transrate 1.0.0.alpha.8.bowtie → 1.0.0.beta1

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Files changed (51) hide show
  1. checksums.yaml +4 -4
  2. data/.gitignore +3 -0
  3. data/README.md +2 -0
  4. data/bin/transrate +3 -5
  5. data/deps/deps.yaml +12 -20
  6. data/lib/transrate.rb +1 -1
  7. data/lib/transrate/assembly.rb +21 -0
  8. data/lib/transrate/contig.rb +33 -3
  9. data/lib/transrate/express.rb +29 -24
  10. data/lib/transrate/read_metrics.rb +40 -28
  11. data/lib/transrate/sam_checker.rb +6 -31
  12. data/lib/transrate/samtools.rb +1 -1
  13. data/lib/transrate/score_optimiser.rb +31 -0
  14. data/lib/transrate/snap.rb +28 -3
  15. data/lib/transrate/transrater.rb +5 -10
  16. data/lib/transrate/version.rb +1 -1
  17. data/test/data/express_results.xprs +5 -0
  18. data/test/test_bin.rb +2 -8
  19. data/test/test_express.rb +22 -0
  20. data/test/test_read_metrics.rb +17 -29
  21. data/test/test_transrater.rb +1 -1
  22. data/test/vagrant/centos_6.5_64/Vagrantfile +122 -0
  23. data/test/vagrant/debian_7.4_64/Vagrantfile +126 -0
  24. data/test/vagrant/debian_7.4_64/provision.sh +28 -0
  25. data/test/vagrant/fedora_20_64/Vagrantfile +122 -0
  26. data/test/vagrant/fedora_20_64/provision.sh +16 -0
  27. data/test/vagrant/fedora_20_64/sample_data/params.xprs +182 -0
  28. data/test/vagrant/fedora_20_64/sample_data/reads_1.fastq +40000 -0
  29. data/test/vagrant/fedora_20_64/sample_data/reads_1.fastq-reads_2.fastq-read_count.txt +1 -0
  30. data/test/vagrant/fedora_20_64/sample_data/reads_2.fastq +40000 -0
  31. data/test/vagrant/fedora_20_64/sample_data/transcripts.fasta +498 -0
  32. data/test/vagrant/fedora_20_64/sample_data/transcripts.fasta_results.xprs +16 -0
  33. data/test/vagrant/fedora_20_64/sample_data/transcripts/Genome +17 -0
  34. data/test/vagrant/fedora_20_64/sample_data/transcripts/GenomeIndex +1 -0
  35. data/test/vagrant/fedora_20_64/sample_data/transcripts/GenomeIndexHash +0 -0
  36. data/test/vagrant/fedora_20_64/sample_data/transcripts/OverflowTable +0 -0
  37. data/test/vagrant/ubuntu_12.04_64/Vagrantfile +126 -0
  38. data/test/vagrant/ubuntu_12.04_64/provision.sh +24 -0
  39. data/test/vagrant/ubuntu_12.04_64/sample_data/params.xprs +182 -0
  40. data/test/vagrant/ubuntu_12.04_64/sample_data/reads_1.fastq +40000 -0
  41. data/test/vagrant/ubuntu_12.04_64/sample_data/reads_1.fastq-reads_2.fastq-read_count.txt +1 -0
  42. data/test/vagrant/ubuntu_12.04_64/sample_data/reads_2.fastq +40000 -0
  43. data/test/vagrant/ubuntu_12.04_64/sample_data/transcripts.fasta +498 -0
  44. data/test/vagrant/ubuntu_12.04_64/sample_data/transcripts.fasta_results.xprs +16 -0
  45. data/test/vagrant/ubuntu_12.04_64/sample_data/transcripts/Genome +17 -0
  46. data/test/vagrant/ubuntu_12.04_64/sample_data/transcripts/GenomeIndex +1 -0
  47. data/test/vagrant/ubuntu_12.04_64/sample_data/transcripts/GenomeIndexHash +0 -0
  48. data/test/vagrant/ubuntu_12.04_64/sample_data/transcripts/OverflowTable +0 -0
  49. data/transrate.gemspec +4 -4
  50. metadata +111 -71
  51. data/lib/transrate/bowtie.rb +0 -103
data/test/vagrant/ubuntu_12.04_64/sample_data/transcripts.fasta_results.xprs ADDED
@@ -0,0 +1,16 @@
1
+ bundle_id target_id length eff_length tot_counts uniq_counts est_counts eff_counts ambig_distr_alpha ambig_distr_beta fpkm fpkm_conf_low fpkm_conf_high solvable tpm
2
+ 1 NM_017409 1959 1781.802609 47 47 47.000000 51.674074 0.000000e+00 0.000000e+00 2.637778e+03 2.637778e+03 2.637778e+03 T 4.385178e+03
3
+ 2 NM_174914 2385 2207.751702 210 210 210.000000 226.859750 0.000000e+00 0.000000e+00 9.511939e+03 9.511939e+03 9.511939e+03 T 1.581314e+04
4
+ 3 NM_006897 1541 1363.852559 664 664 664.000000 750.245320 0.000000e+00 0.000000e+00 4.868561e+04 4.868561e+04 4.868561e+04 T 8.093746e+04
5
+ 4 NM_014620 2300 2122.761860 956 956 956.000000 1035.820382 0.000000e+00 0.000000e+00 4.503567e+04 4.503567e+04 4.503567e+04 T 7.486961e+04
6
+ 5 NM_022658 2288 2110.763294 4881 4881 4881.000000 5290.848118 0.000000e+00 0.000000e+00 2.312434e+05 2.312434e+05 2.312434e+05 T 3.844308e+05
7
+ 6 NM_014212 2037 1859.793288 55 55 55.000000 60.240566 0.000000e+00 0.000000e+00 2.957318e+03 2.957318e+03 2.957318e+03 T 4.916397e+03
8
+ 7 NM_017410 2396 2218.750388 42 42 42.000000 45.355260 0.000000e+00 0.000000e+00 1.892957e+03 1.892957e+03 1.892957e+03 T 3.146949e+03
9
