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
# 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
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__()
1
0
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
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))
1
0
galaxy-dist commit d344c55b4f81: another tiny rgHaploView tool test fix - pdfs differ on Main by 20kb.
by commits-noreply＠bitbucket.org 20 Nov '10
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"/>
1
0
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
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><!-- works with PerM version 0.2.6 --><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><!-- options -->
@@ -170,8 +170,7 @@ PerM
<test><!--
PerM command:
- PerM test-data/phiX.fasta 50 +seed F3 -m -s phiX_F3_50.index +readFormat .fastq
- PerM phiX_F3_50.index -1 test-data/perm_in1.fastqsanger -2 test-data/perm_in2.fastqsanger -U 100000 -L 0 -e +readFormat .fastq -v 0 +seed F2 -A -T 50 +includeReadsWN -o perm_out1.sam +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 /afs/bx.psu.edu/depot/data/genome/phiX/perm_index/phiX_base_F3_50.index -1 test-data/perm_in1.fastqsanger -2 test-data/perm_in2.fastqsanger -U 100000 -L 0 -e +readFormat fastq -v 0 +seed F3 -A -T 50 +includeReadsWN -o perm_out1.sam +outputFormat sam +noSamHeader | tr '\r' '\n' | tr -cd "[:print:]\t\n " | grep "Reads\|Sub0\|Pairs\|single" | sed 's/.*Reads:,//' | sed 's/\/.*dat,_ Sub0/Sub0/'
You need to replace the + with 2 dashes.
--><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><!--
PerM command:
- PerM test-data/chr_m.fasta test-data/perm_in3.fastqsanger +readFormat .fastq -v 2 -u perm_out3.fastqsanger -o perm_out2.sam +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 test-data/chr_m.fasta test-data/perm_in3.fastqsanger +readFormat fastq -v 2 -u perm_out3.fastqsanger -o perm_out2.sam +outputFormat sam +noSamHeader | tr '\r' '\n' | tr -cd "[:print:]\t\n " | grep "Reads\|Sub0\|Pairs\|single" | sed 's/.*Reads:,//' | sed 's/\/.*dat,_ Sub0/Sub0/'
You need to replace the + with 2 dashes.
--><param name="space" value="base" />
@@ -215,7 +214,7 @@ PerM
<test><!--
PerM command:
- PerM test-data/phiX.fasta test-data/perm_in4.fastqcssanger +readFormat .csfastq -v 1 -o perm_out4.sam +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 test-data/phiX.fasta test-data/perm_in4.fastqcssanger +readFormat csfastq -v 1 -o perm_out4.sam +outputFormat sam +noSamHeader | tr '\r' '\n' | tr -cd "[:print:]\t\n " | grep "Reads\|Sub0\|Pairs\|single" | sed 's/.*Reads:,//' | sed 's/\/.*dat,_ Sub0/Sub0/'
You need to replace the + with 2 dashes.
--><param name="space" value="color" />
@@ -231,14 +230,12 @@ PerM
<test><!--
PerM command:
- PerM equCab2.fasta 50 +seed F4 -m -s equCab2_F3_50.index +readFormat .csfastq
- PerM equCab2_F3_50.index -1 test-data/perm_in5.fastqcssanger -2 test-data/perm_in6.fastqcssanger -U 90000 -L 10000 +readFormat .csfastq -v 3 -o perm_out5.sam +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 /afs/bx.psu.edu/depot/data/genome/equCab2/perm_index/equCab2_chrM_color_F2_50.index -1 test-data/perm_in5.fastqcssanger -2 test-data/perm_in6.fastqcssanger -U 90000 -L 10000 +readFormat csfastq -v 3 +seed F2-o perm_out5.sam +outputFormat sam +noSamHeader | tr '\r' '\n' | tr -cd "[:print:]\t\n " | grep "Reads\|Sub0\|Pairs\|single" | sed 's/.*Reads:,//' | sed 's/\/.*dat,_ Sub0/Sub0/'
You need to replace the + with 2 dashes.
- hg19.fasta needs to be supplied.
--><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><!--
- Lastz command:
- lastz phiX.2bit/PHIX174[nickname=Ref] test-data/b1.fasta +nogfextend +nochain +gapped +strand=both +seed=12of19 +transition O=400 E=30 X=910 Y=9370 K=3000 L=3000 +noentropy +ambiguousn +nolaj +identity=0..100 +coverage=0 +format=sam- > lastz_wrapper_out2.sam
- You need to point to phiX.2bit somewhere on your system. b1.fasta is located in galaxy's test-data. You will have to replace all the pluses before the
- commands with 2 dashes, as double-dash can't appear in an XML comment.
