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galaxy-dist commit 264c608b48d9: Fixed inconsistency in PerM loc.sample files
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 1290012220 18000
# Node ID 264c608b48d9b0db2a142d820e32ec1d1fa550dd
# Parent 5ec30f459e8e4a1186f666f4879e14f082f17352
Fixed inconsistency in PerM loc.sample files
--- a/tool-data/perm_color_index.loc.sample
+++ b/tool-data/perm_color_index.loc.sample
@@ -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 phiX: seed=F3, read length=50 /depot/data/galaxy/phiX/perm_index/phiX_color_F3_50.index
+#phiX_F3_50 phiX: seed=F3, read length=50 /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:
@@ -21,8 +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 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index
+#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index
+#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index
+#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index
#
--- a/tool-data/perm_base_index.loc.sample
+++ b/tool-data/perm_base_index.loc.sample
@@ -21,8 +21,7 @@
#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 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index
+#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index
+#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index
+#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index
1
0
galaxy-dist commit 5ec30f459e8e: Merge with d1baa724b393de6871df7249ebe35ecfe2054e31
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 rc
# Date 1290011973 18000
# Node ID 5ec30f459e8e4a1186f666f4879e14f082f17352
# Parent 7d46c23bb276790160fe05560aa87c3d41185a27
# Parent d1baa724b393de6871df7249ebe35ecfe2054e31
Merge with d1baa724b393de6871df7249ebe35ecfe2054e31
1
0
galaxy-dist commit 7d46c23bb276: Merge with 39f41821aa4eec15b04509d24715946552bb14a6
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 rc
# Date 1290011867 18000
# Node ID 7d46c23bb276790160fe05560aa87c3d41185a27
# Parent 8ce82d60b2ab55966d133db136fcb2f809201c4b
# Parent 39f41821aa4eec15b04509d24715946552bb14a6
Merge with 39f41821aa4eec15b04509d24715946552bb14a6
1
0
galaxy-dist commit 1ee9e2490e19: Modifed tophat wrapper to work with data tables and fixed problem with index path; also got tests working
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 1290013305 18000
# Node ID 1ee9e2490e1968957f5f440a9dd08fb75aa3eb70
# Parent 264c608b48d9b0db2a142d820e32ec1d1fa550dd
Modifed tophat wrapper to work with data tables and fixed problem with index path; also got tests working
--- /dev/null
+++ b/test-data/tophat_in1.fasta
@@ -0,0 +1,14 @@
+>test_chromosome
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+ACTACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCC
+ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC
+AGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCT
+ACGTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCC
+GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG
+ACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACT
+GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG
+TTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
--- /dev/null
+++ b/test-data/tophat_in2.fastqsanger
@@ -0,0 +1,400 @@
+@test_mRNA_150_290_0/1
+TCCTAAAAAGTCCGCCTCGGTCTCAGTCTCAAGTAGAAAAAGTCCCGTTGGCGATCCGTCTACGTCCGAGTAAGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_8_197_1/1
+TCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGACACTACGGGGATGGCGACTAGGACTACGGACGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_82_255_2/1
+GAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAATATAGTAAAGTAATAGTGGCGTATCGCAAGCTCGACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_96_238_3/1
+GATCCGTCTACGTCCGCGTAAGATAATAAAGTACTAGTAGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_72_258_4/1
+GTAGAAAAAGTCCCGTTGCCCATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_107_286_5/1
+AAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_122_299_6/1
+CAAGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGCTCCGTCTACGTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_58_234_7/1
+AGTCTACGTCCGAGTCAGATAATAAACTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_57_231_8/1
+GGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCACCGACTGGACTATTTAGGACGATCGGACTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_8_155_9/1
+TACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTACAGTCGCTGCATCTGACGCTCGAAGTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_51_237_a/1
+ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_89_230_b/1
+TACGTCCGAGTGAGTTAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_105_276_c/1
+CCTCGATCCCAGTCTCAAGTAGAAAAAGCCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_111_268_d/1
+CCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAATAATAGTGGCGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_151_286_e/1
+ACGTATTTGGCGCGCGGCCGTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_118_297_f/1
+AGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_16_194_10/1
+TCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_28_188_11/1
+TTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGAACGGACTTAGAGCGTCAGATGCAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_36_218_12/1
+GAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGCCTTAGAGCGTCAGATGCAGCGACTGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_105_266_13/1
+AGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGGATCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_51_248_14/1
+ACTACGGGGATGACGACGAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGAACTTTTTAGGACGATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_89_245_15/1
+AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_58_218_16/1
+AGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_46_195_17/1
+ATCCCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGACAAATATGTAGCGTCCTACTGCCCTCCTCAGTCCAATCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_126_282_18/1
+AGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_53_212_19/1
+TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGAATATTTAGGACGATCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_11_190_1a/1
+GACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_52_261_1b/1
+CTACGGGAATGACGACTAGGGCTACGGAGGGACTTACAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_104_274_1c/1
+TCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_151_297_1d/1
+ACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_44_225_1e/1
+CCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCATATACGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_28_206_1f/1
+TTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGACGCAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_48_249_20/1
+GTCCCGTTGCCGATCCGTCTCCGTCCGAGTAAGATAGTAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_75_235_21/1
+ACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGCACGATCGGACTGAGGAGGGCAGTAGAACGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_110_267_22/1
+CAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_69_229_23/1
+ACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTAGACGCTCAGCCGTAGGGCCGCGCGCCAAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_21_208_24/1
+GTAATAGTGGCGTATCGCAAGCTCGACGCTCAGGCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_42_209_25/1
+GGACGTGCCACTACGTGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_97_275_26/1
+ATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_36_146_27/1
+ACCTACTGCACTCCTCAGTCCGATCGTCCTAAATAGTCCAGTCGCTGCATCTGACGCTCTAAGTCCGTCCGTAGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_110_271_28/1
+ACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_38_199_29/1
+GCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_103_284_2a/1
+AAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_116_271_2b/1
+ATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCTGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_77_256_2c/1
+GGACGGACTTAGAGCATCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_50_224_2d/1
+CGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_65_238_2e/1
+GACTAGGACTACGGACGGACTTAGAGCGTCAGAAGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_46_232_2f/1
+GTGCCACTACGGGGATGACGACTAGGACTACGGCCGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_26_189_30/1
+AGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTACCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_79_256_31/1
+AGAAAAAGTCCCGTTGCCGATCCGGCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATGGCAAGCTCGAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_89_267_32/1
+CAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGAAAGATAATAAAGTAATAGTGCCGTATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_131_260_33/1
+GAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_73_240_34/1
+CTACGGACGGACTTAGAGCGTCAGATGCAGCGAATGGACTATTTAGGACGCTCGGACTGAGGAGGGCAGTAGGAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_44_197_35/1
+ACGTGCAACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_128_252_36/1
+ACTGAGGAGGGCAGTAGGACGCTACGCATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATAGGCCAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_145_300_37/1
+GCAAGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTTCCGATCCGTCTACGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_85_275_38/1
+TTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGAAGCTACGTCTTTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_48_207_39/1
+GCCCCTACGGGGATGACGACTAGGACTACGGACGGATTTAGACCGTCAGATGCAGCGACTGGACTATTTAGGACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_81_228_3a/1
+CCTACGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCATAGGGCCGCGCGCCAAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_75_277_3b/1
+ACGGACGGACTTAAAGCTTCAGATGCAGCGACAGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_30_231_3c/1
+CTACGTGCGAGTAAGATATTAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTTAGCCGTAGGGCCGCGCGCCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_58_220_3d/1
+GAAGATAATAAAGTAATAGTGGCGTATCGCAACCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_104_278_3e/1
+CGCCTCGATTCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_44_193_3f/1
+ACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGTCTATTTAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_94_291_40/1
+CAGATGCAGCGACTGTACTATTTAGGACGACCTGACTGAGGAGGGTAGTAGGACGCTACGTATTTGGCGCGCGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_91_256_41/1
+CGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_23_186_42/1
+TCGACGCTCAGTCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTTCTGCCCTCCTCCGTCCGATCGTCCTAAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_92_266_43/1
+GTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTCAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_92_250_44/1
+GTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_106_253_45/1
+AAAAGTCCCGTTGCCGATCCGTTTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_5_197_46/1
+CTATCTGACTAGACTCGAGGCGCTTGCGTCTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_51_194_47/1
+TCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_125_280_48/1
+CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGAAACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_51_194_49/1
+ACTACGGGGATGACGACTAGGCCTACGGATGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_33_189_4a/1
+AGCCCGACGCTCAGCCGTAGGGCCGCGCGCCAAATAGGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_78_276_4b/1
+GACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGGCGCTAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_63_229_4c/1
+ACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACACTCAGCCGTAGGGCCGCGCGCCAAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_81_245_4d/1
+CGTTGCCGATCCGTCTACGTCCGAGTAAGATTATAAAGTAATAGTGGCGTATCGCAACCTCGACGCTCAGCCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_33_223_4e/1
+ACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_172_294_4f/1
+ACGGATGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTCCTCGGACGTAGACGGATCGCCAACGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_88_257_50/1
+TAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_3_187_51/1
+TACTATTTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_9_179_52/1
+TCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATGGTCCAGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_85_268_53/1
+TTAGTGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_75_204_54/1
+ACGGACGGACTTCGAGCCTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_41_236_55/1
+AGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGAATATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_56_183_56/1
+GGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTGGGACGATCGGACT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_87_250_57/1
+AGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_82_271_58/1
+GACTTAGAGCGTCAGTTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_6_182_59/1
+TATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAGTACGGGGATGACGACTAGGACTACGGAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_53_272_5a/1
+GATCCCAGTGTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_114_277_5b/1
+GCCTCGATCCCAGTCTCAAGCAGAAAAAGTCCCGTTGCCGTTCCGTCTACCTCCGAGTAAGATAATAAAGTAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_39_219_5c/1
+CTAGGACGTCCCACTATGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGGCTGGACTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_4_191_5d/1
+CAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGTGTCCTACTGCCCTACTCAGTCCGATCGTCCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_73_259_5e/1
+CTACGGACGGACTTAGAGCGTCAGATGCTGCGACTGGACTATTTGGGACGATCGGACTGAGGAGGGCAGTAGGAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_87_279_5f/1
+CCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_125_293_60/1
+CCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_111_297_61/1
+AGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCGGATCCGTCTACGTCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_22_173_62/1
+AGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_116_295_63/1
+TCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
Binary file test-data/tophat_out1h.bam has changed
--- a/test-data/tophat_in1.fq
+++ /dev/null
@@ -1,400 +0,0 @@
-@test_mRNA_150_290_0/1
-TCCTAAAAAGTCCGCCTCGGTCTCAGTCTCAAGTAGAAAAAGTCCCGTTGGCGATCCGTCTACGTCCGAGTAAGA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_8_197_1/1
-TCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGACACTACGGGGATGGCGACTAGGACTACGGACGG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_82_255_2/1
-GAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAATATAGTAAAGTAATAGTGGCGTATCGCAAGCTCGACG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_96_238_3/1
-GATCCGTCTACGTCCGCGTAAGATAATAAAGTACTAGTAGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_72_258_4/1
-GTAGAAAAAGTCCCGTTGCCCATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_107_286_5/1
-AAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAAT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_122_299_6/1
-CAAGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGCTCCGTCTACGTC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_58_234_7/1
-AGTCTACGTCCGAGTCAGATAATAAACTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_57_231_8/1
-GGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCACCGACTGGACTATTTAGGACGATCGGACTG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_8_155_9/1
-TACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTACAGTCGCTGCATCTGACGCTCGAAGTCC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_51_237_a/1
-ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_89_230_b/1
-TACGTCCGAGTGAGTTAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAGA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_105_276_c/1
-CCTCGATCCCAGTCTCAAGTAGAAAAAGCCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_111_268_d/1
-CCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAATAATAGTGGCGTAT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_151_286_e/1
-ACGTATTTGGCGCGCGGCCGTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_118_297_f/1
-AGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_16_194_10/1
-TCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_28_188_11/1
-TTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGAACGGACTTAGAGCGTCAGATGCAG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_36_218_12/1
-GAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGCCTTAGAGCGTCAGATGCAGCGACTGGA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_105_266_13/1
-AGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGGATCG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_51_248_14/1
-ACTACGGGGATGACGACGAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGAACTTTTTAGGACGATC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_89_245_15/1
-AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_58_218_16/1
-AGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_46_195_17/1
-ATCCCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGACAAATATGTAGCGTCCTACTGCCCTCCTCAGTCCAATCG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_126_282_18/1
-AGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_53_212_19/1
-TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGAATATTTAGGACGATCGG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_11_190_1a/1
-GACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_52_261_1b/1
-CTACGGGAATGACGACTAGGGCTACGGAGGGACTTACAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_104_274_1c/1
-TCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_151_297_1d/1
-ACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_44_225_1e/1
-CCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCATATACGT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_28_206_1f/1
-TTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGACGCAG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_48_249_20/1
-GTCCCGTTGCCGATCCGTCTCCGTCCGAGTAAGATAGTAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_75_235_21/1
-ACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGCACGATCGGACTGAGGAGGGCAGTAGAACGT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_110_267_22/1
-CAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_69_229_23/1
-ACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTAGACGCTCAGCCGTAGGGCCGCGCGCCAAAG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_21_208_24/1
-GTAATAGTGGCGTATCGCAAGCTCGACGCTCAGGCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_42_209_25/1
-GGACGTGCCACTACGTGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_97_275_26/1
-ATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_36_146_27/1
-ACCTACTGCACTCCTCAGTCCGATCGTCCTAAATAGTCCAGTCGCTGCATCTGACGCTCTAAGTCCGTCCGTAGT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_110_271_28/1
-ACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_38_199_29/1
-GCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_103_284_2a/1
-AAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_116_271_2b/1
-ATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCTGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_77_256_2c/1
-GGACGGACTTAGAGCATCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_50_224_2d/1
-CGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_65_238_2e/1
-GACTAGGACTACGGACGGACTTAGAGCGTCAGAAGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_46_232_2f/1
-GTGCCACTACGGGGATGACGACTAGGACTACGGCCGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_26_189_30/1
-AGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTACCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_79_256_31/1
-AGAAAAAGTCCCGTTGCCGATCCGGCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATGGCAAGCTCGAC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_89_267_32/1
-CAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGAAAGATAATAAAGTAATAGTGCCGTATC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_131_260_33/1
-GAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTAT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_73_240_34/1
-CTACGGACGGACTTAGAGCGTCAGATGCAGCGAATGGACTATTTAGGACGCTCGGACTGAGGAGGGCAGTAGGAC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_44_197_35/1
-ACGTGCAACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_128_252_36/1
-ACTGAGGAGGGCAGTAGGACGCTACGCATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATAGGCCAC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_145_300_37/1
-GCAAGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTTCCGATCCGTCTACGT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_85_275_38/1
-TTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGAAGCTACGTCTTTC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_48_207_39/1
-GCCCCTACGGGGATGACGACTAGGACTACGGACGGATTTAGACCGTCAGATGCAGCGACTGGACTATTTAGGACG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_81_228_3a/1
-CCTACGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCATAGGGCCGCGCGCCAAATA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_75_277_3b/1
-ACGGACGGACTTAAAGCTTCAGATGCAGCGACAGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_30_231_3c/1
-CTACGTGCGAGTAAGATATTAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTTAGCCGTAGGGCCGCGCGCCAA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_58_220_3d/1
-GAAGATAATAAAGTAATAGTGGCGTATCGCAACCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_104_278_3e/1
-CGCCTCGATTCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAAT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_44_193_3f/1
-ACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGTCTATTTAG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_94_291_40/1
-CAGATGCAGCGACTGTACTATTTAGGACGACCTGACTGAGGAGGGTAGTAGGACGCTACGTATTTGGCGCGCGGC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_91_256_41/1
-CGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_23_186_42/1
-TCGACGCTCAGTCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTTCTGCCCTCCTCCGTCCGATCGTCCTAAATA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_92_266_43/1
-GTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTCAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_92_250_44/1
-GTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_106_253_45/1
-AAAAGTCCCGTTGCCGATCCGTTTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_5_197_46/1
-CTATCTGACTAGACTCGAGGCGCTTGCGTCTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_51_194_47/1
-TCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_125_280_48/1
-CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGAAACGC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_51_194_49/1
-ACTACGGGGATGACGACTAGGCCTACGGATGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_33_189_4a/1
-AGCCCGACGCTCAGCCGTAGGGCCGCGCGCCAAATAGGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_78_276_4b/1
-GACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGGCGCTAC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_63_229_4c/1
-ACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACACTCAGCCGTAGGGCCGCGCGCCAAAT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_81_245_4d/1
-CGTTGCCGATCCGTCTACGTCCGAGTAAGATTATAAAGTAATAGTGGCGTATCGCAACCTCGACGCTCAGCCGTA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_33_223_4e/1
-ACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_172_294_4f/1
-ACGGATGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTCCTCGGACGTAGACGGATCGCCAACGG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_88_257_50/1
-TAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_3_187_51/1
-TACTATTTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_9_179_52/1
-TCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATGGTCCAGT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_85_268_53/1
-TTAGTGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_75_204_54/1
-ACGGACGGACTTCGAGCCTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_41_236_55/1
-AGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGAATATT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_56_183_56/1
-GGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTGGGACGATCGGACT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_87_250_57/1
-AGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_82_271_58/1
-GACTTAGAGCGTCAGTTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_6_182_59/1
-TATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAGTACGGGGATGACGACTAGGACTACGGAC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_53_272_5a/1
-GATCCCAGTGTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_114_277_5b/1
-GCCTCGATCCCAGTCTCAAGCAGAAAAAGTCCCGTTGCCGTTCCGTCTACCTCCGAGTAAGATAATAAAGTAATA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_39_219_5c/1
-CTAGGACGTCCCACTATGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGGCTGGACTA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_4_191_5d/1
-CAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGTGTCCTACTGCCCTACTCAGTCCGATCGTCCT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_73_259_5e/1
-CTACGGACGGACTTAGAGCGTCAGATGCTGCGACTGGACTATTTGGGACGATCGGACTGAGGAGGGCAGTAGGAC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_87_279_5f/1
-CCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_125_293_60/1
-CCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_111_297_61/1
-AGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCGGATCCGTCTACGTCCG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_22_173_62/1
-AGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_116_295_63/1
-TCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
--- a/tools/ngs_rna/tophat_wrapper.py
+++ b/tools/ngs_rna/tophat_wrapper.py
@@ -30,7 +30,7 @@ def __main__():
parser.add_option( '-g', '--max_multihits', dest='max_multihits', help='Maximum number of alignments to be allowed' )
parser.add_option( '', '--seg-mismatches', dest='seg_mismatches', help='Number of mismatches allowed in each segment alignment for reads mapped independently' )
parser.add_option( '', '--seg-length', dest='seg_length', help='Minimum length of read segments' )
-
+
# Options for supplying own junctions
parser.add_option( '-G', '--GTF', dest='gene_model_annotations', help='Supply TopHat with a list of gene model annotations. \
TopHat will use the exon records in this file to build \
@@ -58,18 +58,18 @@ def __main__():
parser.add_option( '', '--max-closure-intron', dest='max_closure_intron', help='Maximum intron length that may be found during closure search' )
parser.add_option( '', '--min-coverage-intron', dest='min_coverage_intron', help='Minimum intron length that may be found during coverage search' )
parser.add_option( '', '--max-coverage-intron', dest='max_coverage_intron', help='Maximum intron length that may be found during coverage search' )
-
+
# Wrapper options.
parser.add_option( '-1', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format' )
parser.add_option( '-2', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format' )
parser.add_option( '', '--single-paired', dest='single_paired', help='' )
parser.add_option( '', '--settings', dest='settings', help='' )
-
+
(options, args) = parser.parse_args()
-
+
# Creat bowtie index if necessary.
tmp_index_dir = tempfile.mkdtemp()
- if options.own_file != 'None':
+ if options.own_file:
index_path = os.path.join( tmp_index_dir, os.path.split( options.own_file )[1] )
cmd_index = 'bowtie-build -f %s %s' % ( options.own_file, index_path )
try:
@@ -98,12 +98,12 @@ def __main__():
stop_err( 'Error indexing reference sequence\n' + str( e ) )
else:
