2/galaxy/blastdb/wgs/wgs.chunk -#test 20 Sep 2008 /depot/data2/galaxy/blastdb/test/test +#nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk +#wgs_30_Nov_2009 wgs 30 Nov 2009 /depot/data2/galaxy/blastdb/wgs/wgs.chunk +#test_20_Sep_2008 test 20 Sep 2008 /depot/data2/galaxy/blastdb/test/test #...etc... # #See also blastdb_p.loc which is for any protein BLAST database. +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. +# --- a/test-data/bwa_wrapper_out2.sam +++ b/test-data/bwa_wrapper_out2.sam @@ -1,30 +1,30 @@ -seq1 16 phiX 322 25 36M * 0 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 -seq10 0 phiX 4149 37 17M1D19M * 0 0 ATTCTTTCTTTTCGTATCAGGGCGTTGAGTTCGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:5G11^G19 -seq11 0 phiX 4072 37 18M1D18M * 0 0 GCATTTCTACTCCTTCTCATCCCCAATGCTTGGCTT II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:12T5^A18 +seq1 16 phiX174 322 25 36M * 0 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 +seq10 0 phiX174 4149 37 17M1D19M * 0 0 ATTCTTTCTTTTCGTATCAGGGCGTTGAGTTCGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:5G11^G19 +seq11 0 phiX174 4072 37 18M1D18M * 0 0 GCATTTCTACTCCTTCTCATCCCCAATGCTTGGCTT II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:12T5^A18 seq12 4 * 0 0 * * 0 0 CGCGCTTCGATAAAAATGGGATTGGCGTTTCCAACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII seq13 4 * 0 0 * * 0 0 ATTTCTACTCTTTCTCATCCCCAATCCTTGCCTTCC IIIIIIIIIIIIIIIIIIIIIAAIIIIIIIIIIIII -seq14 0 phiX 3998 37 21M1D15M * 0 0 CCCTTTTGAATGTCACGCTGATATTTTGACTTTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:5C15^T15 +seq14 0 phiX174 3998 37 21M1D15M * 0 0 CCCTTTTGAATGTCACGCTGATATTTTGACTTTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:5C15^T15 seq15 4 * 0 0 * * 0 0 CCAACTTACCAAGGTGGGTTACGAAACGCGACGCCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII seq16 4 * 0 0 * * 0 0 TCAGGGTATTAAAAGAGATTATTTTTCTCCAGCCAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -seq17 0 phiX 3034 37 19M1D17M * 0 0 GTGATGTGCTTGCTACCGAAACAATACTTTAGGCAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:19^T9G7 +seq17 0 phiX174 3034 37 19M1D17M * 0 0 GTGATGTGCTTGCTACCGAAACAATACTTTAGGCAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:19^T9G7 seq18 4 * 0 0 * * 0 0 TCAATCCCCCATGCTTGGCCGTTCCATAAGCAGATG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII seq19 4 * 0 0 * * 0 0 TTCCTGCGCTTAATGCTTGAGCGTCCTGGTGCTGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -seq2 0 phiX 141 37 36M * 0 0 ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 -seq20 0 phiX 1082 37 36M * 0 0 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 -seq21 0 phiX 1344 37 15M1D21M * 0 0 CTGATACCAATAAAACCCTAAGCATTTGGTTCAGGG II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:15^T13T7 +seq2 0 phiX174 141 37 36M * 0 0 ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq20 0 phiX174 1082 37 36M * 0 0 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq21 0 phiX174 1344 37 15M1D21M * 0 0 CTGATACCAATAAAACCCTAAGCATTTGGTTCAGGG II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:15^T13T7 seq22 4 * 0 0 * * 0 0 AATCAAACTTACCAAGGGGTTACGACGCGACGCCGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII seq23 4 * 0 0 * * 0 0 TGTGCTTCCCCAACTTGATTTAATAACCCTATAGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -seq24 0 phiX 4084 37 17M1I18M * 0 0 TTTCTCAATCCCCAATGCCTTGGCTTCCCTAAGCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:27A7 -seq25 0 phiX 520 37 16M1I19M * 0 0 TTGCTACTGACCGCTCTTCGTGCTCGTTGCTGCGTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:26C8 -seq26 0 phiX 1976 37 36M * 0 0 CCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 -seq27 0 phiX 2598 37 20M1I15M * 0 0 CGCTAATCAAGTTGTTTCTGTTTGGTGCTGATATTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:9G25 +seq24 0 phiX174 4084 37 17M1I18M * 0 0 TTTCTCAATCCCCAATGCCTTGGCTTCCCTAAGCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:27A7 +seq25 0 phiX174 520 37 16M1I19M * 0 0 TTGCTACTGACCGCTCTTCGTGCTCGTTGCTGCGTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:26C8 +seq26 0 phiX174 1976 37 36M * 0 0 CCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq27 0 phiX174 2598 37 20M1I15M * 0 0 CGCTAATCAAGTTGTTTCTGTTTGGTGCTGATATTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:9G25 seq28 4 * 0 0 * * 0 0 AAAGAGATTATTTGTCGGTCCAGCCACTAAAGTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII seq29 4 * 0 0 * * 0 0 CAAATTAATGCGCGCTTCGATAATGATTGGGGTATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -seq3 0 phiX 505 37 36M * 0 0 GTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 -seq30 0 phiX 4091 37 18M1I17M * 0 0 ATCCCCTATGCTTGGCTTACCATAAGCAGATGGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:6A28 +seq3 0 phiX174 505 37 36M * 0 0 GTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq30 0 phiX174 4091 37 18M1I17M * 0 0 ATCCCCTATGCTTGGCTTACCATAAGCAGATGGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:6A28 seq4 4 * 0 0 * * 0 0 AGCCGCTCGTCTTTTATGTAGGTGGTCAACCATTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -seq5 0 phiX 4985 25 36M * 0 0 CAGTTATATGGCTTTTGGTTTCTATGTGGCTTAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:13G17A4 -seq6 0 phiX 925 37 11M1D25M * 0 0 AGGCGCTCGTCTTGGTATGTAGGTGGTCAACAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:1 X0:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:11^T25 -seq7 0 phiX 943 37 13M1I22M * 0 0 TGTAGGTGGTCAACCAATTTTAATTGCAGGGGCTTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:1 X0:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:35 +seq5 0 phiX174 4985 25 36M * 0 0 CAGTTATATGGCTTTTGGTTTCTATGTGGCTTAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:13G17A4 +seq6 0 phiX174 925 37 11M1D25M * 0 0 AGGCGCTCGTCTTGGTATGTAGGTGGTCAACAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:1 X0:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:11^T25 +seq7 0 phiX174 943 37 13M1I22M * 0 0 TGTAGGTGGTCAACCAATTTTAATTGCAGGGGCTTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:1 X0:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:35 seq8 4 * 0 0 * * 0 0 ACACCCGTCCTTTACGTCATGCGCTCTATTCTCTGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -seq9 0 phiX 2596 37 16M1I19M * 0 0 GCCGCTATTCAGGTTGTTTTCTGTTGGTGCTGATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:7A27 +seq9 0 phiX174 2596 37 16M1I19M * 0 0 GCCGCTATTCAGGTTGTTTTCTGTTGGTGCTGATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:7A27 --- a/test-data/lastz_wrapper_out3.tabular +++ b/test-data/lastz_wrapper_out3.tabular @@ -1,26 +1,22 @@ -phiX 1164 1165 + 5386 HWI-EAS91_1_306UPAAXX:6:1:112:1280 26 27 + 36 G T GTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTG GTTGGCGCTCTCCGTCTTTCTCCATTTCGTCGTG -phiX 2490 2491 + 5386 HWI-EAS91_1_306UPAAXX:6:1:486:822 10 11 - 36 C A ACCTGTTTTACAGACACCTAAAGCTACATCGTCAAC ACCTGTTTTAAAGACACCTAAAGCTACATCGTCAAC -phiX 2205 2206 + 5386 HWI-EAS91_1_306UPAAXX:6:1:217:737 14 15 + 36 G T GTTCAGTTGTTGCAGTGGAATA