+ Lastz command:
+ lastz phiX.2bit/phiX174[nickname=Ref] test-data/b1.fasta +nogfextend +nochain +gapped +strand=both +seed=12of19 +transition O=400 E=30 X=910 Y=9370 K=3000 L=3000 +noentropy +ambiguousn +nolaj +identity=0..100 +coverage=0 +format=sam- > lastz_wrapper_out2.sam
+ You need to point to phiX.2bit somewhere on your system. b1.fasta is located in galaxy's test-data. You will have to replace all the pluses before the
+ commands with 2 dashes, as double-dash can't appear in an XML comment.
-->
- <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" />
+ <!-- this is the backwards-compatible "unique value" for this file, not an actual path -->
+ <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" /><!--
- how_to_name is not the default. It is changed to modify
- input1_2bit by adding the ref_name as a nickname
+ how_to_name is not the default. It is changed to modify
+ input1_2bit by adding the ref_name as a nickname
--><param name="how_to_name" value="yes" /><param name="ref_name" value="Ref" />
@@ -163,10 +178,10 @@
</test><test><!--
- Lastz command:
- lastz test-data/phiX.fasta test-data/b1.fasta[fullnames] +yasra95short +ambiguousn +nolaj +identity=0..100 +coverage=0 +format=diffs > lastz_wrapper_out3.tabular
- phiX.fasta and b1.fasta are located in galaxy's test-data. You will have to replace all the pluses before the commands with 2 dashes,
- as double-dash can't appear in an XML comment.
+ Lastz command:
+ lastz test-data/phiX.fasta test-data/b1.fasta[fullnames] +yasra95short +ambiguousn +nolaj +identity=0..100 +coverage=0 +format=diffs > lastz_wrapper_out3.tabular
+ phiX.fasta and b1.fasta are located in galaxy's test-data. You will have to replace all the pluses before the commands with 2 dashes,
+ as double-dash can't appear in an XML comment.
--><param name="input2" value="b1.fasta" ftype="fasta" /><param name="ref_source" value="history" />
@@ -183,17 +198,17 @@
</test><test><!--
- Lastz command: first you will need to split the file phiX_split.fasta into two files,
- phiX1.fasta and phiX2.fasta, each with 1 sequence (phiX1 and phiX2, respectively). Then:
- lastz phiX1.fasta test-data/b1.fasta *yasra95short *ambiguousn *nolaj *identity=0..100 *coverage=0 *format=general-:score,name1,strand1,size1,start1,zstart1,end1,length1,text1,name2,strand2,size2,start2,zstart2,end2,start2+,zstart2+,end2+,length2,text2,diff,cigar,identity,coverage,gaprate,diagonal,shingle > lastz_wrapper_out4.tabular
- lastz phiX2.fasta test-data/b1.fasta *yasra95short *ambiguousn *nolaj *identity=0..100 *coverage=0 *format=general-:score,name1,strand1,size1,start1,zstart1,end1,length1,text1,name2,strand2,size2,start2,zstart2,end2,start2+,zstart2+,end2+,length2,text2,diff,cigar,identity,coverage,gaprate,diagonal,shingle >> lastz_wrapper_out4.tabular
- You need to point to phiX1.fasta and phiX2.fasta somewhere on your system.
- phiX_split.fasta and b1.fasta are located in galaxy's test-data
- You will have to replace all the asterisks before the commands with 2 dashes,
- as double-dash can't appear in an XML comment
-
- NOTE: since the input file include more than 1 sequence, the output must be sorted in
- order for functional test to pass. This is done using the sort="True" attribute on the output.
+ Lastz command: first you will need to split the file phiX_split.fasta into two files,
+ phiX1.fasta and phiX2.fasta, each with 1 sequence (phiX1 and phiX2, respectively). Then:
+ lastz phiX1.fasta test-data/b1.fasta *yasra95short *ambiguousn *nolaj *identity=0..100 *coverage=0 *format=general-:score,name1,strand1,size1,start1,zstart1,end1,length1,text1,name2,strand2,size2,start2,zstart2,end2,start2+,zstart2+,end2+,length2,text2,diff,cigar,identity,coverage,gaprate,diagonal,shingle > lastz_wrapper_out4.tabular
+ lastz phiX2.fasta test-data/b1.fasta *yasra95short *ambiguousn *nolaj *identity=0..100 *coverage=0 *format=general-:score,name1,strand1,size1,start1,zstart1,end1,length1,text1,name2,strand2,size2,start2,zstart2,end2,start2+,zstart2+,end2+,length2,text2,diff,cigar,identity,coverage,gaprate,diagonal,shingle >> lastz_wrapper_out4.tabular
+ You need to point to phiX1.fasta and phiX2.fasta somewhere on your system.
+ phiX_split.fasta and b1.fasta are located in galaxy's test-data
+ You will have to replace all the asterisks before the commands with 2 dashes,
+ as double-dash can't appear in an XML comment
+
+ NOTE: since the input file include more than 1 sequence, the output must be sorted in
+ order for functional test to pass. This is done using the sort="True" attribute on the output.