index_path = options.index_path
-
+
# Build tophat command.
tmp_output_dir = tempfile.mkdtemp()
cmd = 'tophat -o %s %s %s %s'
reads = options.input1
- if options.input2 != 'None':
+ if options.input2:
reads += ' ' + options.input2
opts = '-p %s' % options.num_threads
if options.single_paired == 'paired':
@@ -129,7 +129,7 @@ def __main__():
opts += ' -j %s' % options.raw_juncs
if options.no_novel_juncs:
opts += ' --no-novel-juncs'
-
+
# Search type options.
if options.coverage_search:
opts += ' --coverage-search --min-coverage-intron %s --max-coverage-intron %s' % ( options.min_coverage_intron, options.max_coverage_intron )
@@ -143,13 +143,13 @@ def __main__():
opts += ' --microexon-search'
if options.single_paired == 'paired':
opts += ' --mate-std-dev %s' % options.mate_std_dev
- if options.seg_mismatches != None:
+ if options.seg_mismatches:
opts += ' --segment-mismatches %d' % int(options.seg_mismatches)
- if options.seg_length != None:
+ if options.seg_length:
opts += ' --segment-length %d' % int(options.seg_length)
- if options.min_segment_intron != None:
+ if options.min_segment_intron:
opts += ' --min-segment-intron %d' % int(options.min_segment_intron)
- if options.max_segment_intron != None:
+ if options.max_segment_intron:
opts += ' --max-segment-intron %d' % int(options.max_segment_intron)
cmd = cmd % ( tmp_output_dir, opts, index_path, reads )
except Exception, e:
@@ -160,7 +160,7 @@ def __main__():
shutil.rmtree( tmp_output_dir )
stop_err( 'Something is wrong with the alignment parameters and the alignment could not be run\n' + str( e ) )
print cmd
-
+
# Run
try:
tmp_out = tempfile.NamedTemporaryFile( dir=tmp_output_dir ).name
@@ -185,10 +185,10 @@ def __main__():
tmp_stderr.close()
if returncode != 0:
raise Exception, stderr
-
+
# TODO: look for errors in program output.
-
- # Copy output files from tmp directory to specified files.
+
+ # Copy output files from tmp directory to specified files.
shutil.copyfile( os.path.join( tmp_output_dir, "junctions.bed" ), options.junctions_output_file )
shutil.copyfile( os.path.join( tmp_output_dir, "accepted_hits.bam" ), options.accepted_hits_output_file )
except Exception, e:
--- a/test-data/tophat_in2.fq
+++ /dev/null
@@ -1,400 +0,0 @@
-@test_mRNA_150_290_0/2
-TACGTATTTGTCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATCCGCCACTATTACTTTATTATCTTACTCG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_8_197_1/2
-GTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGAT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_82_255_2/2
-GACTTAGAGCGTCAGATGCAGCGACTGGACTTTTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_96_238_3/2
-GATGCAGCGACTGGACTATTTAGGACGATCGGACGGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGACC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_72_258_4/2
-ACTACGGACGGACTTAGAGCGTCAGATGCAGCAACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_107_286_5/2
-TGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGCATTTGGCGCGCGGCCCTACGGCTGAGC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_122_299_6/2
-GATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_58_234_7/2
-GGATGACGCCTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_57_231_8/2
-CTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCCTAGGGCCGCGCGCCAA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_8_155_9/2
-TGTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_51_237_a/2
-ATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_89_230_b/2
-AGCGTCAGGTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_105_276_c/2
-ACTGGACTATTTAGGACGATCGGACTGAGGAAGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_111_268_d/2
-CTATTTAAGACGTTCCGCCTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_151_286_e/2
-AAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGATAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAAT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_118_297_f/2
-GGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_16_194_10/2
-GACTGGATGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACGGACGGACTTAAAG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_28_188_11/2
-GCTCGACGCTCAGCCGTAGGGCCTCGCGCCAAATACGAAGCGTCCTACTGCCTTCCTCAGTCCGATCGTCCTAAA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_36_218_12/2
-AGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_105_266_13/2
-ACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_51_248_14/2
-TCCCGTTGCCGTTCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_89_245_15/2
-CGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAGAGAAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_58_218_16/2
-GGATGACGACTAGGACTACGGACGGACTTAGAACGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_46_195_17/2
-GTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_126_282_18/2
-GGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_53_212_19/2
-TAAAGAAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_11_190_1a/2
-AAGCTCGACGCTCAGCCGTAGGGCCACGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCCATCGACCTA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_52_261_1b/2
-CAAGTAGAAAAAGTCCCGTTGCCGATCCTTCTACGTCCGAGTAAGATAATTAAGTAATAGTGGCGTATCGCAAGC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_104_274_1c/2
-GAGTGTACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATGTGCCGCGCGGCCCTACGGCTG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_151_297_1d/2
-AGTCCCGTCCTAAAATGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_44_225_1e/2
-ACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCGGGTGCAGCGACTGGACTATTTAG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_28_206_1f/2
-AATAGTGGCTTATCGCAAGCTCGACTCTCAGCCGTAGGGCCGCGCGCCAAATACGTGGCGTCCTACTGCCCTCCT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_48_249_20/2
-GCCACTACGGGGATGACGACTAGGACGACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_75_235_21/2
-CCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCAACGCTCAGCCGTAGGGCCGTGCG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_110_267_22/2
-ACTAGTTAGGGCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAGTTGGCGCGCGGCCCTACGACTGAGCGTC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_69_229_23/2
-AGGACTACGGACGGACTTATAGGGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_21_208_24/2
-GAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_42_209_25/2
-AGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_97_275_26/2
-CTCGATCCCAGTCTCAAGTAGAAAGAGTCCCGTTTCCGATCCGTCTACGTCCGACTAAGATAATAAAGTAATAGT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_36_146_27/2
-GCGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACAGACGGACTTAGAGCGTCAGATGCAGCGACTGGA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_110_271_28/2
-ATCCCAGTCTCAAGTAGAAAAAGCCCCGTTGCCGATCCGTCTTCGTCCGAGTAAGATAATAAAGTAATAGTGGCG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_38_199_29/2
-GCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_103_284_2a/2
-CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_116_271_2b/2
-TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_77_256_2c/2
-AGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGAC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_50_224_2d/2
-CACTACGAGGATGACGTCTAGGACTACGGACGGACTTAGAGCGTCAGACGCAGCGACTGGACTATTTAGGACGAT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_65_238_2e/2
-GATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCGCAGCCGTAGGGCCGC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_46_232_2f/2
-TCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_26_189_30/2
-GCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_79_256_31/2
-ACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_89_267_32/2
-AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGAGTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_131_260_33/2
-AAGTAAAAAAAGTCCCGTGGCCGATCCGTTTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCACAAGCT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_73_240_34/2
-CCGATCCGTCTACGTCCGAGAAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_44_197_35/2
-GTATCGCAAGCTCGACGATCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGAT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_128_252_36/2
-AAAGTCCCGTTCCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_145_300_37/2
-GACGCTACGTATTTGGCGCGGGGCCCTATGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTAGTATATT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_85_275_38/2
-CTCGATCCCAGTCTCAAGTAGTAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAAGAGT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_48_207_39/2
-TAAGAGTGGCGTATCGCAAGATCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTTCCCTCC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_81_228_3a/2
-GGACTGAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGTAGTAGGACGCTACGTA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_75_277_3b/2
-GCCTCGATCCCAGTCTCAGGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_30_231_3c/2
-GCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_58_220_3d/2
-GGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_104_278_3e/2
-GACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTTTTTGGCGCGCGGCCCTACGGCTG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_44_193_3f/2
-CGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCTCTCCCCAGTCCGATCGTC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_94_291_40/2
-GTCCCAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAATGTCGCGTTGCCGATCCGTCTACGTCCCAGGAAG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_91_256_41/2
-AGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGAC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_23_186_42/2
-GGCGCTTGTGACTGAGCTAGGACGTGCCACTACGGGGATGAAGACTAGGACTACGGACGGACTTAGAGCGTCAGA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_92_266_43/2
-GGTCTCAAGTAGAAAAAGTCCCGTTGCCGCTCCGTCTACGTCCGAGTAAGATAAGAAAGTAATAGTGGCGTATCG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_92_250_44/2
-AGTCCCGTACCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_106_253_45/2
-CTGGACTATTTAGGTCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_5_197_46/2
-GTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCCCGCCAAATACGTAGCGTCCTACTGCCCTCCTCCGTCCGAT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_51_194_47/2
-ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_125_280_48/2
-TCCGCCTCGCTCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCAGAGTAAGATAATAAAGTA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_51_194_49/2
-CCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTGGCGTCCTACTGCCCTCCTCAGTCCGAACGT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_33_189_4a/2
-ACTGAGCTAGGACGTGCCACTACGGGGATTACCACTAGGGCTACGGACGGACTTAGAGCGTCAGATGCAGCGACT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_78_276_4b/2
-CCTCGATCCTAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_63_229_4c/2
-ACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGGGACTGGACTATTTAGGACGATCGGACTGAGGAGG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_81_245_4d/2
-GGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGATGAGGGCAGTAGGACGCTACGTA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_33_223_4e/2
-GAGTTAGATAATAAAGTAATAGTGGCTTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACCTAG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_172_294_4f/2
-CCCGTCCTAAAACGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGCTGCCGACCCGTCTACGTCCGAGT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_88_257_50/2
-GAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_3_187_51/2
-CTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAAT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_9_179_52/2
-CTGACTAGACTGGAGGCGCTCGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_85_268_53/2
-CCAGTCTCAAGTAGAAAAAGTCCCGTTGACGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTAT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_75_204_54/2
-TCGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_41_236_55/2
-TCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_56_183_56/2
-ACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_87_250_57/2
-AGAGCGTCAGATGCAGAGACTGGACTATTTAGGACGATCGGACTGAGGAGTGCAGTAGGACGCTACGTATTTGGC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_82_271_58/2
-ATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATGCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_6_182_59/2
-CGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTCC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_53_272_5a/2
-TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_114_277_5b/2
-TTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGCCTGAGCGTCGAGC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_39_219_5c/2
-AAGATAATAAAGTAATAGTGGCGTATCGCAAGCTGGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_4_191_5d/2
-ACTATCTGACGAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTACCATTACGCGGATGACGACTAGGACTACGG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_73_259_5e/2
-AGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATACAGTAATAGTGGCGTATCGCAAGCTC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_87_279_5f/2
-AGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACCGAGGAGGGCAGTAGGACGCTACGTATTTGGC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_125_293_60/2
-CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCTTCGAGGTTGCGATACGC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_111_297_61/2
-CTATTTAGGACGATCGGACTGGGGAGGGCAGTAGGACGCTACGGATTTGGCGCGCGGCCCTACGGCTGAGCGTCG
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_22_173_62/2
-GTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTCCAGTCGCTGC
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-@test_mRNA_116_295_63/2
-TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
--- /dev/null
+++ b/test-data/tophat_out1j.bed
@@ -0,0 +1,3 @@
+track name=junctions description="TopHat junctions"
+test_chromosome 180 400 JUNC00000001 24 + 180 400 255,0,0 2 70,50 0,170
+test_chromosome 349 550 JUNC00000002 22 + 349 550 255,0,0 2 51,50 0,151
--- a/test-data/tophat_out1.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
--- /dev/null
+++ b/test-data/tophat_out2j.bed
@@ -0,0 +1,3 @@
+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
--- /dev/null
+++ b/test-data/tophat_out3j.bed
@@ -0,0 +1,3 @@
+track name=junctions description="TopHat junctions"
+test_chromosome 180 400 JUNC00000001 24 + 180 400 255,0,0 2 70,50 0,170
+test_chromosome 349 550 JUNC00000002 22 + 349 550 255,0,0 2 51,50 0,151
--- /dev/null
+++ b/test-data/tophat_in3.fastqsanger
@@ -0,0 +1,400 @@
+@test_mRNA_150_290_0/2
+TACGTATTTGTCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATCCGCCACTATTACTTTATTATCTTACTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_8_197_1/2
+GTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_82_255_2/2
+GACTTAGAGCGTCAGATGCAGCGACTGGACTTTTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_96_238_3/2
+GATGCAGCGACTGGACTATTTAGGACGATCGGACGGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGACC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_72_258_4/2
+ACTACGGACGGACTTAGAGCGTCAGATGCAGCAACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_107_286_5/2
+TGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGCATTTGGCGCGCGGCCCTACGGCTGAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_122_299_6/2
+GATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_58_234_7/2
+GGATGACGCCTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_57_231_8/2
+CTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCCTAGGGCCGCGCGCCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_8_155_9/2
+TGTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_51_237_a/2
+ATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_89_230_b/2
+AGCGTCAGGTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_105_276_c/2
+ACTGGACTATTTAGGACGATCGGACTGAGGAAGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_111_268_d/2
+CTATTTAAGACGTTCCGCCTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_151_286_e/2
+AAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGATAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_118_297_f/2
+GGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_16_194_10/2
+GACTGGATGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACGGACGGACTTAAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_28_188_11/2
+GCTCGACGCTCAGCCGTAGGGCCTCGCGCCAAATACGAAGCGTCCTACTGCCTTCCTCAGTCCGATCGTCCTAAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_36_218_12/2
+AGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_105_266_13/2
+ACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_51_248_14/2
+TCCCGTTGCCGTTCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_89_245_15/2
+CGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAGAGAAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_58_218_16/2
+GGATGACGACTAGGACTACGGACGGACTTAGAACGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_46_195_17/2
+GTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_126_282_18/2
+GGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_53_212_19/2
+TAAAGAAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_11_190_1a/2
+AAGCTCGACGCTCAGCCGTAGGGCCACGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCCATCGACCTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_52_261_1b/2
+CAAGTAGAAAAAGTCCCGTTGCCGATCCTTCTACGTCCGAGTAAGATAATTAAGTAATAGTGGCGTATCGCAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_104_274_1c/2
+GAGTGTACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATGTGCCGCGCGGCCCTACGGCTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_151_297_1d/2
+AGTCCCGTCCTAAAATGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_44_225_1e/2
+ACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCGGGTGCAGCGACTGGACTATTTAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_28_206_1f/2
+AATAGTGGCTTATCGCAAGCTCGACTCTCAGCCGTAGGGCCGCGCGCCAAATACGTGGCGTCCTACTGCCCTCCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_48_249_20/2
+GCCACTACGGGGATGACGACTAGGACGACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_75_235_21/2
+CCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCAACGCTCAGCCGTAGGGCCGTGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_110_267_22/2
+ACTAGTTAGGGCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAGTTGGCGCGCGGCCCTACGACTGAGCGTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_69_229_23/2
+AGGACTACGGACGGACTTATAGGGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_21_208_24/2
+GAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_42_209_25/2
+AGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_97_275_26/2
+CTCGATCCCAGTCTCAAGTAGAAAGAGTCCCGTTTCCGATCCGTCTACGTCCGACTAAGATAATAAAGTAATAGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_36_146_27/2
+GCGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACAGACGGACTTAGAGCGTCAGATGCAGCGACTGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_110_271_28/2
+ATCCCAGTCTCAAGTAGAAAAAGCCCCGTTGCCGATCCGTCTTCGTCCGAGTAAGATAATAAAGTAATAGTGGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_38_199_29/2
+GCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_103_284_2a/2
+CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_116_271_2b/2
+TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_77_256_2c/2
+AGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_50_224_2d/2
+CACTACGAGGATGACGTCTAGGACTACGGACGGACTTAGAGCGTCAGACGCAGCGACTGGACTATTTAGGACGAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_65_238_2e/2
+GATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCGCAGCCGTAGGGCCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_46_232_2f/2
+TCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_26_189_30/2
+GCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_79_256_31/2
+ACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_89_267_32/2
+AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGAGTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_131_260_33/2
+AAGTAAAAAAAGTCCCGTGGCCGATCCGTTTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCACAAGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_73_240_34/2
+CCGATCCGTCTACGTCCGAGAAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_44_197_35/2
+GTATCGCAAGCTCGACGATCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_128_252_36/2
+AAAGTCCCGTTCCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_145_300_37/2
+GACGCTACGTATTTGGCGCGGGGCCCTATGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTAGTATATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_85_275_38/2
+CTCGATCCCAGTCTCAAGTAGTAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAAGAGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_48_207_39/2
+TAAGAGTGGCGTATCGCAAGATCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTTCCCTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_81_228_3a/2
+GGACTGAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGTAGTAGGACGCTACGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_75_277_3b/2
+GCCTCGATCCCAGTCTCAGGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_30_231_3c/2
+GCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_58_220_3d/2
+GGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_104_278_3e/2
+GACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTTTTTGGCGCGCGGCCCTACGGCTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_44_193_3f/2
+CGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCTCTCCCCAGTCCGATCGTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_94_291_40/2
+GTCCCAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAATGTCGCGTTGCCGATCCGTCTACGTCCCAGGAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_91_256_41/2
+AGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_23_186_42/2
+GGCGCTTGTGACTGAGCTAGGACGTGCCACTACGGGGATGAAGACTAGGACTACGGACGGACTTAGAGCGTCAGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_92_266_43/2
+GGTCTCAAGTAGAAAAAGTCCCGTTGCCGCTCCGTCTACGTCCGAGTAAGATAAGAAAGTAATAGTGGCGTATCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_92_250_44/2
+AGTCCCGTACCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_106_253_45/2
+CTGGACTATTTAGGTCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_5_197_46/2
+GTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCCCGCCAAATACGTAGCGTCCTACTGCCCTCCTCCGTCCGAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_51_194_47/2
+ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_125_280_48/2
+TCCGCCTCGCTCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCAGAGTAAGATAATAAAGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_51_194_49/2
+CCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTGGCGTCCTACTGCCCTCCTCAGTCCGAACGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_33_189_4a/2
+ACTGAGCTAGGACGTGCCACTACGGGGATTACCACTAGGGCTACGGACGGACTTAGAGCGTCAGATGCAGCGACT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_78_276_4b/2
+CCTCGATCCTAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_63_229_4c/2
+ACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGGGACTGGACTATTTAGGACGATCGGACTGAGGAGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_81_245_4d/2
+GGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGATGAGGGCAGTAGGACGCTACGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_33_223_4e/2
+GAGTTAGATAATAAAGTAATAGTGGCTTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACCTAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_172_294_4f/2
+CCCGTCCTAAAACGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGCTGCCGACCCGTCTACGTCCGAGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_88_257_50/2
+GAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_3_187_51/2
+CTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_9_179_52/2
+CTGACTAGACTGGAGGCGCTCGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_85_268_53/2
+CCAGTCTCAAGTAGAAAAAGTCCCGTTGACGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_75_204_54/2
+TCGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_41_236_55/2
+TCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_56_183_56/2
+ACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_87_250_57/2
+AGAGCGTCAGATGCAGAGACTGGACTATTTAGGACGATCGGACTGAGGAGTGCAGTAGGACGCTACGTATTTGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_82_271_58/2
+ATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATGCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_6_182_59/2
+CGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_53_272_5a/2
+TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_114_277_5b/2
+TTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGCCTGAGCGTCGAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_39_219_5c/2
+AAGATAATAAAGTAATAGTGGCGTATCGCAAGCTGGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_4_191_5d/2
+ACTATCTGACGAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTACCATTACGCGGATGACGACTAGGACTACGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_73_259_5e/2
+AGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATACAGTAATAGTGGCGTATCGCAAGCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_87_279_5f/2
+AGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACCGAGGAGGGCAGTAGGACGCTACGTATTTGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_125_293_60/2
+CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCTTCGAGGTTGCGATACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_111_297_61/2
+CTATTTAGGACGATCGGACTGGGGAGGGCAGTAGGACGCTACGGATTTGGCGCGCGGCCCTACGGCTGAGCGTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_22_173_62/2
+GTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTCCAGTCGCTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_116_295_63/2
+TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
--- a/tools/ngs_rna/tophat_wrapper.xml
+++ b/tools/ngs_rna/tophat_wrapper.xml
@@ -1,4 +1,4 @@
-<tool id="tophat" name="Tophat" version="1.1.2">
+<tool id="tophat" name="Tophat" version="1.2.0"><description>Find splice junctions using RNA-seq data</description><requirements><requirement type="package">tophat</requirement>
@@ -7,46 +7,41 @@
tophat_wrapper.py
## Change this to accommodate the number of threads you have available.
--num-threads="4"
-
+
## Provide outputs.
--junctions-output=$junctions
--hits-output=$accepted_hits
-
+
## Handle reference file.
#if $refGenomeSource.genomeSource == "history":
--own-file=$refGenomeSource.ownFile
- --indexes-path="None"
#else:
- --own-file="None"
- --indexes-path=$refGenomeSource.index
+ --indexes-path="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'tophat_indexes' ].get_fields() )[0][-1] }"
#end if
-
+
## Are reads single-end or paired?
--single-paired=$singlePaired.sPaired
-
+
## First input file always required.
--input1=$singlePaired.input1
-
+
## Set parms based on whether reads are single-end or paired.
#if $singlePaired.sPaired == "single":
- --input2="None"
- -r "None"
- --settings=$singlePaired.sParams.sSettingsType
- #if $singlePaired.sParams.sSettingsType == "full":
- --mate-std-dev="None"
- -a $singlePaired.sParams.anchor_length
- -m $singlePaired.sParams.splice_mismatches
- -i $singlePaired.sParams.min_intron_length
- -I $singlePaired.sParams.max_intron_length
- -F $singlePaired.sParams.junction_filter
- -g $singlePaired.sParams.max_multihits
- --min-segment-intron $singlePaired.sParams.min_segment_intron
- --max-segment-intron $singlePaired.sParams.max_segment_intron
- --seg-mismatches=$singlePaired.sParams.seg_mismatches
- --seg-length=$singlePaired.sParams.seg_length
-
- ## Supplying junctions parameters.