GTTCAGTTGTTGCATTGGAATA -phiX 2173 2174 + 5386 HWI-EAS91_1_306UPAAXX:6:1:259:1389 26 27 + 36 G T GCGTACTTATTCGCCACCATGATTATGACCAGTGTT GCGTACTTATTCGCCACCATGATTATTACCAGTGTT -phiX 578 579 + 5386 HWI-EAS91_1_306UPAAXX:6:1:317:1411 8 9 + 36 G T GTACGCTGGACTTTGTGGGATACCCTCGCTTTCCT GTACGCTGTACTTTGTGGGATACCCTCGCTTTCCT -phiX 2992 2993 + 5386 HWI-EAS91_1_306UPAAXX:6:1:458:1629 23 24 + 36 G T GCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGT GCTGGTGGCGCCATGTCTAAATTTTTTGGAGGCGGT -phiX 4783 4784 + 5386 HWI-EAS91_1_306UPAAXX:6:1:646:59 18 19 - 36 C T CATTTCCATGCGGTGCACTTTATGCGGACACTTCC CATTTCCATGCGGTGCATTTTATGCGGACACTTCC -phiX 1649 1650 + 5386 HWI-EAS91_1_306UPAAXX:6:1:295:694 24 25 + 36 A G GTGATTACTTCATGCAGCGTTACCATGATGTTATTT GTGATTACTTCATGCAGCGTTACCGTGATGTTATTT -phiX 1995 1996 + 5386 HWI-EAS91_1_306UPAAXX:6:1:590:331 14 15 + 36 G T GAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGAT GAAATTTCTATGAATGATGTTTTCCGTTCTGGTGAT -phiX 3261 3262 + 5386 HWI-EAS91_1_306UPAAXX:6:1:221:1238 17 18 - 36 C A AAGTCTGCCGCTGATAAAGGAAAGGATAC AAGTCTGCCGATGATAAAGGAAAGGATAC -phiX 4109 4110 + 5386 HWI-EAS91_1_306UPAAXX:6:1:478:252 12 13 - 36 C A ATGCTTGGCTTCCATAAGCAGATGGATAACCGCATC ATGCTTGGCTTCAATAAGCAGATGGATAACCGCATC -phiX 3126 3127 + 5386 HWI-EAS91_1_306UPAAXX:6:1:589:96 28 29 - 36 A G CAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCC CAAGGCTCTAATGTTCCTAACCCTGATGGGGCCGCC -phiX 2569 2570 + 5386 HWI-EAS91_1_306UPAAXX:6:1:1472:716 23 24 + 36 G T TGGTAATGGTGGTTTTCTTCATTGCATTCAG TGGTAATGGTGGTTTTCTTCATTTCATTCAG -phiX 2972 2973 + 5386 HWI-EAS91_1_306UPAAXX:6:1:836:1204 17 18 + 36 G T TTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAAT TTGCTTCTGCTCTTGCTTGTGGCGCCATGTCTAAAT -phiX 2234 2235 + 5386 HWI-EAS91_1_306UPAAXX:6:1:172:1412 13 14 - 36 C A AAATTTAATGTGACCGTTTATCGCAATCTGCCGACC AAATTTAATGTGAACGTTTATCGCAATCTGCCGACC -phiX 2902 2903 + 5386 HWI-EAS91_1_306UPAAXX:6:1:540:1415 18 19 + 36 G T TTATTAAAGAGATTATTTGTCTCCAGCCACTTA TTATTAAAGAGATTATTTTTCTCCAGCCACTTA -phiX 2837 2838 + 5386 HWI-EAS91_1_306UPAAXX:6:1:253:1162 14 15 - 36 T A ATGGTTTGGTCTAACTTTACCGCTACTAAATGC ATGGTTTGGTCAAACTTTACCGCTACTAAATGC -phiX 4662 4663 + 5386 HWI-EAS91_1_306UPAAXX:6:1:828:754 26 27 + 36 G T TTTGCGTGACTATTTTCGTGATATTGGTCGTATGGT TTTGCGTGACTATTTTCGTGATATTGTTCGTATGGT -phiX 4202 4203 + 5386 HWI-EAS91_1_306UPAAXX:6:1:891:1437 19 20 + 36 G T TAATGGTGATATGTATGTTGACGGCCATAAGGCTG TAATGGTGATATGTATGTTTACGTCCATAAGGCTG -phiX 4206 4207 + 5386 HWI-EAS91_1_306UPAAXX:6:1:891:1437 23 24 + 36 G T TAATGGTGATATGTATGTTGACGGCCATAAGGCTG TAATGGTGATATGTATGTTTACGTCCATAAGGCTG -phiX 430 431 + 5386 HWI-EAS91_1_306UPAAXX:6:1:203:667 9 10 - 36 T C AGACCGCTTTGGCCTCTATTAAGC AGACCGCCTTGGCCTCTATTAAGC -phiX 4783 4784 + 5386 HWI-EAS91_1_306UPAAXX:6:1:1566:499 9 10 + 36 C T TGCGGTGCACTTTATGCGGACACTTCCTACAGGTAG TGCGGTGCATTTTATGCGGACACTTCCTACAGGTAG -phiX 2857 2858 + 5386 HWI-EAS91_1_306UPAAXX:6:1:578:971 15 16 + 36 G T CGCTACTAAATGCCGCGGATTGGTTTCG CGCTACTAAATTCCGCGGATTGGTTTCG -phiX 3112 3113 + 5386 HWI-EAS91_1_306UPAAXX:6:1:1721:1800 27 28 - 36 T C TCAAGGCTCTAATGTTCCTAACCC TCAAGGCTCTAATGTCCCTAACCC -phiX 4825 4826 + 5386 HWI-EAS91_1_306UPAAXX:6:1:815:1640 9 10 - 36 T G CCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCA CCCTAATTTGGGTCGTCGGGTACGCAATCGCCGCCA -phiX 4517 4518 + 5386 HWI-EAS91_1_306UPAAXX:6:1:1485:741 19 20 - 36 G A GAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGAT GAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGAT +phiX174 1164 1165 + 5386 HWI-EAS91_1_306UPAAXX:6:1:112:1280 26 27 + 36 G T GTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTG GTTGGCGCTCTCCGTCTTTCTCCATTTCGTCGTG +phiX174 2490 2491 + 5386 HWI-EAS91_1_306UPAAXX:6:1:486:822 10 11 - 36 C A ACCTGTTTTACAGACACCTAAAGCTACATCGTCAAC ACCTGTTTTAAAGACACCTAAAGCTACATCGTCAAC +phiX174 2205 2206 + 5386 HWI-EAS91_1_306UPAAXX:6:1:217:737 14 15 + 36 G T GTTCAGTTGTTGCAGTGGAATA GTTCAGTTGTTGCATTGGAATA +phiX174 2173 2174 + 5386 HWI-EAS91_1_306UPAAXX:6:1:259:1389 26 27 + 36 G T GCGTACTTATTCGCCACCATGATTATGACCAGTGTT GCGTACTTATTCGCCACCATGATTATTACCAGTGTT +phiX174 578 579 + 5386 HWI-EAS91_1_306UPAAXX:6:1:317:1411 8 9 + 36 G T GTACGCTGGACTTTGTGGGATACCCTCGCTTTCCT GTACGCTGTACTTTGTGGGATACCCTCGCTTTCCT +phiX174 2992 2993 + 5386 HWI-EAS91_1_306UPAAXX:6:1:458:1629 23 24 + 36 G T GCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGT GCTGGTGGCGCCATGTCTAAATTTTTTGGAGGCGGT +phiX174 1995 1996 + 5386 HWI-EAS91_1_306UPAAXX:6:1:590:331 14 15 + 36 G T GAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGAT GAAATTTCTATGAATGATGTTTTCCGTTCTGGTGAT +phiX174 3261 3262 + 5386 HWI-EAS91_1_306UPAAXX:6:1:221:1238 17 18 - 36 C A AAGTCTGCCGCTGATAAAGGAAAGGATAC AAGTCTGCCGATGATAAAGGAAAGGATAC +phiX174 4109 4110 + 5386 HWI-EAS91_1_306UPAAXX:6:1:478:252 12 13 - 36 C A ATGCTTGGCTTCCATAAGCAGATGGATAACCGCATC ATGCTTGGCTTCAATAAGCAGATGGATAACCGCATC +phiX174 3126 3127 + 5386 HWI-EAS91_1_306UPAAXX:6:1:589:96 28 29 - 36 A G CAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCC CAAGGCTCTAATGTTCCTAACCCTGATGGGGCCGCC +phiX174 2569 2570 + 5386 HWI-EAS91_1_306UPAAXX:6:1:1472:716 23 24 + 36 G T TGGTAATGGTGGTTTTCTTCATTGCATTCAG TGGTAATGGTGGTTTTCTTCATTTCATTCAG +phiX174 2972 2973 + 5386 HWI-EAS91_1_306UPAAXX:6:1:836:1204 17 18 + 36 G T TTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAAT TTGCTTCTGCTCTTGCTTGTGGCGCCATGTCTAAAT +phiX174 2234 2235 + 5386 HWI-EAS91_1_306UPAAXX:6:1:172:1412 13 14 - 36 C A AAATTTAATGTGACCGTTTATCGCAATCTGCCGACC AAATTTAATGTGAACGTTTATCGCAATCTGCCGACC +phiX174 2902 2903 + 5386 HWI-EAS91_1_306UPAAXX:6:1:540:1415 18 19 + 36 G T TTATTAAAGAGATTATTTGTCTCCAGCCACTTA TTATTAAAGAGATTATTTTTCTCCAGCCACTTA +phiX174 2837 2838 + 5386 HWI-EAS91_1_306UPAAXX:6:1:253:1162 14 15 - 36 T A ATGGTTTGGTCTAACTTTACCGCTACTAAATGC ATGGTTTGGTCAAACTTTACCGCTACTAAATGC +phiX174 4662 4663 + 5386 HWI-EAS91_1_306UPAAXX:6:1:828:754 26 27 + 36 G T TTTGCGTGACTATTTTCGTGATATTGGTCGTATGGT TTTGCGTGACTATTTTCGTGATATTGTTCGTATGGT +phiX174 4202 4203 + 5386 HWI-EAS91_1_306UPAAXX:6:1:891:1437 19 20 + 36 G T TAATGGTGATATGTATGTTGACGGCCATAAGGCTG TAATGGTGATATGTATGTTTACGTCCATAAGGCTG +phiX174 4206 4207 + 5386 HWI-EAS91_1_306UPAAXX:6:1:891:1437 23 24 + 36 G T TAATGGTGATATGTATGTTGACGGCCATAAGGCTG TAATGGTGATATGTATGTTTACGTCCATAAGGCTG +phiX174 430 431 + 5386 HWI-EAS91_1_306UPAAXX:6:1:203:667 9 10 - 36 T C AGACCGCTTTGGCCTCTATTAAGC AGACCGCCTTGGCCTCTATTAAGC +phiX174 2857 2858 + 5386 HWI-EAS91_1_306UPAAXX:6:1:578:971 15 16 + 36 G T CGCTACTAAATGCCGCGGATTGGTTTCG CGCTACTAAATTCCGCGGATTGGTTTCG +phiX174 3112 3113 + 5386 HWI-EAS91_1_306UPAAXX:6:1:1721:1800 27 28 - 36 T C TCAAGGCTCTAATGTTCCTAACCC TCAAGGCTCTAATGTCCCTAACCC +phiX174 4825 4826 + 5386 HWI-EAS91_1_306UPAAXX:6:1:815:1640 9 10 - 36 T G CCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCA CCCTAATTTGGGTCGTCGGGTACGCAATCGCCGCCA --- a/tools/metag_tools/megablast_wrapper.py +++ b/tools/metag_tools/megablast_wrapper.py @@ -29,15 +29,12 @@ def stop_err( msg ): def __main__(): #Parse Command Line options, args = doc_optparse.parse( __doc__ ) - - db_build = options.db_build query_filename = options.input.strip() output_filename = options.output.strip() mega_word_size = options.word_size # -W mega_iden_cutoff = options.identity_cutoff # -p mega_evalue_cutoff = options.eval_cutoff # -e mega_temp_output = tempfile.NamedTemporaryFile().name - mega_filter = options.filter_query # -F GALAXY_DATA_INDEX_DIR = options.index_dir DB_LOC = "%s/blastdb.loc" % GALAXY_DATA_INDEX_DIR @@ -47,30 +44,20 @@ def __main__(): except: stop_err( 'Invalid value for word size' ) try: - float(mega_iden_cutoff) + float( mega_iden_cutoff ) except: stop_err( 'Invalid value for identity cut-off' ) try: - float(mega_evalue_cutoff) + float( mega_evalue_cutoff ) except: stop_err( 'Invalid value for Expectation value' ) - # prepare the database - db = {} - for i, line in enumerate( file( DB_LOC ) ): - line = line.rstrip( '\r\n' ) - if not line or line.startswith( '#' ): - continue - fields = line.split( '\t' ) - db[ fields[0] ] = fields[1] + if not os.path.exists( os.path.split( options.db_build )[0] ): + stop_err( 'Cannot locate the target database directory. Please check your location file.' ) - if not db.has_key( db_build ): - stop_err( 'Cannot locate the target database. Please check your location file.' ) - - # arguments for megablast - chunk = db[ ( db_build ) ] - megablast_command = "megablast -d %s -i %s -o %s -m 8 -a 8 -W %s -p %s -e %s -F %s > /dev/null " \ - % ( chunk, query_filename, mega_temp_output, mega_word_size, mega_iden_cutoff, mega_evalue_cutoff, mega_filter ) + # arguments for megablast + megablast_command = "megablast -d %s -i %s -o %s -m 8 -a 8 -W %s -p %s -e %s -F %s > /dev/null" \ + % ( options.db_build, query_filename, mega_temp_output, mega_word_size, mega_iden_cutoff, mega_evalue_cutoff, options.filter_query ) print megablast_command --- a/tool-data/srma_index.loc.sample +++ b/tool-data/srma_index.loc.sample @@ -3,15 +3,15 @@ #to create these data files and then create a srma_index.loc file #similar to this one (store it in this directory) that points to #the directories in which those files are stored. The srma_index.loc -#file has this format (white space is the TAB character): +#file has this format (longer white space is the TAB character): # -#<build><fasta_file> +#<unique_build_id><dbkey><display_name><fasta_file_path> # #So, for example, if you had hg18 indexed and stored in #/depot/data2/galaxy/srma/hg18/, #then the srma_index.loc entry would look like this: # -#hg18 /depot/data2/galaxy/srma/hg18/hg18.fa +#hg18 hg18 hg18 Pretty /depot/data2/galaxy/srma/hg18/hg18.fa # #and your /depot/data2/galaxy/srma/hg18/ directory #would contain the following three files: @@ -23,3 +23,4 @@ #created via Picard (http://picard.sourceforge.net) Note that #the dict file does not have the .fa extension although the #path list in the loc file does include it. +# --- a/tools/sr_mapping/lastz_paired_reads_wrapper.xml +++ b/tools/sr_mapping/lastz_paired_reads_wrapper.xml @@ -1,20 +1,21 @@ -<tool id="lastz_paired_reads_wrapper" name="Lastz paired reads" version="1.0.0"> +<tool id="lastz_paired_reads_wrapper" name="Lastz paired reads" version="1.1.0"><description> map short paired reads against reference sequence</description><command interpreter="python">lastz_paired_reads_wrapper.py -#if $seq_name.how_to_name=="yes": ---ref_name=$seq_name.ref_name -#else: ---ref_name="None" -#end if ---ref_source=$source.ref_source --input2=$input2 --input3=$input3 --input4=$input4 -#if $source.ref_source=="history": ---input1=$source.input1 ---ref_sequences=$input1.metadata.sequences -#else: ---input1=$source.input1_2bit ---ref_sequences="None" -#end if ---output=$output1 --lastz_seqs_file_dir=${GALAXY_DATA_INDEX_DIR} + #if $seq_name.how_to_name=="yes": + --ref_name=$seq_name.ref_name + #end if + --ref_source=$source.ref_source + --input2=$input2 + --input3=$input3 + --input4=$input4 + #if $source.ref_source=="history": + --input1=$source.input1 + --ref_sequences=$input1.metadata.sequences + #else: + --input1="${ filter( lambda x: str( x[0] ) == str( $source.input1_2bit ), $__app__.tool_data_tables[ 'lastz_seqs' ].get_fields() )[0][-1] }" + #end if + --output=$output1 + --lastz_seqs_file_dir=${GALAXY_DATA_INDEX_DIR} </command><inputs><param name="input2" format="fasta" type="data" label="Align sequencing reads in" /> @@ -25,10 +26,7 @@ </param><when value="cached"><param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> - <options from_file="lastz_seqs.loc"> - <column name="value" index="1" /> - <column name="name" index="0" /> - </options> + <options from_data_table="lastz_seqs" /></param></when><when value="history"> @@ -64,7 +62,7 @@ --><param name="input2" value="lastz_paired_input2.fasta" ftype="fasta" /><param name="ref_source" value="cached" /> - <param name="input1_2bit" value="hg18Chr21" /> + <param name="input1_2bit" value="/galaxy/data/hg18/seq/chr21.2bit" /><param name="input3" value="lastz_paired_input3.fasta" ftype="fasta" /><param name="input4" value="lastz_paired_input4.qual454" ftype="qual454" /><param name="how_to_name" value="no" /> --- a/tools/sr_mapping/lastz_wrapper.py +++ b/tools/sr_mapping/lastz_wrapper.py @@ -156,7 +156,7 @@ def __main__(): unmask = '[unmask]' else: unmask = '' - if options.ref_name != 'None': + if options.ref_name: ref_name = '[nickname=%s]' % options.ref_name else: ref_name = '' --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.1"> +<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.5"><description>Search translated nucleotide database with translated nucleotide query sequence(s)</description><command> ## The command is a Cheetah template which allows some Python based syntax. @@ -35,9 +35,10 @@ tblastx </param><when value="db"><param name="database" type="select" label="Nucleotide BLAST database"> + <options from_file="blastdb.loc"> - <column name="name" index="0"/> - <column name="value" index="1"/> + <column name="name" index="2"/> + <column name="value" index="0"/></options></param><param name="subject" type="hidden" value="" /> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.1"> +<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.5"><description>Search protein database with translated nucleotide query sequence(s)</description><command> ## The command is a Cheetah template which allows some Python based syntax. @@ -36,9 +36,10 @@ blastx </param><when value="db"><param name="database" type="select" label="Protein BLAST database"> + <options from_file="blastdb_p.loc"> - <column name="name" index="0"/> - <column name="value" index="1"/> + <column name="name" index="2"/> + <column name="value" index="0"/></options></param><param name="subject" type="hidden" value="" /> --- a/test-data/perm_in1.fastqsanger +++ b/test-data/perm_in1.fastqsanger @@ -1,76 +1,76 @@ @HWI-EAS91_1_30788AAXX:1:1:1761:343/1 TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA -+/1 ++ IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII @HWI-EAS91_1_30788AAXX:1:1:1578:331/1 TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1647:512/1 TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1570:620/1 GAGTAACAAAGTaaaGTTTGGAccGTTTTTGTCTCGTGCTCGTCGCTGCG -+/1 ++ IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1599:330/1 AGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTC -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1652:270/1 AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGacTTTGCATTGTTTAATTG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1746:351/1 CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1582:633/1 CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1598:534/1 GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1572:324/1 AAGGTGCTTaaaTTCgtGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1749:466/1 TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1629:446/1 AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1763:587/1 AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1616:363/1 TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1768:715/1 ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT -+/1 ++ IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1572:270/1 TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1785:1272/1 TATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCT -+/1 ++ III""""""IIIIIIIII""FI"IIII""II+ICI"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1673:514/1 ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1634:330/1 GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII --- a/tool_data_table_conf.xml.sample +++ b/tool_data_table_conf.xml.sample @@ -1,17 +1,37 @@ <tables> +  + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table><table name="bfast_indexes" comment_char="#"><columns>value, dbkey, formats, name, path</columns><file path="tool-data/bfast_indexes.loc" /></table> +  + <table name="blastdb" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/blastdb.loc" /> + </table> +  + <table name="blastdb_p" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/blastdb_p.loc" /> + </table> - <table name="bowtie_indexes"> - <columns>name, value</columns> + <table name="bowtie_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns><file path="tool-data/bowtie_indices.loc" /></table> +  + <table name="bowtie_indexes_color" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bowtie_indices_color.loc" /> + </table> - <table name="bwa_indexes"> - <columns>name, value</columns> + <table name="bwa_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns><file path="tool-data/bwa_index.loc" /></table> @@ -24,4 +44,30 @@ <columns>value, dbkey, name, path</columns><file path="tool-data/ngs_sim_fasta.loc" /></table> +  + <table name="lastz_seqs" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/lastz_seqs.loc" /> + </table> +  + <table name="perm_base_indexes" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/perm_base_index.loc" /> + </table> +  + <table name="perm_color_indexes" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/perm_color_index.loc" /> + </table> +  + <table name="srma_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/srma_index.loc" /> + </table> +  +</tables> --- a/test-data/phiX.fasta +++ b/test-data/phiX.fasta @@ -1,109 +1,79 @@ ->phiX -GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTG -ATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTA -CGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTA -TCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACT -AACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATA -TGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTT -CATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC -TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGT -TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA -TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG -ACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTG -CGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCT -TTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT -CCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC -GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGT -TCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGAC -GCAGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATG -TCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTT -GCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTG -GTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATT -ATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA -TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTA -CTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTC -CGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACAT -TTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTA -AGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACT -ACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATAC -CAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA -ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAAT -GAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAA -AAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAA -TGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTAT -GCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCg -TGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACC -GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT -GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACA -GACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTA -TGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATT -CAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGA -CCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATG -TTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAG -TGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA -AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCG -TACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTG -TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT -GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG -AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT -TGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTT -CAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT -TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTA -AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT -AATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGC -TAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTA -AATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACC -CTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATGGTGG -TTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC -CGGGCAATAAtGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCT -ACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTAT -TTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGG -CGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAG -GCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACC -GATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCA -AGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG -GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCT -GGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGG -CAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTG -CATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCT -GCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAAT -GCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAA -AAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC -CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTAC -TGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGC -AGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGT -CAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGC -TGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTT -CTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCT -GCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA -TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTA -ATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTT -TTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCC -TTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTA -AACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATG -CTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGAT -TCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG -TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTT -ACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCA -ACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAAT -GGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCT -GCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAA -GAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGA -AATCGCGTAGAGGCTTTaCTATTCAGCGTTTGATGAATGCAATGCGACAG -GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGA -CGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATT -TTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAAT -GATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTAC -AGCTAATGGCCGTCTTCATTTCCATGCGGTGCAtTTTATGCGGACACTTC -CTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGC -CAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT -CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGC -CTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTT -GGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGC -TGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGC -TGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTC -GGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCA -ACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC -AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCC -GACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCG -CGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA +>phiX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT +GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA +ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG +TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA +GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT +TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT +CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT +TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG +TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC +GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA +CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG +TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT +AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC +CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA +TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC +TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA +CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA +GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT +GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA +ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC +TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT +TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC +ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC +CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT +GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC +CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC +TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG +TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT +TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA +AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT +TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT +ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC +GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC +TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT +TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA +TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG +TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC +CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG +AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC +CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT +TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG +CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA +AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT +GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA +TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT +CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG +TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA +GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC +CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA +TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA +AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC +TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT +CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA +TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG +TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT +CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT +TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC +ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG +TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA +ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG +GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC +CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT +GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG +GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT +ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG +CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC +CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC +GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT +CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG +CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA +TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT +TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG +TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC +AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC +TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA +

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galaxy-dist commit 3ea6ee14a8b7: Remove debugging statement from previous commit.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1289243761 18000 # Node ID 3ea6ee14a8b71cd7ac48da98a6ecdb50b9067040 # Parent c61ec9e333d5a0ade7a23b3f4b55ae3deb3aa0bb Remove debugging statement from previous commit. --- a/lib/galaxy/tools/util/gff_util.py +++ b/lib/galaxy/tools/util/gff_util.py @@ -53,7 +53,6 @@ def parse_gff_attributes( attr_str ): pair = name_value_pair.strip().split(" ") if len( pair ) == 1: pair = name_value_pair.strip().split("=") - print pair if pair == '': continue name = pair[0].strip()

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galaxy-dist commit c61ec9e333d5: Enable gff2bed tool to convert GFF3 files to BED and add functional test for this conversion.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1289243703 18000 # Node ID c61ec9e333d5a0ade7a23b3f4b55ae3deb3aa0bb # Parent 629e14c5f561446c963b05560f245e2ed7041ff0 Enable gff2bed tool to convert GFF3 files to BED and add functional test for this conversion. --- a/tools/filters/gff2bed.xml +++ b/tools/filters/gff2bed.xml @@ -16,6 +16,11 @@ <param name="input" value="gff2bed_in2.gff" ftype="gff"/><output name="out_file1" file="gff2bed_out2.bed"/></test> + <test> +  + <param name="input" value="5.gff3" ftype="gff"/> + <output name="out_file1" file="gff2bed_out3.bed"/> + </test></tests><help> --- /dev/null +++ b/test-data/gff2bed_out3.bed @@ -0,0 +1,145 @@ +ctgA 22131 24633 my_feature 0 + +ctgA 46989 48410 my_feature 0 - +ctgA 44704 47713 my_feature 0 - +ctgA 36648 40440 my_feature 0 - +ctgA 23071 23185 my_feature 0 + +ctgA 37241 38653 my_feature 0 + +ctgA 37496 40559 motif 0 - +ctgA 36033 38167 my_feature 0 + +ctgA 28331 30033 motif 0 - +ctgA 4714 5968 my_feature 0 - +ctgA 48252 48366 motif 0 + +ctgA 999 20000 BAC 0 + +ctgA 19499 20000 right_end_read 0 - +ctgA 999 1500 left_end_read 0 + +ctgA 13800 14007 motif 0 - +ctgA 1049 9000 coding 0 + +ctgA 1200 1500 CDS 0 + +ctgA 2999 3902 CDS 0 + +ctgA 4999 5500 CDS 0 + +ctgA 6999 7608 CDS 0 + +ctgA 1049 9000 processed_transcript 0 + +ctgA 1049 1200 5'-UTR 0 + +ctgA 7608 9000 3'-UTR 0 + +ctgA 5409 7503 match 0 - +ctgA 6999 7503 HSP 0 - +ctgA 5409 5500 HSP 0 - +ctgA 46011 48851 motif 0 + +ctgA 6884 8999 match 0 - +ctgA 8305 8999 HSP 0 - +ctgA 8054 8080 HSP 0 - +ctgA 7409 7737 HSP 0 - +ctgA 6884 7241 HSP 0 - +ctgA 13279 16394 my_feature 0 + +ctgA 29770 32937 match 0 + +ctgA 29770 29942 HSP 0 + +ctgA 30041 30340 HSP 0 + +ctgA 30809 31307 HSP 0 + +ctgA 31760 31984 HSP 0 + +ctgA 32373 32937 HSP 0 + +ctgA 36615 37227 match 0 - +ctgA 37207 37227 HSP 0 - +ctgA 36615 37057 HSP 0 - +ctgA 11910 15561 motif 0 + +ctgA 1049 3202 match 0 + +ctgA 1049 1500 HSP 0 + +ctgA 2999 3202 HSP 0 + +ctgA 15395 16159 motif 0 + +ctgA 1149 7200 match 0 + +ctgA 1149 1500 HSP 0 + +ctgA 4999 5500 HSP 0 + +ctgA 6999 7200 HSP 0 + +ctgA 1049 7300 match 0 + +ctgA 1049 1500 HSP 0 + +ctgA 4999 5500 HSP 0 + +ctgA 6999 7300 HSP 0 + +ctgA 19156 22915 my_feature 0 - +ctgA 7999 9000 match 0 - +ctgA 7999 9000 HSP 0 - +ctgA 28341 28447 motif 0 - +ctgA 17666 17690 motif 0 + +ctgA 44400 45925 trace 0 + +ctgA 26121 34466 match 0 + +ctgA 26121 26126 HSP 0 + +ctgA 26496 26869 HSP 0 + +ctgA 27200 27325 HSP 0 + +ctgA 27371 27433 HSP 0 + +ctgA 27564 27565 HSP 0 + +ctgA 27812 28091 HSP 0 + +ctgA 28092 28201 HSP 0 + +ctgA 28328 28377 HSP 0 + +ctgA 28828 29194 HSP 0 + +ctgA 29516 29702 HSP 0 + +ctgA 29712 30061 HSP 0 + +ctgA 30328 30774 HSP 0 + +ctgA 30807 31306 HSP 0 + +ctgA 31515 31729 HSP 0 + +ctgA 31752 32154 HSP 0 + +ctgA 32594 32696 HSP 0 + +ctgA 32891 32901 HSP 0 + +ctgA 33126 33388 HSP 0 + +ctgA 33438 33443 HSP 0 + +ctgA 33758 34209 HSP 0 + +ctgA 34400 34466 HSP 0 + +ctgA 0 50000 contig 0 + +ctgA 41136 47829 match 0 - +ctgA 47448 47829 HSP 0 - +ctgA 46815 46992 HSP 0 - +ctgA 46091 46318 HSP 0 - +ctgA 45789 46022 HSP 0 - +ctgA 45230 45488 HSP 0 - +ctgA 44762 45030 HSP 0 - +ctgA 44064 44556 HSP 0 - +ctgA 43394 43811 HSP 0 - +ctgA 42889 43270 HSP 0 - +ctgA 42056 42474 HSP 0 - +ctgA 41753 41948 HSP 0 - +ctgA 41136 41318 HSP 0 - +ctgA 12530 15870 match 0 + +ctgA 12530 12895 HSP 0 + +ctgA 13121 13449 HSP 0 + +ctgA 13451 13745 HSP 0 + +ctgA 13907 13965 HSP 0 + +ctgA 13997 14488 HSP 0 + +ctgA 14563 14899 HSP 0 + +ctgA 15184 15276 HSP 0 + +ctgA 15638 15736 HSP 0 + +ctgA 15744 15870 HSP 0 + +ctgA 7499 8000 match 0 - +ctgA 7499 8000 HSP 0 - +ctgA 1299 9000 coding 0 + +ctgA 3300 3902 CDS 0 + +ctgA 4999 5500 CDS 0 + +ctgA 6999 7600 CDS 0 + +ctgA 1299 9000 processed_transcript 0 + +ctgA 1299 1500 5'-UTR 0 + +ctgA 2999 3300 5'-UTR 0 + +ctgA 7600 9000 3'-UTR 0 + +ctgA 26502 35904 match 0 - +ctgA 35641 35904 HSP 0 - +ctgA 35332 35507 HSP 0 - +ctgA 34604 34983 HSP 0 - +ctgA 34243 34313 HSP 0 - +ctgA 33437 33868 HSP 0 - +ctgA 33052 33325 HSP 0 - +ctgA 32207 32680 HSP 0 - +ctgA 32009 32057 HSP 0 - +ctgA 31420 31817 HSP 0 - +ctgA 31231 31236 HSP 0 - +ctgA 30464 30798 HSP 0 - +ctgA 30107 30216 HSP 0 - +ctgA 29512 29647 HSP 0 - +ctgA 28776 29058 HSP 0 - +ctgA 28224 28316 HSP 0 - +ctgA 27886 28076 HSP 0 - +ctgA 27447 27860 HSP 0 - +ctgA 27171 27185 HSP 0 - +ctgA 26502 26799 HSP 0 - +ctgA 49405 50000 match 0 + +ctgA 49405 49476 HSP 0 + +ctgA 49761 50000 HSP 0 + +ctgA 1049 9000 gene 0 + +ctgA 33324 35791 motif 0 + +ctgA 31784 32359 match 0 + +ctgA 31784 31939 HSP 0 + +ctgA 32328 32359 HSP 0 + --- a/lib/galaxy/tools/util/gff_util.py +++ b/lib/galaxy/tools/util/gff_util.py @@ -42,13 +42,18 @@ def convert_gff_coords_to_bed( interval def parse_gff_attributes( attr_str ): """ - Parses a GFF attribute string and returns a dictionary of name-value pairs. - The general format for a GFF attribute string is name1 "value1" ; name2 "value2" + Parses a GFF/GTF attribute string and returns a dictionary of name-value pairs. + The general format for a GFF3 attributes string is name1=value1;name2=value2 + The general format for a GTF attribute string is name1 "value1" ; name2 "value2" """ attributes_list = attr_str.split(";") attributes = {} for name_value_pair in attributes_list: + # Try splitting by space and, if necessary, by '=' sign. pair = name_value_pair.strip().split(" ") + if len( pair ) == 1: + pair = name_value_pair.strip().split("=") + print pair if pair == '': continue name = pair[0].strip()