--><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_data_table="blastdb" /> --><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><!-- Commands to run to prepare test files (uses built-in index)
- Prepare bam index file:
- samtools index srma_in1.bam
- Run SRMA:
- java -jar "srma.jar" I=srma_in1.bam O=srma_out1.bam R=/afs/bx.psu.edu/depot/data/genome/hg18/srma_index/chr21.fa
- To create the bam file first, start with a sam file (srma_in1.sam) generated with a run using the chr21 fasta file and which contains the header. Run before samtools index:
- samtools view -bt /afs/bx.psu.edu/depot/data/genome/hg18/sam_index/chr21.fa -o srma_in1.u.bam srma_in1.sam
- samtools sort srma_in1.u.bam srma_in1
+ Prepare bam index file:
+ samtools index srma_in1.bam
+ Run SRMA:
+ java -jar "srma.jar" I=srma_in1.bam O=srma_out1.bam R=/afs/bx.psu.edu/depot/data/genome/hg18/srma_index/chr21.fa
+ To create the bam file first, start with a sam file (srma_in1.sam) generated with a run using the chr21 fasta file and which contains the header. Run before samtools index:
+ samtools view -bt /afs/bx.psu.edu/depot/data/genome/hg18/sam_index/chr21.fa -o srma_in1.u.bam srma_in1.sam
+ samtools sort srma_in1.u.bam srma_in1
--><param name="refGenomeSource_type" value="built-in" /><param name="ref" value="hg18chr21" />
@@ -87,16 +95,16 @@
</test><test><!-- Commands to run to prepare test files (uses custom genome):
- Prepare custom dict/index files:
- samtools faidx srma_in2.fa
- java -cp "srma.jar" net.sf.picard.sam.CreateSequenceDictionary R=srma_in2.fa O=srma_in2.dict
- Prepare bam index file:
- samtools index srma_in3.bam
- Run SRMA:
- java -jar "srma.jar" I=srma_in3.bam O=srma_out2.bam R=srma_in2.fa OFFSET=20 MIN_MAPQ=0 MINIMUM_ALLELE_PROBABILITY=0.1 MINIMUM_ALLELE_COVERAGE=2 RANGES=null RANGE=null CORRECT_BASES=true USE_SEQUENCE_QUALITIES=true MAX_HEAP_SIZE=8192
- To create the bam file first, the sam file needs to have been run with the same reference file (srma_in2.fa) and have the header present. Run these commands before samtools index:
- samtools view -bt srma_in2.fa -o srma_in3.u.bam srma_in1.sam
- samtools sort srma_in3.u.bam srma_in3
+ Prepare custom dict/index files:
+ samtools faidx srma_in2.fa
+ java -cp "srma.jar" net.sf.picard.sam.CreateSequenceDictionary R=srma_in2.fa O=srma_in2.dict
+ Prepare bam index file:
+ samtools index srma_in3.bam
+ Run SRMA:
+ java -jar "srma.jar" I=srma_in3.bam O=srma_out2.bam R=srma_in2.fa OFFSET=20 MIN_MAPQ=0 MINIMUM_ALLELE_PROBABILITY=0.1 MINIMUM_ALLELE_COVERAGE=2 RANGES=null RANGE=null CORRECT_BASES=true USE_SEQUENCE_QUALITIES=true MAX_HEAP_SIZE=8192
+ To create the bam file first, the sam file needs to have been run with the same reference file (srma_in2.fa) and have the header present. Run these commands before samtools index:
+ samtools view -bt srma_in2.fa -o srma_in3.u.bam srma_in1.sam
+ samtools sort srma_in3.u.bam srma_in3
--><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_data_table="blastdb" /> --><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"/>
- <!--
- <options from_file="bowtie_indices.loc">
- <column name="value" index="1" />
- <column name="name" index="0" />
- </options>
- --></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" />
+ <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
+ <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" />
+ <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
+ <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"/><!-- source_select needs to match the entry in the blastdb.loc file, which includes the last update date if appropriate -->
- <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"/>
- <!--
- <options from_file="bwa_index.loc">
- <column name="value" index="1" />
- <column name="name" index="0" />
- </options>
- --></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 @@
<!--
BWA commands:
bwa aln -t 4 phiX test-data/bwa_wrapper_in1.fastq > bwa_wrapper_out1.sai
- bwa samse phiX bwa_wrapper_out1.sai test-data/bwa_wrapper_in1.fastq >> bwa_wrapper_out1.sam
+ bwa samse phiX bwa_wrapper_out1.sai test-data/bwa_wrapper_in1.fastq > bwa_wrapper_out1.sam
phiX.fa is the prefix for the reference files (phiX.fa.amb, phiX.fa.ann, phiX.fa.bwt, ...)