- #if $singlePaired.sParams.own_junctions.use_junctions == "Yes":
+ --settings=$singlePaired.sParams.sSettingsType
+ #if $singlePaired.sParams.sSettingsType == "full":
+ -a $singlePaired.sParams.anchor_length
+ -m $singlePaired.sParams.splice_mismatches
+ -i $singlePaired.sParams.min_intron_length
+ -I $singlePaired.sParams.max_intron_length
+ -F $singlePaired.sParams.junction_filter
+ -g $singlePaired.sParams.max_multihits
+ --min-segment-intron $singlePaired.sParams.min_segment_intron
+ --max-segment-intron $singlePaired.sParams.max_segment_intron
+ --seg-mismatches=$singlePaired.sParams.seg_mismatches
+ --seg-length=$singlePaired.sParams.seg_length
+
+ ## Supplying junctions parameters.
+ #if $singlePaired.sParams.own_junctions.use_junctions == "Yes":
#if $singlePaired.sParams.own_junctions.gene_model_ann.use_annotations == "Yes":
-G $singlePaired.sParams.own_junctions.gene_model_ann.gene_annotation_model
#end if
@@ -57,47 +52,47 @@
#if str($singlePaired.sParams.own_junctions.no_novel_juncs) == "Yes":
--no-novel-juncs
#end if
- #end if
-
- #if $singlePaired.sParams.closure_search.use_search == "Yes":
+ #end if
+
+ #if $singlePaired.sParams.closure_search.use_search == "Yes":
--closure-search
--min-closure-exon $singlePaired.sParams.closure_search.min_closure_exon
--min-closure-intron $singlePaired.sParams.closure_search.min_closure_intron
--max-closure-intron $singlePaired.sParams.closure_search.max_closure_intron
- #else:
+ #else:
--no-closure-search
- #end if
- #if $singlePaired.sParams.coverage_search.use_search == "Yes":
+ #end if
+ #if $singlePaired.sParams.coverage_search.use_search == "Yes":
--coverage-search
--min-coverage-intron $singlePaired.sParams.coverage_search.min_coverage_intron
--max-coverage-intron $singlePaired.sParams.coverage_search.max_coverage_intron
- #else:
+ #else:
--no-coverage-search
- #end if
- ## TODO: No idea why the type conversion is necessary, but it seems to be.
- #if str($singlePaired.sParams.microexon_search) == "Yes":
+ #end if
+ ## TODO: No idea why the type conversion is necessary, but it seems to be.
+ #if str($singlePaired.sParams.microexon_search) == "Yes":
--microexon-search
- #end if
- #end if
- #else:
- --input2=$singlePaired.input2
- -r $singlePaired.mate_inner_distance
- --settings=$singlePaired.pParams.pSettingsType
- #if $singlePaired.pParams.pSettingsType == "full":
- --mate-std-dev=$singlePaired.pParams.mate_std_dev
- -a $singlePaired.pParams.anchor_length
- -m $singlePaired.pParams.splice_mismatches
- -i $singlePaired.pParams.min_intron_length
- -I $singlePaired.pParams.max_intron_length
- -F $singlePaired.pParams.junction_filter
- -g $singlePaired.pParams.max_multihits
- --min-segment-intron $singlePaired.pParams.min_segment_intron
- --max-segment-intron $singlePaired.pParams.max_segment_intron
- --seg-mismatches=$singlePaired.pParams.seg_mismatches
- --seg-length=$singlePaired.pParams.seg_length
-
- ## Supplying junctions parameters.
- #if $singlePaired.pParams.own_junctions.use_junctions == "Yes":
+ #end if
+ #end if
+ #else:
+ --input2=$singlePaired.input2
+ -r $singlePaired.mate_inner_distance
+ --settings=$singlePaired.pParams.pSettingsType
+ #if $singlePaired.pParams.pSettingsType == "full":
+ --mate-std-dev=$singlePaired.pParams.mate_std_dev
+ -a $singlePaired.pParams.anchor_length
+ -m $singlePaired.pParams.splice_mismatches
+ -i $singlePaired.pParams.min_intron_length
+ -I $singlePaired.pParams.max_intron_length
+ -F $singlePaired.pParams.junction_filter
+ -g $singlePaired.pParams.max_multihits
+ --min-segment-intron $singlePaired.pParams.min_segment_intron
+ --max-segment-intron $singlePaired.pParams.max_segment_intron
+ --seg-mismatches=$singlePaired.pParams.seg_mismatches
+ --seg-length=$singlePaired.pParams.seg_length
+
+ ## Supplying junctions parameters.
+ #if $singlePaired.pParams.own_junctions.use_junctions == "Yes":
#if $singlePaired.pParams.own_junctions.gene_model_ann.use_annotations == "Yes":
-G $singlePaired.pParams.own_junctions.gene_model_ann.gene_annotation_model
#end if
@@ -108,29 +103,29 @@
#if str($singlePaired.pParams.own_junctions.no_novel_juncs) == "Yes":
--no-novel-juncs
#end if
- #end if
-
- #if $singlePaired.pParams.closure_search.use_search == "Yes":
+ #end if
+
+ #if $singlePaired.pParams.closure_search.use_search == "Yes":
--closure-search
--min-closure-exon $singlePaired.pParams.closure_search.min_closure_exon
--min-closure-intron $singlePaired.pParams.closure_search.min_closure_intron
--max-closure-intron $singlePaired.pParams.closure_search.max_closure_intron
- #else:
+ #else:
--no-closure-search
- #end if
- #if $singlePaired.pParams.coverage_search.use_search == "Yes":
+ #end if
+ #if $singlePaired.pParams.coverage_search.use_search == "Yes":
--coverage-search
--min-coverage-intron $singlePaired.pParams.coverage_search.min_coverage_intron
--max-coverage-intron $singlePaired.pParams.coverage_search.max_coverage_intron
- #else:
+ #else:
--no-coverage-search
- #end if
- ## TODO: No idea why the type conversion is necessary, but it seems to be.
- #if str ($singlePaired.pParams.microexon_search) == "Yes":
+ #end if
+ ## TODO: No idea why the type conversion is necessary, but it seems to be.
+ #if str ($singlePaired.pParams.microexon_search) == "Yes":
--microexon-search
#end if
- #end if
- #end if
+ #end if
+ #end if
</command><inputs><conditional name="refGenomeSource">
@@ -140,10 +135,7 @@
</param><when value="indexed"><param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
- <options from_file="bowtie_indices.loc">
- <column name="value" index="1" />
- <column name="name" index="0" />
- </options>
+ <options from_data_table="tophat_indexes" /></param></when><when value="history">
@@ -186,7 +178,7 @@
<conditional name="gene_model_ann"><param name="use_annotations" type="select" label="Use Gene Annotation Model"><option value="No">No</option>
- <option value="Yes">Yes</option>
+ <option value="Yes">Yes</option></param><when value="No" /><when value="Yes">
@@ -196,7 +188,7 @@
<conditional name="raw_juncs"><param name="use_juncs" type="select" label="Use Raw Junctions"><option value="No">No</option>
- <option value="Yes">Yes</option>
+ <option value="Yes">Yes</option></param><when value="No" /><when value="Yes">
@@ -242,7 +234,7 @@
</param></when><!-- full --></conditional><!-- sParams -->
- </when>
+ </when><!-- single --><when value="paired"><param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/><param format="fastqsanger" name="input2" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
@@ -276,7 +268,7 @@
<conditional name="gene_model_ann"><param name="use_annotations" type="select" label="Use Gene Annotation Model"><option value="No">No</option>
- <option value="Yes">Yes</option>
+ <option value="Yes">Yes</option></param><when value="No" /><when value="Yes">
@@ -286,7 +278,7 @@
<conditional name="raw_juncs"><param name="use_juncs" type="select" label="Use Raw Junctions"><option value="No">No</option>
- <option value="Yes">Yes</option>
+ <option value="Yes">Yes</option></param><when value="No" /><when value="Yes">
@@ -325,14 +317,14 @@
<param name="max_coverage_intron" type="integer" value="20000" label="Maximum intron length that may be found during coverage search" /></when><when value="No" />
- </conditional>
+ </conditional><param name="microexon_search" type="select" label="Use Microexon Search" help="With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer."><option value="No">No</option><option value="Yes">Yes</option></param></when><!-- full --></conditional><!-- pParams -->
- </when>
+ </when><!-- paired --></conditional></inputs>
@@ -342,38 +334,46 @@
</outputs><tests>
-<!-- <test>
- <param name="genomeSource" value="indexed"/>
- <param name="index" value="equCab2chrM"/>
- <param name="sPaired" value="single"/>
- <param name="input1" ftype="fastqsanger" value="tophat_in1.fq"/>
- <param name="sSettingsType" value="preSet"/>
---><!--
- Can't test this right now because first lines of file are run-specific.