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galaxy-dist commit d46ccc650084: Eliminate check_user flag from tool menu and workflow methods.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1289046578 14400 # Node ID d46ccc650084224553b3b48c11df64d43d7673ef # Parent 702f4717a8f3fe38758c54136f81935f7679c937 Eliminate check_user flag from tool menu and workflow methods. --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -1206,14 +1206,13 @@ class WorkflowController( BaseController ## % ( workflow_name, web.url_for( action='editor', id=trans.security.encode_id(stored.id) ) ) ) @web.expose - def run( self, trans, id, check_user=True, **kwargs ): + def run( self, trans, id, **kwargs ): stored = self.get_stored_workflow( trans, id, check_ownership=False ) - if check_user: - user = trans.get_user() - if stored.user != user: - if trans.sa_session.query( model.StoredWorkflowUserShareAssociation ) \ - .filter_by( user=user, stored_workflow=stored ).count() == 0: - error( "Workflow is not owned by or shared with current user" ) + user = trans.get_user() + if stored.user != user: + if trans.sa_session.query( model.StoredWorkflowUserShareAssociation ) \ + .filter_by( user=user, stored_workflow=stored ).count() == 0: + error( "Workflow is not owned by or shared with current user" ) # Get the latest revision workflow = stored.latest_workflow # It is possible for a workflow to have 0 steps @@ -1343,14 +1342,13 @@ class WorkflowController( BaseController incoming=kwargs ) @web.expose - def tag_outputs( self, trans, id, check_user=True, **kwargs ): + def tag_outputs( self, trans, id, **kwargs ): stored = self.get_stored_workflow( trans, id, check_ownership=False ) - if check_user: - user = trans.get_user() - if stored.user != user: - if trans.sa_session.query( model.StoredWorkflowUserShareAssociation ) \ - .filter_by( user=user, stored_workflow=stored ).count() == 0: - error( "Workflow is not owned by or shared with current user" ) + user = trans.get_user() + if stored.user != user: + if trans.sa_session.query( model.StoredWorkflowUserShareAssociation ) \ + .filter_by( user=user, stored_workflow=stored ).count() == 0: + error( "Workflow is not owned by or shared with current user" ) # Get the latest revision workflow = stored.latest_workflow # It is possible for a workflow to have 0 steps --- a/templates/root/tool_menu.mako +++ b/templates/root/tool_menu.mako @@ -32,7 +32,7 @@ <div class="toolTitleNoSection"> %endif <% encoded_id = key.lstrip( 'workflow_' ) %> - <a id="link-${workflow.id}" href="${ h.url_for( controller='workflow', action='run', id=encoded_id, check_user=False )}" target="_parent">${_(workflow.name)}</a> + <a id="link-${workflow.id}" href="${ h.url_for( controller='workflow', action='run', id=encoded_id )}" target="_parent">${_(workflow.name)}</a></div></%def>

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galaxy-dist commit fb55bfc792b1: Trackster UI tweaks, mainly moving the navigation to the top, still needs to be compressed and cleaned up. Also, getting borders and spacing a little more even. Some intial keyboard navigation
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User James Taylor <james(a)jamestaylor.org> # Date 1289163413 18000 # Node ID fb55bfc792b1d087783055a736d9fb439e5bb41c # Parent d46ccc650084224553b3b48c11df64d43d7673ef Trackster UI tweaks, mainly moving the navigation to the top, still needs to be compressed and cleaned up. Also, getting borders and spacing a little more even. Some intial keyboard navigation --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -15,8 +15,8 @@ ${h.css( "history", "autocomplete_tagging", "trackster", "overcast/jquery-ui-1.8.5.custom" )} <style type="text/css"> - #center { - overflow: auto; + #center, #browser-container { + overflow: none; } ul#sortable-ul { list-style: none; @@ -29,10 +29,7 @@ background: #eee; } .nav-container { - position: fixed; width: 100%; - left: 0; - bottom: 0; } # Styles for filters. .filter-name { @@ -57,6 +54,7 @@ <a id="add-track" class="panel-header-button right-float" href="javascript:void(0);">Add Tracks</a></div></div> +<div id="browser-container" class="unified-panel-body"></div></%def> @@ -79,7 +77,7 @@ $(function() { %if config: - view = new View( $("#center"), "${config.get('title') | h}", "${config.get('vis_id')}", "${config.get('dbkey')}" ); + view = new View( $("#browser-container"), "${config.get('title') | h}", "${config.get('vis_id')}", "${config.get('dbkey')}" ); view.editor = true; %for track in config.get('tracks'): view.add_track( @@ -215,6 +213,16 @@ error: function() { alert("Could not save visualization"); } }); }); + + $(document).keydown( function( e ) { + // 37 == left + if ( e.which == 39 ) { + view.move_fraction( -0.25 ); + // 39 == right + } else if ( e.which == 37 ) { + view.move_fraction( 0.25 ); + } + }); }; }); --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -103,15 +103,25 @@ var View = function( container, title, v // Create DOM elements var parent_element = this.container, view = this; - this.top_labeltrack = $("<div/>").addClass("top-labeltrack").appendTo(parent_element); + // Top container for things that are fixed at the top + this.top_container = $("<div/>").addClass("top-container").appendTo(parent_element); + // Content container, primary tracks are contained in here this.content_div = $("<div/>").addClass("content").css("position", "relative").appendTo(parent_element); + // Bottom container for things that are fixed at the bottom + this.bottom_container = $("<div/>").addClass("bottom-container").appendTo(parent_element); + // Label track fixed at top + this.top_labeltrack = $("<div/>").addClass("top-labeltrack").appendTo(this.top_container); + // Viewport for dragging tracks in center this.viewport_container = $("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div); - this.intro_div = $("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide(); // Future overlay - - this.nav_container = $("<div/>").addClass("nav-container").appendTo(parent_element); - this.nav_labeltrack = $("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container); + // Future overlay? + this.intro_div = $("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide(); + // Another label track at bottom + this.nav_labeltrack = $("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container); + // Navigation at top + this.nav_container = $("<div/>").addClass("nav-container").prependTo(this.top_container); this.nav = $("<div/>").addClass("nav").appendTo(this.nav_container); - this.overview = $("<div/>").addClass("overview").appendTo(this.nav); + // Overview (scrollbar and overview plot) at bottom + this.overview = $("<div/>").addClass("overview").appendTo(this.bottom_container); this.overview_viewport = $("<div/>").addClass("overview-viewport").appendTo(this.overview); this.overview_close = $("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport); this.overview_highlight = $("<div />").addClass("overview-highlight").hide().appendTo(this.overview_viewport); @@ -327,6 +337,11 @@ var View = function( container, title, v } view.change_chrom(chrom, new_low, new_high); }, + move_fraction : function( fraction ) { + var view = this; + var span = view.high - view.low; + this.move_delta( fraction * span ); + }, move_delta: function(delta_chrom) { var view = this; var current_chrom_span = view.high - view.low; @@ -439,7 +454,7 @@ var View = function( container, title, v this.redraw(); }, resize_window: function() { - this.viewport_container.height( this.container.height() - this.nav_container.height() - 45 ); + this.viewport_container.height( this.container.height() - this.top_container.height() - this.bottom_container.height() ); this.nav_container.width( this.container.width() ); this.redraw(); }, --- a/static/june_2007_style/blue/trackster.css +++ b/static/june_2007_style/blue/trackster.css @@ -1,7 +1,7 @@ .viewport-container{overflow-x:hidden;overflow-y:auto;} -.nav{padding:0 0;color:#333;font-weight:bold;} -.content{font:9px verdana;} -.nav-controls{text-align:center;position:relative;background:#cccccc;background-image:url(panel_header_bg.png);background-position:top center;background-repeat:repeat-x;padding:2px 0;} +.nav{padding:0 0;color:#333;font-weight:bold;background:#cccccc;background-image:url(panel_header_bg.png);background-position:bottom center;background-repeat:repeat-x;height:2.5em;border-bottom:solid #333 1px;} +.content{font:10px verdana;} +.nav-controls{text-align:center;position:relative;padding:2px 0;} .nav-controls input{margin:0 5px;} .nav-controls a{padding:0 0.4em;} .nav-input{font-size:12px;width:30em;z-index:1000;} @@ -9,24 +9,23 @@ .draghandle{cursor:move;float:left;background:transparent url(../images/visualization/draggable_horizontal.png) center center no-repeat;width:10px;height:12px;} .intro{z-index:1000;margin-left:auto;margin-right:auto;color:#555;text-align:center;font-size:16px;} .overview{width:100%;margin:0px;color:white;} -.overview-viewport{position:relative;height:14px;background:white;border-bottom:solid gray 1px;margin:0;} +.overview-viewport{position:relative;height:14px;background:white;margin:0;} .overview-close{font:9px verdana;position:absolute;top:0px;right:0px;padding:5px;z-index:500;background-color:white;} -.overview-highlight{opacity:0.5;top:0px;position:absolute;z-index:100;border-style:solid;border-color:#484848;border-width:0px 1px;} -.overview-boxback{width:100%;bottom:0px;z-index:50;position:absolute;height:14px;background:#eee;} -.overview-box{cursor:pointer;opacity:0.5;bottom:0px;z-index:100;position:absolute;margin-top:0px;height:14px;background:#484848 url(../images/visualization/draggable_horizontal.png) center center no-repeat;border-style:solid;border-color:#484848;border-width:0px 1px;-moz-border-radius:3px;border-radius:3px;} -.overview-box:hover{background-color:#838383;border-color:#838383;} +.overview-highlight{top:0px;position:absolute;z-index:100;border-style:solid;border-color:#666;border-width:0px 1px;} +.overview-boxback{width:100%;bottom:0px;z-index:50;position:absolute;height:14px;background:#eee;border:solid #999 1px;} +.overview-box{cursor:pointer;bottom:0px;z-index:100;position:absolute;margin-top:0px;height:14px;background:#C1C9E5 url(../images/visualization/draggable_horizontal.png) center center no-repeat;border:solid #666 1px;} .viewport-canvas{width:100%;height:100px;} .yaxislabel{color:#777;z-index:100;} .line-track .track-content{border-top:1px solid #ddd;border-bottom:1px solid #ddd;} -.track{background:white;margin-bottom:1px;} +.track{background:white;margin-bottom:1px;padding-bottom:4px;border-bottom:#eee solid 1px;} .track-header{text-align:left;padding:4px 0px;color:#666;} .track-header .menubutton{margin-left:3px;} .track-content{overflow:hidden;text-align:center;} -.track.error{background-color:#ECB4AF;} -.track.nodata{background-color:#ddd;} +.track.error .track-content{background-color:#ECB4AF;} +.track.nodata .track-content{background-color:#ddd;} .loading{min-height:100px;} -.label-track{} -.label-track .label{border-left:solid #999 1px;padding:1px;display:inline-block;} +.label-track{font-size:10px;border:none;padding:0;margin:0;height:1.3em;} +.label-track .label{border-left:solid #999 1px;padding:1px;padding-bottom:2px;display:inline-block;} .right-float{float:right;margin-left:5px;} .top-labeltrack{position:relative;border-bottom:solid #999 1px;} -.nav-labeltrack{border-top:solid #999 1px;border-bottom:solid #999 1px;} +.nav-labeltrack{border-top:solid #999 1px;border-bottom:solid #333 1px;} --- a/static/june_2007_style/trackster.css.tmpl +++ b/static/june_2007_style/trackster.css.tmpl @@ -5,17 +5,19 @@ .nav { padding: 0 0; color:#333;font-weight:bold; + background:#cccccc; + background-image:url(panel_header_bg.png); + background-position: bottom center; + background-repeat:repeat-x; + height: 2.5em; + border-bottom: solid #333 1px; } .content { - font: 9px verdana; + font: 10px verdana; } .nav-controls { text-align: center; position: relative; - background:#cccccc; - background-image:url(panel_header_bg.png); - background-position:top center; - background-repeat:repeat-x; padding: 2px 0; } .nav-controls input { @@ -61,7 +63,6 @@ /* border-top: solid #666 1px;*/ /* border-bottom: solid #aaa 1px;*/ background: white; - border-bottom: solid gray 1px; margin: 0; } .overview-close { @@ -74,12 +75,11 @@ background-color: white; } .overview-highlight { - opacity: 0.5; top: 0px; position: absolute; z-index: 100; border-style: solid; - border-color: #484848; + border-color: #666; border-width: 0px 1px; } .overview-boxback { @@ -89,25 +89,17 @@ position: absolute; height: 14px; background: #eee; + border: solid #999 1px; } .overview-box { cursor: pointer; - opacity: 0.5; bottom: 0px; z-index: 100; position: absolute; margin-top: 0px; height: 14px; - background: #484848 url(../images/visualization/draggable_horizontal.png) center center no-repeat; - border-style: solid; - border-color: #484848; - border-width: 0px 1px; - -moz-border-radius: 3px; - border-radius: 3px; -} -.overview-box:hover { - background-color: #838383; - border-color: #838383; + background: #C1C9E5 url(../images/visualization/draggable_horizontal.png) center center no-repeat; + border: solid #666 1px; } .viewport-canvas { width: 100%; @@ -129,6 +121,8 @@ /* border-bottom: solid #DDDDDD 1px; */ background: white; margin-bottom: 1px; + padding-bottom: 4px; + border-bottom: #eee solid 1px; } .track-header { @@ -146,10 +140,10 @@ text-align: center; } -.track.error { +.track.error .track-content { background-color: #ECB4AF; } -.track.nodata { +.track.nodata .track-content { background-color: #ddd; } @@ -159,11 +153,16 @@ .label-track { /* font-weight: bold; */ - /* font-size: 10px; */ + font-size: 10px; + border: none; + padding: 0; + margin: 0; + height: 1.3em; } .label-track .label { border-left: solid #999 1px; padding: 1px; + padding-bottom: 2px; display: inline-block; } .right-float { @@ -178,5 +177,5 @@ .nav-labeltrack { border-top: solid #999 1px; - border-bottom: solid #999 1px; + border-bottom: solid #333 1px; }

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