remove the comment lines (beginning with '@') from the resulting sam file
--><param name="refGenomeSource" value="indexed" />
- <param name="indices" value="phiX" />
+ <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
+ <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><!--
BWA commands:
bwa aln -n 0.04 -o 1 -e -1 -d 16 -i 5 -k 2 -t 4 -M 3 -O 11 -E 4 -R -N phiX.fa test-data/bwa_wrapper_in2.fastq > bwa_wrapper_out3a.sai
bwa aln -n 0.04 -o 1 -e -1 -d 16 -i 5 -k 2 -t 4 -M 3 -O 11 -E 4 -R -N phiX.fa test-data/bwa_wrapper_in3.fastq > bwa_wrapper_out3b.sai
- bwa sampe -a 500 -o 100000 phiX.fasta bwa_wrapper_out3a.sai bwa_wrapper_out3b.sai test-data/bwa_wrapper_in2.fastq test-data/bwa_wrapper_in3.fastq > bwa_wrapper_out3.sam
+ bwa sampe -a 500 -o 100000 phiX.fa bwa_wrapper_out3a.sai bwa_wrapper_out3b.sai test-data/bwa_wrapper_in2.fastq test-data/bwa_wrapper_in3.fastq > bwa_wrapper_out3.sam
phiX.fa is the prefix for the reference
remove the comment lines (beginning with '@') from the resulting sam file
--><param name="refGenomeSource" value="indexed" />
- <param name="indices" value="phiX" />
+ <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
+ <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" />
+ <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
+ <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" />
+ <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
+ <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_data_table="blastdb_p" /> --><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_data_table="blastdb" /> --><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_data_table="blastdb_p" /> --><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>
+ <!-- Locations of all fasta files under genome directory -->
+ <table name="all_fasta" comment_char="#">
+ <columns>value, dbkey, name, path</columns>
+ <file path="tool-data/all_fasta.loc" />
+ </table><!-- Locations of indexes in the BFAST mapper format --><table name="bfast_indexes" comment_char="#"><columns>value, dbkey, formats, name, path</columns><file path="tool-data/bfast_indexes.loc" /></table>
+ <!-- Locations of nucleotide (mega)blast databases -->
+ <table name="blastdb" comment_char="#">
+ <columns>value, name, path</columns>
+ <file path="tool-data/blastdb.loc" />
+ </table>
+ <!-- Locations of protein (mega)blast databases -->
+ <table name="blastdb_p" comment_char="#">
+ <columns>value, name, path</columns>
+ <file path="tool-data/blastdb_p.loc" />
+ </table><!-- Locations of indexes in the Bowtie mapper format -->
- <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>
+ <!-- Locations of indexes in the Bowtie color mapper format -->
+ <table name="bowtie_indexes_color" comment_char="#">
+ <columns>value, dbkey, name, path</columns>
+ <file path="tool-data/bowtie_indices_color.loc" />
+ </table><!-- Locations of indexes in the BWA mapper format -->
- <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><!-- Locations of MAF files that have been indexed with bx-python -->
@@ -24,4 +44,30 @@
<columns>value, dbkey, name, path</columns><file path="tool-data/ngs_sim_fasta.loc" /></table>
+ <!-- Locations of 2bit sequence files for use in Lastz -->
+ <table name="lastz_seqs" comment_char="#">
+ <columns>value, name, path</columns>
+ <file path="tool-data/lastz_seqs.loc" />
+ </table>
+ <!-- Locations of PerM base index files -->
+ <table name="perm_base_indexes" comment_char="#">
+ <columns>value, name, path</columns>
+ <file path="tool-data/perm_base_index.loc" />
+ </table>
+ <!-- Locations of PerM color index files -->
+ <table name="perm_color_indexes" comment_char="#">
+ <columns>value, name, path</columns>
+ <file path="tool-data/perm_color_index.loc" />
+ </table>
+ <!-- Location of SRMA dict file and other files -->
+ <table name="srma_indexes" comment_char="#">
+ <columns>value, dbkey, name, path</columns>
+ <file path="tool-data/srma_index.loc" />
+ </table>
+ <!-- Locations of indexes in the Bowtie mapper format for TopHat to use -->
+<!-- <table name="tophat_indexes" comment_char="#">
+ <columns>value, dbkey, name, path</columns>
+ <file path="tool-data/bowtie_indices.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
+
1
0
galaxy-dist commit 3ea6ee14a8b7: Remove debugging statement from previous commit.
by commits-noreply＠bitbucket.org 20 Nov '10
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()
1
0
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
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>
+ <!-- Test conversion of gff3 file. -->
+ <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()
1
0
galaxy-dist commit d46ccc650084: Eliminate check_user flag from tool menu and workflow methods.
by commits-noreply＠bitbucket.org 20 Nov '10
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>
1
0
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
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;
}
1
0