- <output name="accepted_hits" file="tophat_out1.sam"/>
+ <!-- Test single-end reads with pre-built index and preset parameters -->
+ <test>
+ <!-- TopHat commands:
+ tophat -o tmp_dir -p 1 /afs/bx.psu.edu/depot/data/genome/test/tophat/tophat_in1 test-data/tophat_in2.fastqsanger
-->
-<!-- <output name="coverage" file="tophat_out2.wig"/>
- <output name="junctions" file="tophat_out3.bed"/>
+ <param name="genomeSource" value="indexed" />
+ <param name="index" value="tophat_test" />
+ <param name="sPaired" value="single" />
+ <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger" />
+ <param name="sSettingsType" value="preSet" />
+ <output name="junctions" file="tophat_out1j.bed" ftype="bed" />
+ <output name="accepted_hits" file="tophat_out1h.bam" compare="sim_size" ftype="bam" /></test>
---><!-- Test using test data: paired-end reads, index from history. --><test>
+ <!-- TopHat commands:
+ bowtie-build -f test-data/tophat_in4.fasta tophat_in4
+ tophat -o tmp_dir -p 1 -r 20 tophat_in4 test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger
+ -->
+ <param name="genomeSource" value="history" />
+ <param name="ownFile" ftype="fasta" value="tophat_in1.fasta" />
+ <param name="sPaired" value="paired" />
+ <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger" />
+ <param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger" />
+ <param name="mate_inner_distance" value="20" />
+ <param name="pSettingsType" value="preSet" />
+ <output name="junctions" file="tophat_out2j.bed" ftype="bed" />
+ <output name="accepted_hits" file="tophat_out2h.bam" compare="sim_size" ftype="bam" />
+ </test>
+ <!-- Test single-end reads with user-supplied reference fasta and full parameters -->
+ <test>
+ <!-- Tophat commands:
+ bowtie-build -f test-data/tophat_in1.fasta tophat_in1
+ tophat -o tmp_dir -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +closure-search +min-closure-exon 50 +min-closure-intron 50 +max-closure-intro 5000 +microexon-search tophat_in1 test-data/tophat_in2.fastqsanger
+ Replace the + with double-dash
+ --><param name="genomeSource" value="history"/>
- <param name="ownFile" ftype="fasta" value="tophat_in3.fa"/>
- <param name="sPaired" value="paired"/>
- <param name="input1" ftype="fastqsanger" value="tophat_in1.fq"/>
- <param name="input2" ftype="fastqsanger" value="tophat_in2.fq"/>
- <param name="mate_inner_distance" value="20"/>
- <param name="pSettingsType" value="preSet"/>
- <output name="junctions" file="tophat_out1.bed"/>
- <!-- Bam files always differ (due to magic number?), so can't test this right now. -->
- <output name="accepted_hits" file="tophat_out2.bam" lines_diff="100000"/>
- </test>
-<!-- <test>
- <param name="genomeSource" value="history"/>
- <param name="ownFile" value="phiX.fasta"/>
+ <param name="ownFile" value="tophat_in1.fasta"/><param name="sPaired" value="single"/>
- <param name="input1" ftype="fastqsanger" value="tophat_in1.fq"/>
+ <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger"/><param name="sSettingsType" value="full"/><param name="anchor_length" value="8"/><param name="splice_mismatches" value="0"/>
@@ -386,19 +386,32 @@
<param name="max_segment_intron" value="500000" /><param name="seg_mismatches" value="2"/><param name="seg_length" value="25"/>
---><!--
- Can't test this right now because first lines of file are run-specific.
- <output name="accepted_hits" file="tophat_out1.sam"/>
+ <param name="use_junctions" value="Yes" />
+ <param name="use_annotations" value="No" />
+ <param name="use_juncs" value="No" />
+ <param name="no_novel_juncs" value="No" />
+ <param name="use_search" value="Yes" />
+ <param name="min_closure_exon" value="50" />
+ <param name="min_closure_intron" value="50" />
+ <param name="max_closure_intron" value="5000" />
+ <param name="use_search" value="Yes" />
+ <param name="min_coverage_intron" value="50" />
+ <param name="max_coverage_intron" value="20000" />
+ <param name="microexon_search" value="Yes" />
+ <output name="junctions" file="tophat_out3j.bed" ftype="bed" />
+ <output name="accepted_hits" file="tophat_out3h.bam" compare="sim_size" ftype="bam" />
+ </test>
+ <!-- Test paired-end reads with user-supplied reference fasta and full parameters -->
+ <test>
+ <!-- TopHat commands:
+ tophat -o tmp_dir -r 20 -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +closure-search +min-closure-exon 50 +min-closure-intron 50 +max-closure-intron 5000 +microexon-search /afs/bx.psu.edu/depot/data/genome/test/tophat/tophat_in1 test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger
+ Replace the + with double-dash
-->
-<!-- <output name="coverage" file="tophat_out2.wig"/>
- <output name="junctions" file="tophat_out3.bed"/>
- </test>
- <test><param name="genomeSource" value="indexed"/>
- <param name="index" value="equCab2chrM"/>
+ <param name="index" value="tophat_test"/><param name="sPaired" value="paired"/>
- <param name="input1" ftype="fastqsanger" value="tophat_in1.fq"/>
- <param name="input2" ftype="fastqsanger" value="tophat_in2.fq"/>
+ <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger"/>
+ <param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger"/><param name="mate_inner_distance" value="20"/><param name="pSettingsType" value="full"/><param name="mate_std_dev" value="20"/>
@@ -409,18 +422,26 @@
<param name="quals_scale" value="default"/><param name="junction_filter" value="0.15"/><param name="max_multihits" value="40"/>
+ <param name="min_segment_intron" value="50" />
+ <param name="max_segment_intron" value="500000" />
+ <param name="seg_mismatches" value="2"/>
+ <param name="seg_length" value="25"/>
+ <param name="use_junctions" value="Yes" />
+ <param name="use_annotations" value="No" />
+ <param name="use_juncs" value="No" />
+ <param name="no_novel_juncs" value="No" />
+ <param name="use_search" value="Yes" />
+ <param name="min_closure_exon" value="50" />
+ <param name="min_closure_intron" value="50" />
+ <param name="max_closure_intron" value="5000" />
+ <param name="use_search" value="Yes" /><param name="min_coverage_intron" value="50" /><param name="max_coverage_intron" value="20000" />
- <param name="seg_mismatches" value="2"/>
- <param name="seg_length" value="25"/>
---><!--
- Can't test this right now because first lines of file are run-specific.
- <output name="accepted_hits" file="tophat_out1.sam"/>
- -->
-<!-- <output name="coverage" file="tophat_out2.wig"/>
- <output name="junctions" file="tophat_out3.bed"/>
+ <param name="microexon_search" value="Yes" />
+ <output name="junctions" file="tophat_out4j.bed" ftype="bed" />
+ <output name="accepted_hits" file="tophat_out4h.bam" compare="sim_size" ftype="bam" /></test>
---></tests>
+ </tests><help>
**Tophat Overview**
Binary file test-data/tophat_out3h.bam has changed
Binary file test-data/tophat_out2.bam has changed
--- a/test-data/tophat_in3.fa
+++ /dev/null
@@ -1,14 +0,0 @@
->test_chromosome
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
-ACTACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCC
-ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC
-AGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCT
-ACGTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCC
-GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG
-ACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACT
-GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG
-TTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
--- a/tool_data_table_conf.xml.sample
+++ b/tool_data_table_conf.xml.sample
@@ -1,3 +1,4 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--><tables><!-- Locations of all fasta files under genome directory --><table name="all_fasta" comment_char="#">
@@ -34,7 +35,7 @@
<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 -->
+ <!-- Locations of MAF files that have been indexed with bx-python --><table name="indexed_maf_files"><columns>name, value, dbkey, species</columns><file path="tool-data/maf_index.loc" />
@@ -65,9 +66,8 @@
<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="#">
+ <table name="tophat_indexes" comment_char="#"><columns>value, dbkey, name, path</columns><file path="tool-data/bowtie_indices.loc" /></table>
---></tables>
Binary file test-data/tophat_out4h.bam has changed
--- /dev/null
+++ b/test-data/tophat_out4j.bed
@@ -0,0 +1,3 @@
+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
Binary file test-data/tophat_out2h.bam has changed
1
0
galaxy-dist commit 8ce82d60b2ab: - added the change data library sample operation functional test.
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 rc
# Date 1290011634 18000
# Node ID 8ce82d60b2ab55966d133db136fcb2f809201c4b
# Parent 19b10fff133595cb5cd1851a7f24024c2637ad2b
- added the change data library sample operation functional test.
- renaming dataset now checks for incorrect filename characters
- fixed bugs
--- a/lib/galaxy/web/controllers/requests_common.py
+++ b/lib/galaxy/web/controllers/requests_common.py
@@ -1079,7 +1079,7 @@ class RequestsCommon( BaseController, Us
cntrller=cntrller,
action='update_request_state',
request_id=trans.security.encode_id( request.id ) ) )
- elif sample_operation == trans.model.sample.bulk_operations.SELECT_LIBRARY:
+ elif sample_operation == trans.model.Sample.bulk_operations.SELECT_LIBRARY:
# TODO: fix the code so that the sample_operation_select_field does not use
# sample_0_library_id as it's name. it should use something like sample_operation_library_id
# and sample_operation_folder_id because the name sample_0_library_id should belong to the
--- a/templates/admin/requests/rename_datasets.mako
+++ b/templates/admin/requests/rename_datasets.mako
@@ -16,6 +16,7 @@
<div class="toolForm"><form name="rename_datasets" id="rename_datasets" action="${h.url_for( controller='requests_admin', action='rename_datasets', id_list=id_list, sample_id=trans.security.encode_id( sample.id ) )}" method="post" >
+
<table class="grid"><thead><tr>
@@ -43,9 +44,16 @@
</tbody></table><br/>
+ <div class="form-row">
+ <div class="toolParamHelp" style="clear: both;">
+ A dataset name should only contain the alphanumeric characters or underscore(_).
+ If a dataset name contains any other character, it would be replaced by an underscore(_).
+ </div>
+ </div><div class="form-row"><input type="submit" name="rename_datasets_button" value="Save"/><input type="submit" name="cancel_rename_datasets_button" value="Close"/></div></form>
+
</div>
--- a/scripts/galaxy_messaging/server/setup_rabbitmq.py
+++ b/scripts/galaxy_messaging/server/setup_rabbitmq.py
@@ -24,7 +24,7 @@ def main( config_file ):
cmd_list = [
'add_user %s %s' % ( username, password ),
- 'add_vhost %s' % config.get( 'galaxy_amqp', 'virtual_host' ),
+ 'add_vhost %s' % virtual_host,
'set_permissions -p %s %s ".*" ".*" ".*"' % ( virtual_host, username )
]
--- a/test/functional/test_sample_tracking.py
+++ b/test/functional/test_sample_tracking.py
@@ -430,8 +430,8 @@ class TestFormsAndRequests( TwillTestCas
"""Testing editing the sample information of new request1"""
# logged in as regular_user1
# target data library - change it to library1
- target_library_info = dict(library=self.security.encode_id(library1.id),
- folder=self.security.encode_id(library1_folder1.id) )
+ target_library_info = dict(library=self.security.encode_id( library1.id ),
+ folder=self.security.encode_id( library1_folder1.id ) )
new_sample_value_tuples = \
[ ( 'Sample1_renamed', target_library_info, [ 'option2', 'sample1 field2 value edited', 'sample1 field3 value edited' ] ),
( 'Sample2_renamed', target_library_info, [ 'option1', 'sample2 field2 value edited', 'sample2 field3 value edited' ] ),
@@ -494,6 +494,23 @@ class TestFormsAndRequests( TwillTestCas
strings_displayed_count=strings_displayed_count,
strings_not_displayed=[ request1.states.COMPLETE,
request1.states.REJECTED ] )
+ # change the target data library back to library2 using sample operation user interface
+ self.change_sample_target_data_library( cntrller='requests',
+ request_id=self.security.encode_id( request1.id ),
+ sample_ids=[ sample.id for sample in request1.samples ],
+ new_library_id=self.security.encode_id( library2.id ),
+ new_folder_id=self.security.encode_id( library2_folder1.id ),
+ strings_displayed=[ 'Edit Current Samples of Sequencing Request "%s"' % request1.name ],
+ strings_displayed_after_submit=[ 'Changes made to the samples have been saved.' ] )
+ # check the changed target data library & folder on the request page
+ strings_displayed_count = []
+ strings_displayed_count.append( ( library2.name, len( request1.samples ) ) )
+ strings_displayed_count.append( ( library2_folder1.name, len( request1.samples ) ) )
+ self.view_request( cntrller='requests',
+ request_id=self.security.encode_id( request1.id ),
+ strings_displayed=[],
+ strings_displayed_count=strings_displayed_count )
+
#
# ====== Sequencing request test methods - Admin perspective ================
#
@@ -537,7 +554,7 @@ class TestFormsAndRequests( TwillTestCas
request1.type.states[4].desc ]
# check history of each sample
for sample in request1.samples:
- strings_displayed = [ 'Events for Sample "%s"' % sample.name,
+ strings_displayed = [ 'History of sample "%s"' % sample.name,
'Sequencing request submitted and sample state set to %s' % request1.type.states[0].name,
request1.type.states[0].name,
request1.type.states[1].name ]
--- a/lib/galaxy/web/controllers/requests_admin.py
+++ b/lib/galaxy/web/controllers/requests_admin.py
@@ -361,17 +361,29 @@ class RequestsAdmin( BaseController, Use
sample_dataset = trans.sa_session.query( trans.app.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) )
sample_datasets.append( sample_dataset )
if params.get( 'rename_datasets_button', False ):
+ incorrect_dataset_names = []
for sample_dataset in sample_datasets:
encoded_id = trans.security.encode_id( sample_dataset.id )
selected_option = util.restore_text( params.get( 'rename_datasets_for_sample_%s' % encoded_id, '' ) )
new_name = util.restore_text( params.get( 'new_name_%s' % encoded_id, '' ) )
+ if not new_name:
+ incorrect_dataset_names.append( sample_dataset.name )
+ continue
+ new_name = util.sanitize_for_filename( new_name )
if selected_option == 'none':
sample_dataset.name = new_name
else:
sample_dataset.name = '%s_%s' % ( selected_option, new_name )
trans.sa_session.add( sample_dataset )
trans.sa_session.flush()
- message = 'Changes saved successfully.'
+ if len( sample_datasets ) == len( incorrect_dataset_names ):
+ status = 'error'
+ message = 'All datasets renamed incorrectly.'
+ elif len( incorrect_dataset_names ):
+ status = 'done'
+ message = 'Changes saved successfully. The following datasets were renamed incorrectly: %s.' % str( incorrect_dataset_names )
+ else:
+ message = 'Changes saved successfully.'
return trans.fill_template( '/admin/requests/rename_datasets.mako',
sample=sample,
id_list=id_list,
--- a/test/base/twilltestcase.py
+++ b/test/base/twilltestcase.py
@@ -1638,6 +1638,23 @@ class TwillTestCase( unittest.TestCase )
tc.submit( "save_samples_button" )
for check_str in strings_displayed_after_submit:
self.check_page_for_string( check_str )
+ def change_sample_target_data_library( self, cntrller, request_id, sample_ids, new_library_id, new_folder_id, comment='', strings_displayed=[], strings_displayed_after_submit=[] ):
+ url = "%s/requests_common/edit_samples?cntrller=%s&id=%s&editing_samples=True" % ( self.url, cntrller, request_id )
+ self.visit_url( url )
+ for check_str in strings_displayed:
+ self.check_page_for_string( check_str )
+ for sample_id in sample_ids:
+ tc.fv( "1", "select_sample_%i" % sample_id, True )
+ tc.fv( "1", "sample_operation", 'Select data library and folder' )
+ self.refresh_form( "sample_operation", 'Select data library and folder' )
+ self.check_page_for_string( "Select data library:" )
+ tc.fv( "1", "sample_0_library_id", new_library_id )
+ self.refresh_form( "sample_0_library_id", new_library_id )
+ self.check_page_for_string( "Select folder:" )
+ tc.fv( "1", "sample_0_folder_id", new_folder_id )
+ tc.submit( "save_samples_button" )
+ for check_str in strings_displayed_after_submit:
+ self.check_page_for_string( check_str )
def add_user_address( self, user_id, address_dict ):
self.home()
self.visit_url( "%s/user/new_address?admin_view=False&user_id=%i" % ( self.url, user_id ) )
--- a/lib/galaxy/web/controllers/forms.py
+++ b/lib/galaxy/web/controllers/forms.py
@@ -635,8 +635,8 @@ class Forms( BaseController ):
if form_type == trans.model.FormDefinition.types.SAMPLE:
for ft in trans.model.Sample.supported_field_types:
if ft.__name__ == field[ 'type' ]:
- self.fieldtype.add_option( ft.__name__, ft__name__, selected=True )
- if ft == 'SelectField':
+ self.fieldtype.add_option( ft.__name__, ft.__name__, selected=True )
+ if ft.__name__ == 'SelectField':
self.selectbox_ui( field )
else:
self.fieldtype.add_option( ft.__name__, ft.__name__ )
@@ -644,7 +644,7 @@ class Forms( BaseController ):
for ft in trans.model.FormDefinition.supported_field_types:
if ft.__name__ == field[ 'type' ]:
self.fieldtype.add_option( ft.__name__, ft.__name__, selected=True )
- if ft == 'SelectField':
+ if ft.__name__ == 'SelectField':
self.selectbox_ui( field )
else:
self.fieldtype.add_option( ft.__name__, ft.__name__ )
1
0
galaxy-dist commit 39f41821aa4e: Adding data table configuration file for backwards compatibility with local installs: for people who don't want to update loc file style (changes made in rev 4550:535d276c92bc)
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 1290011565 18000
# Node ID 39f41821aa4eec15b04509d24715946552bb14a6
# Parent 19b10fff133595cb5cd1851a7f24024c2637ad2b
Adding data table configuration file for backwards compatibility with local installs: for people who don't want to update loc file style (changes made in rev 4550:535d276c92bc)
--- /dev/null
+++ b/tool_data_table_conf.xml.oldlocstyle
@@ -0,0 +1,73 @@
+<!-- Use this file if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<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>name, value</columns>
+ <file path="tool-data/blastdb.loc" />
+ </table>
+ <!-- Locations of protein (mega)blast databases -->
+ <table name="blastdb_p" comment_char="#">
+ <columns>name, value</columns>
+ <file path="tool-data/blastdb_p.loc" />
+ </table>
+ <!-- Locations of indexes in the Bowtie mapper format -->
+ <table name="bowtie_indexes" comment_char="#">
+ <columns>name, value</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>name, value</columns>
+ <file path="tool-data/bowtie_indices_color.loc" />
+ </table>
+ <!-- Locations of indexes in the BWA mapper format -->
+ <table name="bwa_indexes" comment_char="#">
+ <columns>name, value</columns>
+ <file path="tool-data/bwa_index.loc" />
+ </table>
+ <!-- Locations of MAF files that have been indexed with bx-python -->
+ <table name="indexed_maf_files">
+ <columns>name, value, dbkey, species</columns>
+ <file path="tool-data/maf_index.loc" />
+ </table>
+ <!-- Locations of fasta files appropriate for NGS simulation -->
+ <table name="ngs_sim_fasta" comment_char="#">
+ <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>name, value</columns>
+ <file path="tool-data/lastz_seqs.loc" />
+ </table>
+ <!-- Locations of PerM base index files -->
+ <table name="perm_base_indexes" comment_char="#">
+ <columns>name, value</columns>
+ <file path="tool-data/perm_base_index.loc" />
+ </table>
+ <!-- Locations of PerM color index files -->
+ <table name="perm_color_indexes" comment_char="#">
+ <columns>name, value</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>name, value</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>name, value</columns>
+ <file path="tool-data/bowtie_indices.loc" />
+ </table>
+</tables>
1
0
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 1290010215 18000
# Node ID 19b10fff133595cb5cd1851a7f24024c2637ad2b
# Parent 918a25ed14f5427f70970b0c436159fc58fd111e
More bug fixes.
--- a/lib/galaxy/web/controllers/forms.py
+++ b/lib/galaxy/web/controllers/forms.py
@@ -602,7 +602,7 @@ class Forms( BaseController ):
self.fieldtype.add_option( ft.__name__, ft.__name__ )
else:
for ft in trans.model.FormDefinition.supported_field_types:
- self.fieldtype.add_option( ft.__name__, ft__name__ )
+ self.fieldtype.add_option( ft.__name__, ft.__name__ )
self.required = SelectField('field_required_'+str(index), display='radio')
self.required.add_option('Required', 'required')
self.required.add_option('Optional', 'optional', selected=True)
@@ -713,7 +713,7 @@ class Forms( BaseController ):
form_details=form_details,
field_details=field_details,
form_definition=form_definition,
- field_types=BaseField.form_field_types(),
+ field_types=trans.model.FormDefinition.supported_field_types,
message=message,
status=status,
current_form_type=current_form[ 'type' ],
1
0
galaxy-dist commit 29227c9c5992: Relax GTF sniffer ever so slightly so that Ensembl GTF files are sniffed correctly.
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 1290019719 18000
# Node ID 29227c9c599292f7608e61cdd4b2be424b7a7bfc
# Parent 1ee9e2490e1968957f5f440a9dd08fb75aa3eb70
Relax GTF sniffer ever so slightly so that Ensembl GTF files are sniffed correctly.
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -965,7 +965,9 @@ class Gtf( Gff ):
if len( attributes ) >= 2:
try:
# Imprecise: should check for a single space per the spec.
- attr_name, attr_value = attributes[0].split(" ")
+ # strip() needed b/c Ensembl GTF files include an (illegal)
+ # space before attributes string.
+ attr_name, attr_value = attributes[0].strip().split(" ")
if attr_name != 'gene_id':
return False
except:
1
0
galaxy-dist commit 918a25ed14f5: Bug fix due to my last commit - Requests do not have supported_field_types, FormDefinitions do.
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 1290008781 18000
# Node ID 918a25ed14f5427f70970b0c436159fc58fd111e
# Parent 7bded9108bd8297ea609e9ec06bbe516b5f0b83a
Bug fix due to my last commit - Requests do not have supported_field_types, FormDefinitions do.
--- a/lib/galaxy/web/controllers/forms.py
+++ b/lib/galaxy/web/controllers/forms.py
@@ -601,7 +601,7 @@ class Forms( BaseController ):
for ft in trans.model.Sample.supported_field_types:
self.fieldtype.add_option( ft.__name__, ft.__name__ )
else:
- for ft in trans.model.Request.supported_field_types:
+ for ft in trans.model.FormDefinition.supported_field_types:
self.fieldtype.add_option( ft.__name__, ft__name__ )
self.required = SelectField('field_required_'+str(index), display='radio')
self.required.add_option('Required', 'required')
@@ -641,7 +641,7 @@ class Forms( BaseController ):
else:
self.fieldtype.add_option( ft.__name__, ft.__name__ )
else:
- for ft in trans.model.Request.supported_field_types:
+ for ft in trans.model.FormDefinition.supported_field_types:
if ft.__name__ == field[ 'type' ]:
self.fieldtype.add_option( ft.__name__, ft.__name__, selected=True )
if ft == 'SelectField':
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galaxy-dist commit 394d8186f666: tool_form: Make radio and select box labels explicitly inline. Workflow: add colons after parameter names where appropriate. Fixes #419
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 Kanwei Li <kanwei(a)gmail.com>
# Date 1289929775 18000
# Node ID 394d8186f666b506cd0a93aefb7a079e0c9ec59b
# Parent 1bf064c8ab88621dd58890f6cd56ad4900d10d6b
tool_form: Make radio and select box labels explicitly inline. Workflow: add colons after parameter names where appropriate. Fixes #419
--- a/static/june_2007_style/base.css.tmpl
+++ b/static/june_2007_style/base.css.tmpl
@@ -210,6 +210,10 @@ div.form-row label {
margin-bottom: .2em;
}
+div.form-row label.inline {
+ display: inline;
+}
+
div.form-row-input {
float: left;
}
--- a/templates/workflow/editor_tool_form.mako
+++ b/templates/workflow/editor_tool_form.mako
@@ -7,8 +7,8 @@ from galaxy.util.expressions import Expr
<% ctx = ExpressionContext( values, ctx ) %>
%for input_index, input in enumerate( inputs.itervalues() ):
%if input.type == "repeat":
- <div class="repeat-group">
- <div class="form-title-row"><b>${input.title_plural}</b></div>
+ <div class="repeat-group form-row">
+ <label>${input.title_plural}:</label><% repeat_values = values[input.name] %>
%for i in range( len( repeat_values ) ):
<%
@@ -19,7 +19,7 @@ from galaxy.util.expressions import Expr
index = repeat_values[i]['__index__']
%><div class="repeat-group-item">
- <div class="form-title-row"><b>${input.title} ${i + 1}</b></div>
+ <div class="form-title-row"><label>${input.title} ${i + 1}</label></div>
${do_inputs( input.inputs, repeat_values[ i ], rep_errors, prefix + input.name + "_" + str(index) + "|", ctx )}
<div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div></div>
@@ -63,7 +63,7 @@ from galaxy.util.expressions import Expr
%else:
%if isinstance( value, RuntimeValue ):
<label>
- ${param.get_label()}
+ ${param.get_label()}:
<span class="popupmenu"><button type="submit" name="make_buildtime" value="${prefix}${param.name}">Set in advance</button></span>
@@ -73,7 +73,7 @@ from galaxy.util.expressions import Expr
</div>
%else:
<label>
- ${param.get_label()}
+ ${param.get_label()}:
%if allow_runtime:
<span class="popupmenu"><button type="submit" name="make_runtime" value="${prefix}${param.name}">Set at runtime</button>
--- a/lib/galaxy/web/form_builder.py
+++ b/lib/galaxy/web/form_builder.py
@@ -248,16 +248,16 @@ class SelectField(BaseField):
>>> t.add_option( "tuti", 1 )
>>> t.add_option( "fruity", "x" )
>>> print t.get_html()
- <div><input type="radio" name="foo" value="1" id="foo|1"><label for="foo|1">tuti</label></div>
- <div><input type="radio" name="foo" value="x" id="foo|x"><label for="foo|x">fruity</label></div>
+ <div><input type="radio" name="foo" value="1" id="foo|1"><label class="inline" for="foo|1">tuti</label></div>
+ <div><input type="radio" name="foo" value="x" id="foo|x"><label class="inline" for="foo|x">fruity</label></div>
>>> t = SelectField( "bar", multiple=True, display="checkboxes" )
>>> t.add_option( "automatic", 3 )
>>> t.add_option( "bazooty", 4, selected=True )
>>> print t.get_html()
<div class="checkUncheckAllPlaceholder" checkbox_name="bar"></div>
- <div><input type="checkbox" name="bar" value="3" id="bar|3"><label for="bar|3">automatic</label></div>
- <div><input type="checkbox" name="bar" value="4" id="bar|4" checked='checked'><label for="bar|4">bazooty</label></div>
+ <div><input type="checkbox" name="bar" value="3" id="bar|3"><label class="inline" for="bar|3">automatic</label></div>
+ <div><input type="checkbox" name="bar" value="4" id="bar|4" checked='checked'><label class="inline" for="bar|4">bazooty</label></div>
"""
def __init__( self, name, multiple=None, display=None, refresh_on_change=False, refresh_on_change_values=[], size=None ):
self.name = name
@@ -302,7 +302,7 @@ class SelectField(BaseField):
selected_text = ""
if selected:
selected_text = " checked='checked'"
- rval.append( '<div%s><input type="checkbox" name="%s%s" value="%s" id="%s"%s%s><label for="%s">%s</label></div>' % \
+ rval.append( '<div%s><input type="checkbox" name="%s%s" value="%s" id="%s"%s%s><label class="inline" for="%s">%s</label></div>' % \
( style, prefix, self.name, escaped_value, uniq_id, selected_text, self.get_disabled_str( disabled ), uniq_id, text ) )
ctr += 1
return "\n".join( rval )
@@ -318,7 +318,7 @@ class SelectField(BaseField):
selected_text = ""
if selected:
selected_text = " checked='checked'"
- rval.append( '<div%s><input type="radio" name="%s%s"%s value="%s" id="%s"%s%s><label for="%s">%s</label></div>' % \
+ rval.append( '<div%s><input type="radio" name="%s%s"%s value="%s" id="%s"%s%s><label class="inline" for="%s">%s</label></div>' % \
( style,
prefix,
self.name,
--- a/static/june_2007_style/blue/base.css
+++ b/static/june_2007_style/blue/base.css
@@ -39,6 +39,7 @@ div.form-title-row{padding:5px 10px;}
div.repeat-group-item{border-left:solid #d8b365 5px;margin-left:10px;margin-bottom:10px;}
div.form-row-error{background:#FFCCCC;}
div.form-row label{font-weight:bold;display:block;margin-bottom:.2em;}
+div.form-row label.inline{display:inline;}
div.form-row-input{float:left;}
div.form-row-input label{font-weight:normal;display:inline;}
div.form-row-error-message{width:300px;float:left;color:red;font-weight:bold;padding:3px 0 0 1em;}
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -515,14 +515,14 @@ class SelectToolParameter( ToolParameter
blah
>>> print p.get_html()
<div class="checkUncheckAllPlaceholder" checkbox_name="blah"></div>
- <div><input type="checkbox" name="blah" value="x" id="blah|x"><label for="blah|x">I am X</label></div>
- <div class="odd_row"><input type="checkbox" name="blah" value="y" id="blah|y" checked='checked'><label for="blah|y">I am Y</label></div>
- <div><input type="checkbox" name="blah" value="z" id="blah|z" checked='checked'><label for="blah|z">I am Z</label></div>
+ <div><input type="checkbox" name="blah" value="x" id="blah|x"><label class="inline" for="blah|x">I am X</label></div>
+ <div class="odd_row"><input type="checkbox" name="blah" value="y" id="blah|y" checked='checked'><label class="inline" for="blah|y">I am Y</label></div>
+ <div><input type="checkbox" name="blah" value="z" id="blah|z" checked='checked'><label class="inline" for="blah|z">I am Z</label></div>
>>> print p.get_html( value=["x","y"])
<div class="checkUncheckAllPlaceholder" checkbox_name="blah"></div>
- <div><input type="checkbox" name="blah" value="x" id="blah|x" checked='checked'><label for="blah|x">I am X</label></div>
- <div class="odd_row"><input type="checkbox" name="blah" value="y" id="blah|y" checked='checked'><label for="blah|y">I am Y</label></div>
- <div><input type="checkbox" name="blah" value="z" id="blah|z"><label for="blah|z">I am Z</label></div>
+ <div><input type="checkbox" name="blah" value="x" id="blah|x" checked='checked'><label class="inline" for="blah|x">I am X</label></div>
+ <div class="odd_row"><input type="checkbox" name="blah" value="y" id="blah|y" checked='checked'><label class="inline" for="blah|y">I am Y</label></div>
+ <div><input type="checkbox" name="blah" value="z" id="blah|z"><label class="inline" for="blah|z">I am Z</label></div>
>>> print p.to_param_dict_string( ["y", "z"] )
y,z
"""
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