+ 8 NM_173860 849 671.935252 962 962 962.000000 1215.501043 0.000000e+00 0.000000e+00 1.431686e+05 1.431686e+05 1.431686e+05 T 2.380108e+05
10
+ 9 NM_153633 1666 1488.837622 12 12 12.000000 13.427925 0.000000e+00 0.000000e+00 8.059979e+02 8.059979e+02 8.059979e+02 T 1.339932e+03
11
+ 10 NM_001168316 2283 2105.763891 1545 1545 1545.000000 1675.038220 0.000000e+00 0.000000e+00 7.337005e+04 7.337005e+04 7.337005e+04 T 1.219741e+05
12
+ 11 NM_004503 1681 1503.835829 383 383 383.000000 428.120535 0.000000e+00 0.000000e+00 2.546821e+04 2.546821e+04 2.546821e+04 T 4.233965e+04
13
+ 12 NM_153693 2072 1894.789105 6 6 6.000000 6.561152 0.000000e+00 0.000000e+00 3.166579e+02 3.166579e+02 3.166579e+02 T 5.264284e+02
14
+ 13 NR_031764 1853 1675.815276 9 9 9.000000 9.951574 0.000000e+00 0.000000e+00 5.370520e+02 5.370520e+02 5.370520e+02 T 8.928228e+02
15
+ 14 NR_003084 1640 0.000000 0 0 0.000000 0.000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 F 0.000000e+00
16
+ 15 NM_018953 1612 1434.844075 228 228 228.000000 256.150481 0.000000e+00 0.000000e+00 1.589023e+04 1.589023e+04 1.589023e+04 T 2.641673e+04
data/test/vagrant/ubuntu_12.04_64/sample_data/transcripts/Genome ADDED
@@ -0,0 +1,17 @@
1
+ 36562 15
2
+ 500 NM_001168316
3
+ 3283 NM_174914
4
+ 6168 NR_031764
5
+ 8521 NM_004503
6
+ 10702 NM_006897
7
+ 12743 NM_014212
8
+ 15280 NM_014620
9
+ 18080 NM_017409
10
+ 20539 NM_017410
11
+ 23435 NM_018953
12
+ 25547 NM_022658
13
+ 28335 NM_153633
14
+ 30501 NM_153693
15
+ 33073 NM_173860
16
+ 34422 NR_003084
17
+ nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnTTAGTGAGGTTGGGGAGAGATAACGCTGTAAACTTTTATTTTTCAGGAAATCTGGAAACCTACAGTCTCCAAGCCTGCTCAGCCAAGAAGGAGCTCACTGTGGGCACCAGAGACAGGGACCCAATGTGGAGACCTGTGAGCCTGTGTCCGGCCCTGAACTCTCAAGCACAGGGCAGGCTTCCTGAGCATTGAAGAGAATATGTGGGAGAACAAAACAGAAACTGAAAGAATATGCAAGGTGTCTTTCTTGGATGTTATTCCATGATAGATAGTAGGGGCAGGAGTGAGAGAGGCTGACTAGGTCTGGACATGGAGGCTGGAAGAGTCAGGGTGTGATTCGGAGAGGCGCATGAGAAGGAAGGTGGATTTTAAGGCTGGAAATCTGAGGGTCAGTGGTCCAAGTCACTCAGAGACAGAATCACAGCATAGCCCTTGCTGATGGCAAACAAAGGAGGACAAGAGGACTGGAAAGAATTCTGCTAGCAGGCAGGAGCTAGTAAGGATGAATTTGTAGCAAAATTAGCAAGTGGAAAGGATGATTTTTGGCCATTTTTCCTGTTCTTCAAGAAAACAGGAGATAACTAGAAGGACTAGAGAATGGGGCTGCCAGAACTAGTGGGAAGCTCCCTAGAAATGGTGACATCGCCCACCAAACAGACCCCGCCAAGGCTGCACCTGGCCTTATGTCTCCTTCACCTTTCTGGCCCCACGCAGCCACCAGACAGCCATGCCCAGCAGCTTCCCACAAAGCCATAGAGTCCCCAGAGTGAGCCCCAGCAGAAACACAAAAACGTCGAGCAGGTACTGCTCATGCCAGGGCTGCTGAAAGACATAGGGCTTGAGGTGCGTCGCGCCCCCTGTCTGGAGGACGTGGTCAATCCAGCCCACCAGCCGCTGTGTGGGGCTGAGCGGGTGGGAGCGCAGGATGACACTGGCAGCCACTGCCGCGGACTTGTATCTCTTGTCTTCCATGATTTGTTTCATCTTAAGAGCCAATGTCTCTGCCTTGAGCTTCTTTAACTGAATAGAAACACCAAACTTTTTGGCTTCTACTCGGACCATGTTTTCAGGCTGGTCTCCAAAGAGAGGGATCCCCACCATGGGCACACCATGCTGGATGGCCTCCATTATGCTATTCTGCCCGCCGTGGGTGACAAACAGACGGATGCTTGGGTGAGCCAGGAGGTCACTCTGAGGAAGCCAGTCCACAATTTTCACATTTGCAGCCAGGTGGACATCTTTGGGCCAATGAGAACACTGACACTTCCATATCACCCCTTGGGGTAGGTGAGCAAAGGCATTGTTCATCTCCTTGAAGATTTCCGGATTCTGACAGGTGTTCACCATGGAGCCCAAGGTCACAAGGACAAAACCAGAGTCCCCAAACTTGGCAATGAAGTTCTCCAAGTCTTGTGGTACTGGTTTAATAGGTTTTTCCATCAAGCCTCCAACATAAACAGTGTTGGGAAGCAGAGGTCGAGCAAAATCAAAGGCAAAGTCAGAGTTAATGAACCACAACTCTGCTTTCAGTAGAAGATGAGACAAAACTGGCCTAGAGCCTTCTGTGAAATGTTCCTTGATGGTGTTGTCAAATGTAGACTGCATGTGCTGTTGCCTCCTGCAGAAACTAAAGAACATCAGAAAATTCTTCACTCGGCCCCAGAAGTCCATGTGATCAGTCAGCAAGGAACGGAATACTGGAACATAAGACAAGGGGATTGGTAGCCCAAATTCCAAAGAGCCGAATGAAGTGGAAAGAATGGCCACAAATGGCTTCCCAAGCTTCTCAGCAATCAGGAAAGGACAGTAGTCAAAAGTTTCAACTATCACCATGTCGAAGTTCTCATTCTTTAAGGAATCCATGATATCCTTTCTATTTAAAAAATGACTGCACTGCAACGCCAAGTATTCTAGAACATTTAATAAGTTTTCAAATTTTCCTCTGCCACCTAAAGTTTCTTCCAGAAAGAAATCAAAACTCTTTTTAAATTCTCTTTGATGATCTTCAGGTGCAAGCCAACTGATAACTTGATATGATTTTTCTTCCTTTTTAAAATCTACTGTAGATATTGTCAGGATTTTGGCAGCCTCTGAGAGCAGGACCCCAGGGAGAAGGAAGCCCACTAGAAGAAGCACTCGCTGCCCAGCCATGCTCACTTCTACGGAAGCCGCGGATCTCAGCCTGGGCTGCGCGCCCTGCGCCCGGCTAAGGGACCCTGTGCACCTCAGTGCGCCAAAGGCACTGGCTGTGGGTAGAGGTAGGAGTAAGGATCCTGCCAGTCTnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnTTAGTGAGGTTGGGGAGAGATAACGCTGTAAACTTTTATTTTTCAGGAAATCTGGAAACCTACAGTCTCCAAGCCTGCTCAGCCAAGAAGGAGCTCACTGTGGGCACCAGAGACAGGGACCCAATGTGGAGACCTGTGAGCCTGTGTCCGGCCCTGAACTCTCAAGCACAGGGCAGGCTTCCTGAGCATTGAAGAGAATATGTGGGAGAACAAAACAGAAACTGAAAGAATATGCAAGGTGTCTTTCTTGGATGTTATTCCATGATAGATAGTAGGGGCAGGAGTGAGAGAGGCTGACTAGGTCTGGACATGGAGGCTGGAAGAGTCAGGGTGTGATTCGGAGAGGCGCATGAGAAGGAAGGTGGATTTTAAGGCTGGAAATCTGAGGGTCAGTGGTCCAAGTCACTCAGAGACAGAATCACAGCATAGCCCTTGCTGATGGCAAACAAAGGAGGACAAGAGGACTGGAAAGAATTCTGCTAGCAGGCAGGAGCTAGTAAGGATGAATTTGTAGCAAAATTAGCAAGTGGAAAGGATGATTTTTGGCCATTTTTCCTGTTCTTCAAGAAAACAGGAGATAACTAGAAGGACTAGAGAATGGGGCTGCCAGAACTAGTGGGAAGCTCCCTAGAAATGGTGACATCGCCCACCAAACAGACCCCGCCAAGGCTGCACCTGGCCTTATGTCTCCTTCACCTTTCTGGCCCCACGCAGCCACCAGACAGCCATGCCCAGCAGCTTCCCACAAAGCCATAGAGTCCCCAGAGTGAGCCCCAGCAGAAACACAAAAACGTCGAGCAGGTACTGCTCATGCCAGGGCTGCTGAAAGACATAGGGCTTGAGGTGCGTCGCGCCCCCTGTCTGGAGGACGTGGTCAATCCAGCCCACCAGCCGCTGTGTGGGGCTGAGCGGGTGGGAGCGCAGGATGACACTGGCAGCCACTGCCGCGGACTTGTATCTCTTGTCTTCCATGATTTGTTTCATCTTAAGAGCCAATGTCTCTGCCTTGAGCTTCTTTAACTGAATAGAAACACCAAACTTTTTGGCTTCTACTCGGACCATGTTTTCAGGCTGGTCTCCAAAGAGAGGGATCCCCACCATGGGCACACCATGCTGGATGGCCTCCATTATGCTATTCTGCCCGCCGTGGGTGACAAACAGACGGATGCTTGGGTGAGCCAGGAGGTCACTCTGAGGAAGCCAGTCCACAATTTTCACATTTGCAGCCAGGTGGACATCTTTGGGCCAATGAGAACACTGACACTTCCATATCACCCCTTGGGGTAGGTGAGCAAAGGCATTGTTCATCTCCTTGAAGATTTCCGGATTCTGACAGGTGTTCACCATGGAGCCCAAGGTCACAAGGACAAAACCAGAGTCCCCAAACTTGGCAATGAAGTTCTCCAAGTCTTGTGGTACTGGTTTAATAGGTTTTTCCATCAAGCCTCCAACATAAACAGTGTTGGGAAGCAGAGGTCGAGCAAAATCAAAGGCAAAGTCAGAGTTAATGAACCACAACTCTGCTTTCAGTAGAAGATGAGACAAAACTGGCCTAGAGCCTTCTGTGAAATGTTCCTTGATGGTGTTGTCAAATGTAGACTGCATGTGCTGTTGCCTCCTGCAGAAACTAAAGAACATCAGAAAATTCTTCACTCGGCCCCAGAAGTCCATGTGATCAGTCAGCAAGGAACGGAATACTGGAACATAAGACAAGGGGATTGGTAGCCCAAATTCCAAAGAGCCGAATGAAGTGGAAAGAATGGCCACAAATGGCTTCCCAAGCTTCTCAGCAATCAGGAAAGGACAGTAGTCAAAAGTTTCAACTATCACCATGTCGAAGTTCTCATTCTTTAAGGAATCCATGATATCCTTTCTATTTAAAAAATGACTGCACTGCAACGCCAAGTATTCTAGAACATTTAATAAGTTTTCAAATTTTCCTCTGCCACCTAAAGTTTCTTCCAGAAAGAAATCAAAACTCTTTTTAAATTCTCTTTGATGATCTTCAGGTGCAAGCCAACTGATAACTTGATATGATTTTTCTTCCTTTTTAAAATCTGGCATAAAAGGACCTCTTTTGTGGTTAAGCATGGTGACATTATGACCGTGATCTTGAAGAATCTGAGAAACCCGGTCCATCAGTAGATAATGGCTTCCACCTACTGTAGATATTGTCAGGATTTTGGCAGCCTCTGAGAGCAGGACCCCAGGGAGAAGGAAGCCCACTAGAAGAAGCACTCGCTGCCCAGCCATGCTCACTTCTACGGAAGCCGCGGATCTCAGCCTGGGCTGCGCGCCCTGCGCCCGGCTAAGGGACCCTGTGCACCTCAGTGCGCCAAAGGCACTGGCTGTGGGTAGAGGTAGGAGTAAGGATCCTGCCAGTCTnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnTTAGTGAGGTTGGGGAGAGATAACGCTGTAAACTTTTATTTTTCAGGAAATCTGGAAACCTACAGTCTCCAAGCCTGCTCAGCCAAGAAGGAGCTCACTGTGGGCACCAGAGACAGGGACCCAATGTGGAGACCTGTGAGCCTGTGTCCGGCCCTGAACTCTCAAGCACAGGGCAGGCTTCCTGAGCATTGAAGAGAATATGTGGGAGAACAAAACAGAAACTGAAAGAATATGCAAGGTGTCTTTCTTGGATGTTATTCCATGATAGATAGTAGGGGCAGGAGTGAGAGAGGCTGACTAGGTCTGGACATGGAGGCTGGAAGAGTCAGGGTGTGATTCGGAGAGGCGCATGAGAAGGAAGGTGGATTTTAAGGCTGGAAATCTGAGGGTCAGTGGTCCAAGTCACTCAGAGACAGAATCACAGCATAGCCCTTGCTGATGGCAAACAAAGGAGGACAAGAGGACTGGAAAGAATTCTGCTAGCAGGCAGGAGCTAGTAAGGATGAATTTGTAGCAAAATTAGCAAGTGGAAAGGATGATTTTTGGCCATTTTTCCTGTTCTTCAAGAAAACAGGAGATAACTAGAAGGACTAGAGAATGGGGCTGCCAGAACTAGTGGGAAGCTCCCTAGAAATGGTGACATCGCCCACCAAACAGACCCCGCCAAGGCTGCACCTGGCCTTATGTCTCCTTCACCTTTCTGGCCCCACGCAGCCACCAGACAGCCATGCCCAGCAGCTTCCCACAAAGCCATAGAGTCCCCAGAGTGAGCCCCAGCAGAAACACAAAAACGTCGAGCAGGTACTGCTCATGCCAGGGCTGCTGAAAGACATAGGGCTTGAGGTGCGTCGCGCCCCCTGTCTGGAGGACGTGGTCAATCCAGCCCACCAGCCGCTGTGTGGGGCTGAGCGGGTGGGAGCGCAGGATGACACTGGCAGCCACTGCCGCGGACTTGTATCTCTTGTCTTCCATGATTTGTTTCATCTTAAGAGCCAATGTCTCTGCCTTGAGCTTCTTTAACTGAATAGAAACACCAAACTTTTTGGCTTCTACTCGGACCATGTTTTCAGGCTGGTCTCCAAAGAGAGGGATCCCCACCATGGGCACACCATGCTGGATGGCCTCCATTATGCTATTCTGCCCGCCGTGGGTGACAAACAGACGGATGCTTGGGTGAGCCAGGAGGTCACTCTGAGGAAGCCAGTCCACAATTTTCACATTTGCAGCCAGGTGGACATCTTTGGGCCAATGAGAACACTGACACTTCCATATCACCCCTTGGGGTAGGTGAGCAAAGGCATTGTTCATCTCCTTGAAGATTTCCGGATTCTGACAGGTGTTCACCATGGAGCCCAAGGTCACAAGGACAAAACCAGAGTCCCCAAACTTGGCAATGAAGTTCTCCAAGTCCTGCCACCTAAAGTTTCTTCCAGAAAGAAATCAAAACTCTTTTTAAATTCTCTTTGATGATCTTCAGGTGCAAGCCAACTGATAACTTGATATGATTTTTCTTCCTTTTTAAAATCTGGCATAAAAGGACCTCTTTTGTGGTTAAGCATGGTGACATTATGACCGTGATCTTGAAGAATCTGAGAAACCCGGTCCATCAGTAGATAATGGCTTCCACCTACTGTAGATATTGTCAGGATTTTGGCAGCCTCTGAGAGCAGGACCCCAGGGAGAAGGAAGCCCACTAGAAGAAGCACTCGCTGCCCAGCCATGCTCACTTCTACGGAAGCCGCGGATCTCAGCCTGGGCTGCGCGCCCTGCGCCCGGCTAAGGGACCCTGTGCACCTCAGTGCGCCAAAGGCACTGGCTGTGGGTAGAGGTAGGAGTAAGGATCCTGCCAGTCTnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnTTTTGTCTGTCCTGGATTGGAGCCGTCCCTATAACCATCTAGTTCCGAGTACAAACTGGAGACAGAAATAAATATTAAAGAAATCATAGACCGACCAGGTAAAGGCAAAGGGATGAATTCCTACTTCACTAACCCTTCCTTATCCTGCCACCTCGCCGGGGGCCAGGACGTCCTCCCCAACGTCGCCCTCAATTCCACCGCCTATGATCCAGTGAGGCATTTCTCGACCTATGGAGCGGCCGTTGCCCAGAACCGGATCTACTCGACTCCCTTTTATTCGCCACAGGAGAATGTCGTGTTCAGTTCCAGCCGGGGGCCGTATGACTATGGATCTAATTCCTTTTACCAGGAGAAAGACATGCTCTCAAACTGCAGACAAAACACCTTAGGACATAACACACAGACCTCAATCGCTCAGGATTTTAGTTCTGAGCAGGGCAGGACTGCGCCCCAGGACCAGAAAGCCAGTATCCAGATTTACCCCTGGATGCAGCGAATGAATTCGCACAGTGGGGTCGGCTACGGAGCGGACCGGAGGCGCGGCCGCCAGATCTACTCGCGGTACCAGACCCTGGAACTGGAGAAGGAATTTCACTTCAATCGCTACCTAACGCGGCGCCGGCGCATCGAGATCGCCAACGCGCTTTGCCTGACCGAGCGACAGATCAAAATCTGGTTCCAGAACCGCCGGATGAAGTGGAAAAAAGAATCTAATCTCACATCCACTCTCTCGGGGGGCGGCGGAGGGGCCACCGCCGACAGCCTGGGCGGAAAAGAGGAAAAGCGGGAAGAGACAGAAGAGGAGAAGCAGAAAGAGTGACCAGGACTGTCCCTGCCACCCCTCTCTCCCTTTCTCCCTCGCTCCCCACCAACTCTCCCCTAATCACACACTCTGTATTTATCACTGGCACAATTGATGTGTTTTGATTCCCTAAAACAAAATTAGGGAGTCAAACGTGGACCTGAAAGTCAGCTCTGGACCCCCTCCCTCACCGCACAACTCTCTTTCACCACGCGCCTCCTCCTCCTCGCTCCCTTGCTAGCTCGTTCTCGGCTTGTCTACAGGCCCTTTTCCCCGTCCAGGCCTTGGGGGCTCGGACCCTGAACTCAGACTCTACAGATTGCCCTCCAAGTGAGGACTTGGCTCCCCCACTCCTTCGACGCCCCCACCCCCGCCCCCCGTGCAGAGAGCCGGCTCCTGGGCCTGCTGGGGCCTCTGCTCCAGGGCCTCAGGGCCCGGCCTGGCAGCCGGGGAGGGCCGGAGGCCCAAGGAGGGCGCGCCTTGGCCCCACACCAACCCCCAGGGCCTCCCCGCAGTCCCTGCCTAGCCCCTCTGCCCCAGCAAATGCCCAGCCCAGGCAAATTGTATTTAAAGAATCCTGGGGGTCATTATGGCATTTTACAAACTGTGACCGTTTCTGTGTGAAGATTTTTAGCTGTATTTGTGGTCTCTGTATTTATATTTATGTTTAGCACCGTCAGTGTTCCTATCCAATTTCAAAAAAGGAAAAAAAAGAGGGAAAATTACAAAAAGAGAGAAAAAAAGTGAATGACGTTTGTTTAGCCAGTAGGAGAAAATAAATAAATAAATAAATCCCTTCGTGTTACCCTCCTGTATAAATCCAACCTCTGGGTCCGTTCTCGAATATTTAATAAAACTGATATTATTTTTAAAACTTTAnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnTGGAAAAATAATTACCTGACTTGATTGTTCTGTGAGCAGATAAAAAGTACATATACAGTTCATACAATAATCTTATGTATGTAAAACCCCGTTACGATGTCGGCGACGGGGCCCATCAGTAACTATTACGTGGACTCGCTCATCTCTCACGACAATGAAGACCTCCTAGCGTCCAGGTTTCCGGCCACCGGGGCTCATCCCGCCGCCGCCAGACCCAGCGGTTTGGTGCCGGACTGTAGCGATTTTCCGTCCTGTAGCTTCGCGCCCAAGCCGGCAGTGTTCAGCACGTCGTGGGCGCCCGTGCCCTCTCAGTCGTCCGTGGTATATCACCCGTACGGCCCCCAGCCCCACCTCGGCGCCGACACGCGCTACATGCGGACTTGGCTCGAGCCGCTGTCCGGCGCCGTCTCCTTCCCCAGCTTCCCGGCCGGGGGCCGTCACTACGCCCTCAAGCCGGACGCCTACCCCGGGCGCCGCGCGGACTGCGGCCCAGGGGAGGGCCGCAGCTACCCGGACTACATGTACGGCTCGCCCGGGGAGCTGCGCGACCGCGCCCCGCAGACACTGCCCTCGCCCGAGGCGGACGCGCTCGCCGGCAGCAAGCACAAAGAGGAGAAGGCCGACCTGGACCCCAGCAACCCCGTGGCCAACTGGATTCACGCCCGCTCCACGAGGAAGAAGCGCTGCCCCTACACCAAGTACCAGACGCTGGAACTGGAGAAGGAGTTTCTCTTCAATATGTATTTAACCAGGGACCGTCGGTATGAGGTGGCCCGGGTTCTCAATCTCACCGAGCGGCAGGTCAAAATCTGGTTTCAGAATCGAAGGATGAAGATGAAAAAGATGAATAAAGAGAAAACCGACAAGGAGCAGTCCTAAACCCTACCCAGCCTGCTGCCTCAGCACAGCCAAGGGAAAAACAAAAACCCCACAAAATACCCCAACACAGGCGGGGGAGAGACGAAAAAGAAAAGGAAAGAGCAAGATAGACAAAAGCCAATCAGCTTAAAAAGAAAAACAAGGAAGGGGAAAAGAAAACTCTTGCGATTTGGGAGGGTTCAGTGTTGAGATATTGGTGTTTTAGAGTTAGTTCTACCCAGCGAGGAGGAGGCGGGGAGAGAAACTGCGTTCTCTTTCCCCAGCGCAACCGAAATAAATGACACATACAAATGTGATTTTTTTCCTCCTTTCTTCAGAGAAGCCAGTACTTGAATCGCTATATTTCTATTTTTTTTTCCCTGTATCGTATTTGGTCCAGGTCATCCCTCCCCGGGCCTGGGGCGCTCTGCGTGCAGATTTTGTACAAAAAAAAAAAAGACACACACACATACATGATAATGATTCCCAGCCCAGGAGCTGAGGGGTGAGGGCTGGGGACCATGCCGCGGGCTAGGTCGGGCCCGTGCAGGCCGGCGCCTTGGGCTGTACATAGTGTTCCCTCTCATCCCCAGGGTTCGTCCCCAGCGTCCGTCCTGTAACGTGCTTCTGTTTGTTATGGTAGAACAGCCCTGTGTTAATATATTGAAGTCACTTAACCAGAAnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnGTGCTCAGAGAGAGAGAGACTAAGACGGATAACGCGTCATCTCGCCTTCCCAAATTTTCCCCCCTCGCTAGACCGGGTCCAAAACCTCCATCCGGAGCCGGCAGGAGAGGAGAACGATGTTTAACTCGGTCAACCTGGGCAACTTCTGCTCTCCGTCGCGCAAGGAGAGGGGCGCAGATTTCGGCGAGCGAGGGAGCTGCGCCTCCAACCTCTATCTGCCCAGTTGCACTTACTACATGCCCGAGTTCTCCACGGTCTCCTCCTTCCTGCCCCAGGCCCCCTCTCGTCAGATCTCCTATCCCTACTCGGCCCAAGTGCCCCCGGTCCGGGAGGTCTCCTACGGCCTGGAGCCATCCGGCAAGTGGCACCATCGGAACAGCTACTCCTCCTGCTATGCGGCGGCCGACGAGCTTATGCACCGGGAGTGCCTGCCTCCTTCCACCGTCACCGAGATCCTCATGAAAAACGAAGGCTCCTACGGCGGCCACCACCACCCCAGCGCCCCGCACGCAACCCCCGCCGGCTTCTACTCCTCAGTCAACAAGAACAGCGTCCTGCCTCAAGCCTTCGACCGTTTCTTCGACAACGCCTACTGCGGTGGCGGCGACCCGCCCGCCGAGCCCCCCTGCTCCGGCAAGGGCGAGGCCAAGGGGGAGCCCGAGGCACCCCCGGCCTCGGGACTGGCGTCCCGGGCTGAGGCGGGTGCCGAGGCGGAGGCTGAGGAGGAGAACACAAATCCCAGCTCGTCCGGTTCAGCCCACTCCGTGGCCAAGGAGCCGGCCAAAGGAGCCGCCCCCAACGCCCCCCGCACCCGCAAGAAGCGCTGCCCTTATTCGAAATTCCAGATCCGGGAACTGGAGCGAGAGTTTTTCTTCAACGTGTATATCAACAAAGAGAAGCGGCTGCAGCTGTCCCGGATGCTGAACCTGACGGACCGACAAGTGAAAATTTGGTTTCAGAACAGAAGGATGAAAGAAAAGAAACTGAGCAGAGACCGGCTGCAGTATTTCTCGGGAAATCCTCTGCTGTAACCTGCAGACCGGGCCCTTTTGGGGGCGGGGGGAGGGGAAAATTATTTTATTTTATTTTTATTTTTTATTTTCTAACTCGTCTTCTTTCCGCCGGTGGAAAACTGGACTGTGGCCAGGGCTGGCCCCCACCGCTGTGGCCGGCACTCCATTCCGGAACCTCCTGGACCCTCTATCTGACTCTCGCTGTGGGACAGGGACCGGGCCTGGAAAGGGGGTGAAGGGAAGTGTCTGATGCACGGCGAGTGAACACCGTTGGCGCCGAGGCCAAGACTTTGATTTAAAAGAAAACACACCTCGGCGACAATGTCTTGCTGCTCGGATTAGGTGGGGGAGGGGCGACAGTAGTGAGCGCCTGAGCCGAACAATCCTCGAACTAAAAGCCTTCCCTTGCCCATGTGAAAAGATCCGCTAAGACAGCATGTCTGCCAGCGGAAACTTCTCGAGCTCCCCCCTCTACCCCGCCCCACCTTGCAGCTAAATGTGATCCTGCCTTGCTGTGAAATTTCTGTACCTTCAACCTGGTGTTAGGTGTGCAAAGTCCGTGTCCTACCTCCGTCTTCGCCAAGGCCCCGCCCGAGCCTAGTTGTTCTCCCCCTGAATGTGTAGAACCTTCCTTTGAAATTTCTTAATCGGTGCATTGAGGTTTCCACATCTTTTTCCAAGCAGTGCCCCACTTCATGGATTTATAGCTATAGTCTATGCAGTCGTTACCTCTTTTTTTTTTTTTTTTAAGAAAATTGAAGATTGGGGTGGTGGAGGCAGTAGGGAGATGGGATTGGGCACCTCCCCCGTGCTGGGGCCTGGATTTTTGTAAATAAATTTCCCAAGCGTTTCTTTCCACCTGGAGGGAAAGGGGGGGACGCCCCCAGTGAGATTCAAATCACGCATCTCTACTCCTCTGCGTGAGTGCGTGTGTACATGTGCACTCCCCACCCTGCTCCCTTCCCAGAGGGATTGCTGTGAAATTTTTTTGGTGGCAAATAAAGATAAATTTCATTCTGTTCAAnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnTTATTGTGGTTTGTCCGTTCCGAGCGCTCCGCAGAACAGTCCTCCCTGTAAGAGCCTAACCATTGCCAGGGAAACCTGCCCTGGGCGCTCCCTTCATTAGCAGTATTTTTTTTAAATTAATCTGATTAATAATTATTTTTCCCCCATTTAATTTTTTTTCCTCCCAGGTGGAGTTGCCGAAGCTGGGGGCAGCTGGGGAGGGTGGGGATGGGAGGGGAGAGACAGAAGTTGAGGGCATCTCTCTCTTCCTTCCCGACCCTCTGGCCCCCAAGGGGCAGGAGGAATGCAGGAGCAGGAGTTGAGCTTGGGAGCTGCAGATGCCTCCGCCCCTCCTCTCTCCCAGGCTCTTCCTCCTGCCCCCTTCTTGCAACTCTCCTTAATTTTGTTTGGCTTTTGGATGATTATAATTATTTTTATTTTTGAATTTATATAAAGTATATGTGTGTGTGTGTGGAGCTGAGACAGGCTCGGCAGCGGCACAGAATGAGGGAAGACGAGAAAGAGAGTGGGAGAGAGAGAGGCAGAGAGGGAGAGAGGGAGAGTGACAGCAGCGCTCGCGGGGGCTCAACCCCCAGACCTCCAGAAATGACGTCAGAATCATTTGCATCCCGCTGCCTCTACCTGCCTGGTCCAGCTGGGACCCTGCCTCGCCGGCCGCATGGCCAGAGGGTTGGAAATTAATGATCATGAGCTCGTATTTGATGGACTCTAACTACATCGATCCGAAATTTCCTCCATGCGAAGAATATTCGCAAAATAGCTACATCCCTGAACACAGTCCGGAATATTACGGCCGGACCAGGGAATCGGGATTCCAGCATCACCACCAGGAGCTGTACCCACCACCGCCTCCGCGCCCTAGCTACCCTGAGCGCCAGTATAGCTGCACCAGTCTCCAGGGGCCCGGCAATTCGCGAGGCCACGGGCCGGCCCAGGCGGGCCACCACCACCCCGAGAAATCACAGTCGCTCTGCGAGCCGGCGCCTCTCTCAGGCGCCTCCGCCTCCCCGTCCCCAGCCCCGCCAGCCTGCAGCCAGCCAGCCCCCGACCATCCCTCCAGCGCCGCCAGCAAGCAACCCATAGTCTACCCATGGATGAAAAAAATTCACGTTAGCACGGTGAACCCCAATTATAACGGAGGGGAACCCAAGCGCTCGAGGACAGCCTATACCCGGCAGCAAGTCCTGGAATTAGAGAAAGAGTTTCATTACAACCGCTACCTGACCCGAAGGAGAAGGATCGAGATCGCCCACTCGCTGTGCCTCTCTGAGAGGCAGATCAAAATCTGGTTCCAAAACCGTCGCATGAAATGGAAGAAGGACCACCGACTCCCCAACACCAAAGTCAGGTCAGCACCCCCGGCCGGCGCTGCGCCCAGCACCCTTTCGGCAGCTACCCCGGGTACTTCTGAAGACCACTCCCAGAGCGCCACGCCGCCGGAGCAGCAACGGGCAGAGGACATTACCAGGTTATAAAACATAACTCACACCCCTGCCCCCACCCCATGCCCCCACCCTCCCCTCACACACAAATTGACTCTTATTTATAGAATTTAATATATATATATATATATATATATATAGGTTCTTTTCTCTCTTCCTCTCACCTTGTCCCTTGTCAGTTCCAAACAGACAAAACAGATAAACAAACAAGCCCCCTGCCCTCCTCTCCCTCCCACTGTTAAGGACCCTTTTAAGCATGTGATGTTGTCTTAGCATGGTACCTGCTGGGTGTTTTTTTTTAAAAGGCCATTTTGGGGGGTTATTTATTTTTTAAGAAAAAAAGCTGCAAAAATTATATATTGCAAGGTGTGATGGTCTGGCTTGGGTGAATTTCAGGGGAAATGAGGAAAAGAAAAAAGGAAAGAAATTTTAAAGCCAATTCTCATCCTTCTCCTCCTCCTCCTTCCCCCCCTCTTTCCTTAGGCCTTTTGCATTGAAAATGCACCAGGGGAGGTTAGTGAGGGGGAAGTCATTTTAAGGAGAACAAAGCTATGAAGTTCTTTTGTATTATTGTTGGGGGGGGGTGTGGGAGGAGAGGGGGCGAAGACAGCAGACAAAGCTAAATGCATCTGGAGAGCCTCTCAGAGCTGTTCAGTTTGAGGAGCCAAAAGAAAATCAAAATGAACTTTCAGTTCAGAGAGGCAGTCTATAGGTAGAATCTCTCCCCACCCCTATCGTGGTTATTGTGTTTTTGGACTGAATTTACTTGATTATTGTAAAACTTGCAATAAAGAATTTTAGTGTCGATGTGAAATGCCCCGTGATCAATAATAAACCAGTGGATGTGAATTAGTTTTAnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnCCTCCCCTCCAACCGCGCCCCCCCTCCCGGATGGGGAAAAAAAAAGATGTCAGCTCCTCCGCTGTAGTATTGCTCCTTAAAAACCCCTCTCTCTGAAAATGACATGCCCTCGCAATGTAACTCCGAACTCGTACGCGGAGCCCTTGGCTGCGCCCGGCGGAGGAGAGCGCTATAGCCGGAGCGCAGGCATGTATATGCAGTCTGGGAGTGACTTCAATTGCGGGGTGATGAGGGGCTGCGGGCTCGCGCCCTCGCTCTCCAAGAGGGACGAGGGCAGCAGCCCCAGCCTCGCCCTCAACACCTATCCGTCCTACCTCTCGCAGCTGGACTCCTGGGGCGACCCCAAAGCCGCCTATCGCCTGGAACAACCTGTTGGCAGGCCGCTGTCCTCCTGCTCCTACCCACCTAGTGTCAAGGAGGAGAATGTCTGCTGCATGTACAGCGCAGAGAAGCGGGCGAAAAGTGGCCCCGAGGCAGCTCTCTACTCCCACCCCTTGCCGGAGTCCTGCCTTGGGGAGCACGAGGTACCCGTGCCCAGCTACTACCGCGCCAGCCCGAGCTACTCCGCGCTGGACAAGACGCCCCACTGTTCTGGGGCCAACGACTTCGAAGCCCCTTTCGAGCAGCGGGCCAGTCTCAACCCGCGCGCCGAACATCTGGAATCGCCTCAGCTGGGGGGCAAAGTGAGTTTCCCTGAGACCCCCAAGTCCGACAGCCAGACCCCCAGCCCCAATGAAATCAAGACGGAGCAGAGCCTGGCGGGCCCTAAAGGGAGCCCCTCGGAGAGCGAAAAGGAGAGGGCCAAAGCTGCCGACTCCAGCCCAGACACCTCGGATAACGAAGCGAAAGAGGAGATAAAGGCAGAAAACACCACAGGAAATTGGCTGACAGCAAAGAGCGGAAGGAAGAAGAGGTGCCCCTATACTAAACACCAGACGCTGGAATTGGAGAAAGAATTTCTGTTCAATATGTATTTGACGCGAGAGCGCCGCCTGGAGATTAGCAAGACCATTAACCTTACAGACAGACAAGTCAAAATCTGGTTTCAAAATCGCAGAATGAAACTCAAGAAAATGAACCGAGAGAATCGGATCCGGGAACTGACCTCCAATTTTAATTTCACCTGAGAGCGCGGCCTCTCCTCCTCCCTTCCCGCTCCTTCCTCTCCCCGCCCCTCCTCCCTTTGTGCCTGGTGATATATTTTTTTTTCCTCCCTGAGTATAAATGCAATGCGACTGCAAAAAAGGCAAAGACCTCAGACTCTCCTTCCAAGGGACCTGTGGTTCGTGCTGCGAAGATGCTTCCACTTAAAGCATGAGAAATGGGGTGCCGGGATGTGGGGTGTGGTGTGTGCCCTCATAGATGGGGGTGGGAGTGTGGCTGGTGTGTGTGTCAAGCCCTCACTCACCCACGCACTCACACACAGCATTCTGTTCTCCATGCAAAGTTAAGATCGAATCCATCCGCTTGTAGGGGAAAAAAAGGAAAAAAATTAACCAGAGAGGGTCTGTAATCTCGCAGAGCACAGGCAGAATCGTTCCTTCCTTGCTGCATTTCCTCCTTAGACTAATAGACGTTTTGGAAAGTTCGGCTAGTGTTCGTGTGTTTGTCGTAGCACCCAGAGCCTCCACCAAACCCTCTCCATGTCTTTACCTCCCAGTCGCTCTAAGAATCTGCTTGAAGTCTCGTATTTGTACTGCTTTCTGCTTTTCTCCCACCCCTCCTAGCACCCCCACATCCCCCATCTAGTAACATCTCAGAAATTTCATCCAGAGGAACAAAAAAATTAAAAATAGAACATAGCAAAGCAAAGACAGAATGCCCCCCCCCCCAAATATTGTCCTGTCCCTGTCTGGGAGTTGTGTTATTTAAAGATATTCTGTATGTTGTATCTTTTGCATGTAGCTTCCTTAATGGAGAAAAAAAAACCTAATAAATTTCCAGAATCATAATCCTCAAnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnAGGGGTGGAGAGAAAAGAGGGGAGGGATGGGGGGAGGGGAAACAGGAGCGAGGTGTCTCCCTAGCTCGCTGCCTCTGGCAAGTGGAGTTTTTAAAAAGCTCCAGCAGATCATGTCATGACGACTTCGCTGCTCCTGCATCCACGCTGGCCGGAGAGCCTTATGTACGTCTATGAGGACAGCGCGGCGGAGAGCGGCATCGGCGGCGGCGGCGGAGGAGGAGGCGGCGGCACGGGCGGAGCGGGGGGTGGCTGCAGCGGAGCGAGCCCCGGCAAAGCCCCGAGCATGGATGGTCTGGGCAGCAGCTGCCCGGCCAGCCACTGCCGCGACCTGCTTCCGCACCCCGTGCTGGGCCGCCCGCCGGCTCCCCTGGGCGCCCCTCAGGGCGCCGTCTATACGGACATCCCGGCCCCGGAGGCGGCGCGCCAGTGTGCCCCGCCGCCCGCACCCCCCACCTCGTCCAGCGCCACCCTGGGCTACGGCTACCCCTTCGGGGGCAGCTACTACGGCTGCCGCCTGTCGCACAACGTGAACCTGCAGCAGAAGCCTTGCGCCTACCACCCGGGCGATAAATACCCGGAGCCGTCGGGCGCCCTGCCCGGTGACGACCTGTCCTCTAGGGCCAAGGAGTTCGCCTTCTACCCCAGCTTCGCCAGCTCCTACCAGGCGATGCCCGGCTACCTGGACGTGTCGGTGGTGCCCGGGATCAGCGGGCACCCGGAGCCGCGTCACGACGCCCTCATCCCCGTCGAAGGCTACCAGCACTGGGCTCTCTCCAATGGCTGGGACAGTCAGGTGTACTGCTCCAAGGAGCAGTCGCAGTCCGCCCACCTCTGGAAGTCTCCCTTCCCAGACGTGGTTCCCCTGCAGCCCGAGGTGAGCAGCTACCGGCGCGGGCGCAAGAAACGCGTGCCCTACACTAAGGTGCAGCTGAAGGAGCTAGAGAAGGAATACGCGGCTAGCAAGTTCATCACCAAAGAGAAGCGCCGGCGCATCTCCGCCACCACGAACCTCTCTGAGCGCCAGGTAACCATCTGGTTCCAGAACCGGCGGGTCAAAGAGAAGAAGGTGGTCAGCAAATCGAAAGCGCCTCATCTCCACTCCACCTGACCACCCACCCGCTGCTTGCCCCATCTATTTATGTCTCCGCTTTGTACCATAACCGAACCCACGGAAAGACGCTGCGCGGGTGCAGAAGAGTATTTAATGTTAAGGAAAGAGAAGAACCGCGCCGCCCGGAGGCAGAGAGGCTCCATGGCCGTGCTGCTGGGCCATCCCCAACTCCCTATCCCATCCCCAGCCTCCACCCCCATCCAGATGGGACTCACGTGGCTTCAACAGCTTTGGAAATGGGTCCCGAGTGGGCCGTGCGAGGAAGGCTGTCGACCTCTACTCCTCCTTGCGCTCACCTTGCCAGAAAGTCTGGTGGCAGCGCAGAGCCCAATCATTCCAACCAAAGCAGGGTTGGGGAATCCCGAATGGCCCCAATTCTTGCCTCATCCTATGACCAGGCTTTTAGAGGACCTTCCCTAAGGGCGCAGCTTCGGAGCAGGATCTGTCCAGCTCATACTTTCCTTCGCTGTCCCTCCCGCACTCCTTAGGCAAGATTTCCCAGTAAAGATTTTCTGTGCGTATTTTAAAAGTCGTGTTAATACTCATGATAATTATTAGGGACCTGGCAGCGTGATTGGAGTATGGATGTTTCCGTAAAAGCTGGAATTCCGTAAAAGCATTGACGCAGCCCCTACACTCCATCCCAACCAAGAAACTGCATTTCCTGGGGCCAGGTGGGAGCTGCCTTTGCCCCACTGCCTCCCCTGTTCTGCTCTCTCAGTCAACATGTGGAAATCCAAGGAGGACAAAGACTCCAGCCACGCTGCTAAATAGGGCTCCTCTCTCCTCTCTCTCTCTCTAGGTGGTAAGGTTGGGGATTAGTCCAGGTACAGAAGCAGAACTTTTTTCTAAGGATAAACATCTCTTCCAAGGGGATGGAGAGTGGGTCCCTCAACAAAGTCCCTGTCCAGTCACCTTTCCATCAGGGCACTAGCCCAGGAATGACTCCTCACACTTTCACCTTTACTGATTTCCAGAGGAAAGCTAGAGGATCTAGTTCAAGAGGCAAGAAGATCTGGCCCTCAATTAGCTAGATGTAGATGCTGCCTAACAGTTCCCTCCTCAAAGGCCACCTTGGTGCTGTGGGGGCCCCTTGCCTCTTCCCTTCCCACTGGTGCATTACAAAACAGTGTTCTTTTGAAATGTTCATCAGGAATAGGCTTTTTTAAAAAATGTTGTGTATCTGTATATAGTATTGTGATGTCTGAATGACAATGTACTGAATGCAAAAAGGAAAAAAACCCACAAACATGTTTTTAAAATAAAATATCTTTTTTTGCCTTGAnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnACCCCTCAACTTCAAAGAGTCACAAATCACCCTTAATCAAAAAGGGTGCAGAAATTTTTTTGGGCCCTCCCCGCCATGAGCTCCTACGTAGCCAATTCATTCTATAAGCAGAGCCCCAATATCCCTGCCTATAACATGCAAACTTGTGGGAACTATGGATCGGCCTCAGAGGTGCAGGCATCCAGGTACTGCTACGGCGGATTGGACTTAAGCATCACTTTCCCACCGCCTGCGCCTTCCAACTCTCTCCACGGGGTAGACATGGCTGCCAACCCCCGGGCTCACCCCGACCGCCCCGCCTGCAGCGCCGCGGCCGCTCCGGGACACGCTCCGGGCAGAGACGAAGCGGCTCCTCTGAACCCCGGGATGTACAGTCAGAAGGCGGCTCGCCCGGCGCTGGAGGAGCGAGCTAAGAGCAGTGGGGAGATCAAAGAGGAGCAGGCGCAGACAGGGCAGCCCGCCGGACTGAGCCAGCCACCGGCCCCGCCACAGATTTACCCGTGGATGACCAAACTGCACATGAGCCACGAGACGGACGGCAAGCGGTCCCGAACCAGTTACACGCGCTACCAGACTCTGGAACTCGAGAAAGAATTCCACTTTAACCGCTACCTCACTCGCCGCAGGCGCATAGAGATCGCCAACAACTTGTGTCTCAATGAGAGACAGATCAAGATCTGGTTCCAGAACCGCAGGATGAAGTGGAAGAAAGATTCCAAAATGAAAAGCAAAGAGGCTCTTTAGAGGCAGCGGGGGAGGCCCGCAGAGCGCGCCCCTAGCCGGTTCCTGTCCCTGCGCCTTTCCTTTTCGCCTTTCCTCTCTATATTTCGGGTCGGGGGCAGGTGCTGGAGCACTGGGCTCCCGGGCCCCACAGACAAAAGCGCTTTTCCTTGGCATTCCGCATCCCTACCGACCCAGGGTTCCCGCGGGGCTGTCGGCGCTGCCCCATCTCCCCTCAGCTCGGCTCAGCTCGGTACCCGGGGCCCAGGGCAAGCTCCGCAGGACTTCCCCGGAGGGCTGCGGCGTACAGGCTGGCGCAGAACGAACCTTGGCCTGGGCCGTATCTCCGGCTCCCAGCCTCAGCGCGGCCCTCCCGAGTTAAGGTGGGCCCGGCCCGCGCCACAGGACCCTCGCCGGACCCTCTAACCTCGCCCTCTCCTTTGTTCCCGGCTGGACGGGTTAGACAGCCAAAGGCTGGCGAGAGTCTGGCCCTAGACTCGGGGTGCTTCCTTGTAGCGACTAAACTAGATTTTCACTTATGAATGATTTGCATATGAAAGGAGAGCATCGGCCTAGGGCCCCCACAGTTGCTCTATGCTTTCCAAACCTTATCTCCACAACCTCTTCCCCCCAAAACCCGGGAACCTCCCCAGCCTGCGCCTGCTGCATGCCCTCTCAGGCCGGCAGCCCCAGCCTGCTAGCTAGCTCAACTAGTGGGGTTTCCTGGCACTGGACCCCAGCAAGTGGTCCTAGAGGCCCTTTGCTGTCCCATAGTCCCTGCCACGAATTTCTGTGCCCTCCTGACCCATTGCTGTTGTCCAACTATTTATTGACTCTGGGTCCTTCCTGAAACTATATTTTGTCATATCAAATAAAGAGAGAACAGGACTAAnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnGCCGAGCTCAGCACCGAGGCGCCCCCCAACCTGCCCAGCCCCCAGCCCACCAGCCCAGCCCAGTCCCGGGGAGCCAGCTGGCCTGGGGTTCGGTCCCGGGGGGAGGGGAGTTTCGGGGGTACTGGGCGGGGTACTCGTGAGCCAGAGGGGAGGGGGCCGCGGGTTTTCATGTACCCAGCATGAGCTCCTACTTCGTCAACCCCCTGTTCTCCAAATACAAAGCCGGCGAGTCCCTGGAACCGGCCTATTACGACTGCCGGTTCCCTCAGAGCGTGGGCAGGAGCCATGCGCTGGTGTACGGGCCCGGCGGCTCGGCGCCCGGCTTCCAGCACGCTTCGCACCACGTTCAAGACTTCTTCCACCACGGCACCTCCGGCATCTCCAACTCAGGCTACCAGCAGAACCCGTGCTCGCTTAGCTGCCACGGAGACGCCTCCAAATTCTATGGCTACGAGGCGCTCCCCAGACAGTCCCTTTATGGGGCTCAGCAAGAGGCGAGCGTGGTGCAATATCCCGACTGTAAATCCTCCGCCAACACTAACAGTAGCGAAGGACAAGGCCACTTAAATCAAAACTCGTCTCCCAGCCTCATGTTTCCATGGATGAGACCCCACGCTCCGGGGAGGCGCAGTGGACGGCAAACTTACAGCCGGTATCAGACCTTGGAACTAGAAAAGGAGTTTCTCTTTAATCCTTATTTGACACGAAAACGTCGGATTGAAGTCTCTCATGCCCTGGGACTGACCGAGAGACAAGTGAAGATCTGGTTCCAGAACCGAAGGATGAAGTGGAAAAAGGAGAACAACAAGGATAAACTGCCGGGAGCCCGAGATGAGGAGAAGGTGGAGGAAGAAGGAAATGAGGAAGAGGAGAAAGAAGAGGAGGAAAAGGAAGAAAACAAGGACTAAGCAAAAAAGAAAGACCCCCCCCCCCTTAGCAACTCCCTTGAAGTTTCGTTTTATGGTAGCAGATAAATTGAGAAGTTTACGACTGTCATTTGCTTTTATAGAGAATAGAATGACACTCACAACTCTAACTACCTGTCAGATACTTGCAGCTCTGGTTTTATTACCTTTGGACTTCCCCCACTCTTTATTTGTTTGGGGGCTGGAGGGGGGAGACGGAGAAACAGTGAAAAGTTCGGACTCTCTGTCTCACTCCTTGCCCCACACACACTTGTCCCTGCCCCCACCCTTCTGAGTCCTTCCTGGATTTTAAGGTCTGAGACCTGGCCTCCGTGCTCCTCGGTCTGTCTCTCACCACACTCCCACCTCCCTGCTTCTCTGGTATTTATTTTAGAGGGGAGCCCCCTCGAAATGCAGAAAAGGACTTGTGGTTTTGTTTTTATGCTAAGGCTAGTGTACTAGATGTACTTTTTCTAAAAAGGAAAGGACAGAAAAAAATGAAGAAAGGAAAGGAAGACAAATGTAAAGAAATAAGGAAAAAAGCAAGGAATATCCCCTCCCCCTCCCCCTCCCCCTCCCCAGGGCTCCCTGCTTAGAAAAACCCCCTTGACTTTCTCTAGGAACCTGATGGAAACCTGAAGGAGATGTGGGTCTTTCCCCTCCCCCCATTTCCAGAAGGGTAGATAGGAGCCTGCAGTCGCCTCTAAAATCCTACCTAACCATCCCATGGTCACTCGGGCCCATGCCTTCCTCTCCTTCGCTGTTTGATTTCTATTCTGTTGGGCCCGCCTTCCTCTGAGCTGCATTAGTGTTAGTGCTCAGAAATCACCATAATCACGAAAATAATAATAATAAATCTTTAACATACTACCTAAAGGGAACCTGCAATAATCTTGAAAAAGAAAAAGAGAAAAATTTTAAAATCCTGCTATAGGAGAAAAAAAGAGAAAAAAATAAAAATCAAAAAAAAAAAAAAGAAAGAAAGAAACCTCCAGCGTATTTTATCACTACCTATAGAAAGAAATCCTGCTTTGAGAGTATTTGTAATGCGGTTTTGTTGTCGTTTGTTGCTGCTTATTTCACTAAGAAAACCCAACAACTGAGACTGCCTAGCCCGCCGGTCCTGTGCGCTTTTATTGTGCTTCTAACCCCAGTAGAGTAGAACTAAATTGCACTGAATGTATAGTTAACTCTGTCTTGAATTCTCTGTTTATGCAATGTGCTCGAAAGAAAAAAATGTTAAAAATATATCTATAATAATAATTTTTTGTCATTTGTCTTTATGTCCAGCTATGAATGTAGATTTTGTGTCCCGACAGCCCTGTTCCTGGTCCAAGTACTTTGTATTGTATACGTGAGTCATAATAATAAAAAGAAGAAGAAnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnAGAAAAACGACAAAGCGAGAAAAATTATTTTCCACTCCAGAAATTAATGATCATGAGCTCGTATTTGATGGACTCTAACTACATCGATCCGAAATTTCCTCCATGCGAAGAATATTCGCAAAATAGCTACATCCCTGAACACAGTCCGGAATATTACGGCCGGACCAGGGAATCGGGATTCCAGCATCACCACCAGGAGCTGTACCCACCACCGCCTCCGCGCCCTAGCTACCCTGAGCGCCAGTATAGCTGCACCAGTCTCCAGGGGCCCGGCAATTCGCGAGGCCACGGGCCGGCCCAGGCGGGCCACCACCACCCCGAGAAATCACAGTCGCTCTGCGAGCCGGCGCCTCTCTCAGGCGCCTCCGCCTCCCCGTCCCCAGCCCCGCCAGCCTGCAGCCAGCCAGCCCCCGACCATCCCTCCAGCGCCGCCAGCAAGCAACCCATAGTCTACCCATGGATGAAAAAAATTCACGTTAGCACGGTGAACCCCAATTATAACGGAGGGGAACCCAAGCGCTCGAGGACAGCCTATACCCGGCAGCAAGTCCTGGAATTAGAGAAAGAGTTTCATTACAACCGCTACCTGACCCGAAGGAGAAGGATCGAGATCGCCCACTCGCTGTGCCTCTCTGAGAGGCAGATCAAAATCTGGTTCCAAAACCGTCGCATGAAATGGAAGAAGGACCACCGACTCCCCAACACCAAAGTCAGGTCAGCACCCCCGGCCGGCGCTGCGCCCAGCACCCTTTCGGCAGCTACCCCGGGTACTTCTGAAGACCACTCCCAGAGCGCCACGCCGCCGGAGCAGCAACGGGCAGAGGACATTACCAGGTTATAAAACATAACTCACACCCCTGCCCCCACCCCATGCCCCCACCCTCCCCTCACACACAAATTGACTCTTATTTATAGAATTTAATATATATATATATATATATATATATAGGTTCTTTTCTCTCTTCCTCTCACCTTGTCCCTTGTCAGTTCCAAACAGACAAAACAGATAAACAAACAAGCCCCCTGCCCTCCTCTCCCTCCCACTGTTAAGGACCCTTTTAAGCATGTGATGTTGTCTTAGCATGGTACCTGCTGGGTGTTTTTTTTTAAAAGGCCATTTTGGGGGGTTATTTATTTTTTAAGAAAAAAAGCTGCAAAAATTATATATTGCAAGGTGTGATGGTCTGGCTTGGGTGAATTTCAGGGGAAATGAGGAAAAGAAAAAAGGAAAGAAATTTTAAAGCCAATTCTCATCCTTCTCCTCCTCCTCCTTCCCCCCCTCTTTCCTTAGGCCTTTTGCATTGAAAATGCACCAGGGGAGGTTAGTGAGGGGGAAGTCATTTTAAGGAGAACAAAGCTATGAAGTTCTTTTGTATTATTGTTGGGGGGGGGTGTGGGAGGAGAGGGGGCGAAGACAGCAGACAAAGCTAAATGCATCTGGAGAGCCTCTCAGAGCTGTTCAGTTTGAGGAGCCAAAAGAAAATCAAAATGAACTTTCAGTTCAGAGAGGCAGTCTATAGGTAGAATCTCTCCCCACCCCTATCGTGGTTATTGTGTTTTTGGACTGAATTTACTTGATTATTGTAAAACTTGCAATAAAGAATTTTAGTGTCGATGTGAAATGCCCCGTGATCAATAATAAACCAGTGGATGTGAATTAGTTTTAnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnTTATTGTGGTTTGTCCGTTCCGAGCGCTCCGCAGAACAGTCCTCCCTGTAAGAGCCTAACCATTGCCAGGGAAACCTGCCCTGGGCGCTCCCTTCATTAGCAGTATTTTTTTTAAATTAATCTGATTAATAATTATTTTTCCCCCATTTAATTTTTTTTCCTCCCAGGTGGAGTTGCCGAAGCTGGGGGCAGCTGGGGAGGGTGGGGATGGGAGGGGAGAGACAGAAGTTGAGGGCATCTCTCTCTTCCTTCCCGACCCTCTGGCCCCCAAGGGGCAGGAGGAATGCAGGAGCAGGAGTTGAGCTTGGGAGCTGCAGATGCCTCCGCCCCTCCTCTCTCCCAGGCTCTTCCTCCTGCCCCCTTCTTGCAACTCTCCTTAATTTTGTTTGGCTTTTGGATGATTATAATTATTTTTATTTTTGAATTTATATAAAGTATATGTGTGTGTGTGTGGAGCTGAGACAGGCTCGGCAGCGGCACAGAATGAGGGAAGACGAGAAAGAGAGTGGGAGAGAGAGAGGCAGAGAGGGAGAGAGGGAGAGTGACAGCAGCGCTCGGACGTCCTCCCCAACGTCGCCCTCAATTCCACCGCCTATGATCCAGTGAGGCATTTCTCGACCTATGGAGCGGCCGTTGCCCAGAACCGGATCTACTCGACTCCCTTTTATTCGCCACAGGAGAATGTCGTGTTCAGTTCCAGCCGGGGGCCGTATGACTATGGATCTAATTCCTTTTACCAGGAGAAAGACATGCTCTCAAACTGCAGACAAAACACCTTAGGACATAACACACAGACCTCAATCGCTCAGGATTTTAGTTCTGAGCAGGGCAGGACTGCGCCCCAGGACCAGAAAGCCAGTATCCAGATTTACCCCTGGATGCAGCGAATGAATTCGCACAGTGGGGTCGGCTACGGAGCGGACCGGAGGCGCGGCCGCCAGATCTACTCGCGGTACCAGACCCTGGAACTGGAGAAGGAATTTCACTTCAATCGCTACCTAACGCGGCGCCGGCGCATCGAGATCGCCAACGCGCTTTGCCTGACCGAGCGACAGATCAAAATCTGGTTCCAGAACCGCCGGATGAAGTGGAAAAAAGAATCTAATCTCACATCCACTCTCTCGGGGGGCGGCGGAGGGGCCACCGCCGACAGCCTGGGCGGAAAAGAGGAAAAGCGGGAAGAGACAGAAGAGGAGAAGCAGAAAGAGTGACCAGGACTGTCCCTGCCACCCCTCTCTCCCTTTCTCCCTCGCTCCCCACCAACTCTCCCCTAATCACACACTCTGTATTTATCACTGGCACAATTGATGTGTTTTGATTCCCTAAAACAAAATTAGGGAGTCAAACGTGGACCTGAAAGTCAGCTCTGGACCCCCTCCCTCACCGCACAACTCTCTTTCACCACGCGCCTCCTCCTCCTCGCTCCCTTGCTAGCTCGTTCTCGGCTTGTCTACAGGCCCTTTTCCCCGTCCAGGCCTTGGGGGCTCGGACCCTGAACTCAGACTCTACAGATTGCCCTCCAAGTGAGGACTTGGCTCCCCCACTCCTTCGACGCCCCCACCCCCGCCCCCCGTGCAGAGAGCCGGCTCCTGGGCCTGCTGGGGCCTCTGCTCCAGGGCCTCAGGGCCCGGCCTGGCAGCCGGGGAGGGCCGGAGGCCCAAGGAGGGCGCGCCTTGGCCCCACACCAACCCCCAGGGCCTCCCCGCAGTCCCTGCCTAGCCCCTCTGCCCCAGCAAATGCCCAGCCCAGGCAAATTGTATTTAAAGAATCCTGGGGGTCATTATGGCATTTTACAAACTGTGACCGTTTCTGTGTGAAGATTTTTAGCTGTATTTGTGGTCTCTGTATTTATATTTATGTTTAGCACCGTCAGTGTTCCTATCCAATTTCAAAAAAGGAAAAAAAAGAGGGAAAATTACAAAAAGAGAGAAAAAAAGTGAATGACGTTTGTTTAGCCAGTAGGAGAAAATAAATAAATAAATAAATCCCTTCGTGTTACCCTCCTGTATAAATCCAACCTCTGGGTCCGTTCTCGAATATTTAATAAAACTGATATTATTTTTAAAACTTTAnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnATGGGCGAGCATAATCTCCTGAATCCCGGGTTTGTGGGGCCGCTGGTAAACATCCACACGGGAGACACCTTCTACTTCCCCAACTTCCGCGCGTCCGGGGCGCAGCTTCCCGGGCTGCCTTCGCTGTCCTACCCACGCCGCGACAACGTGTGCTCCCTGTCCTGGCCGTCGGCGGAGCCGTGCAATGGCTACCCGCAGCCCTACCTCGGCAGCCCAGTGTCTCTCAACCCTCCCTTCGGCCGCACGTGCGAGCTGGCGCGCGTGGAGGACGGCAAGGGTTACTACCGCGAGCCGTGCGCCGAGGGTGGCGGCGGGGGCCTGAAGCGTGAGGAGCGCGGGCGCGACCCGGGAGCCGGGCCCGGGGCAGCGCTGCTCCCGCTGGAGCCGTCGGGGCCGCCTGCGCTCGGCTTCAAGTACGACTACGCGGCGGGCGGCGGCGGTGGCGACGGCGGCGGCGGCGCAGGACCTCCGCACGACCCGCCCTCCTGCCAGTCGCTGGAATCCGACTCCAGTTCGTCCCTGCTCAACGAGGGCAACAAGGGCGCCGGCGCAGGCGACCCCGGCAGCTTGGTATCGCCGTTGAACCCCGGCGGCGGGCTCTCGGCCAGCGGCGCGCCCTGGTACCCGATCAACAGCCGCTCTCGGAAGAAGCGCAAGCCCTATTCGAAGTTGCAACTGGCAGAGCTGGAGGGCGAGTTTCTGGTCAACGAGTTCATCACACGCCAGCGCCGGAGGGAACTCTCAGACCGCTTGAATCTTAGTGACCAGCAGGTCAAGATCTGGTTTCAGAACCGGAGAATGAAAAAGAAAAGACTTCTGTTGAGGGAGCAAGCTCTCTCCTTCTTTTAAnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnTTATTGTGGTTTGTCCGTTCCGAGCGCTCCGCAGAACAGTCCTCCCTGTAAGAGCCTAACCATTGCCAGGGAAACCTGCCCTGGGCGCTCCCTTCATTAGCAGTATTTTTTTTAAATTAATCTGATTAATAATTATTTTTCCCCCATTTAATTTTTTTTCCTCCCAGGTGGAGTTGCCGAAGCTGGGGGCAGCTGGGGAGGGTGGGGATGGGAGGGGAGAGACAGAAGTTGAGGGCATCTCTCTCTTCCTTCCCGACCCTCTGGCCCCCAAGGGGCAGGAGGAATGCAGGAGCAGGAGTTGAGCTTGGGAGCTGCAGATGCCTCCGCCCCTCCTCTCTCCCAGGCTCTTCCTCCTGCCCCCTTCTTGCAACTCTCCTTAATTTTGTTTGGCTTTTGGATGATTATAATTATTTTTATTTTTGAATTTATATAAAGTATATGTGTGTGTGTGTGGAGCTGAGACAGGCTCGGCAGCGGCACAGAATGAGGGAAGACGAGAAAGAGAGTGGGAGAGAGAGAGGCAGAGAGGGAGAGAGGGAGAGTGACAGCAGCGCTCGAGACGGACGGCAAGCGGTCCCGAACCAGTTACACGCGCTACCAGACTCTGGAACTCGAGAAAGAATTCCACTTTAACCGCTACCTCACTCGCCGCAGGCGCATAGAGATCGCCAACAACTTGTGTCTCAATGAGAGACAGATCAAGATCTGGTTCCAGAACCGCAGGATGAAGTGGAAGAAAGATTCCAAAATGAAAAGCAAAGAGGCTCTTTAGAGGCAGCGGGGGAGGCCCGCAGAGCGCGCCCCTAGCCGGTTCCTGTCCCTGCGCCTTTCCTTTTCGCCTTTCCTCTCTATATTTCGGGTCGGGGGCAGGTGCTGGAGCACTGGGCTCCCGGGCCCCACAGACAAAAGCGCTTTTCCTTGGCATTCCGCATCCCTACCGACCCAGGGTTCCCGCGGGGCTGTCGGCGCTGCCCCATCTCCCCTCAGCTCGGCTCAGCTCGGTACCCGGGGCCCAGGGCAAGCTCCGCAGGACTTCCCCGGAGGGCTGCGGCGTACAGGCTGGCGCAGAACGAACCTTGGCCTGGGCCGTATCTCCGGCTCCCAGCCTCAGCGCGGCCCTCCCGAGTTAAGGTGGGCCCGGCCCGCGCCACAGGACCCTCGCCGGACCCTCTAACCTCGCCCTCTCCTTTGTTCCCGGCTGGACGGGTTAGACAGCCAAAGGCTGGCGAGAGTCTGGCCCTAGACTCGGGGTGCTTCCTTGTAGCGACTAAACTAGATTTTCACTTATGAATGATTTGCATATGAAAGGAGAGCATCGGCCTAGGGCCCCCACAGTTGCTCTATGCTTTCCAAACCTTATCTCCACAACCTCTTCCCCCCAAAACCCGGGAACCTCCCCAGCCTGCGCCTGCTGCATGCCCTCTCAGGCCGGCAGCCCCAGCCTGCTAGCTAGCTCAACTAGTGGGGTTTCCTGGCACTGGACCCCAGCAAGTGGTCCTAGAGGCCCTTTGCTGTCCCATAGTCCCTGCCACGAATTTCTGTGCCCTCCTGACCCATTGCTGTTGTCCAACTATTTATTGACTCTGGGTCCTTCCTGAAACTATATTTTGTCATATCAAATAAAGAGAGAACAGGACTAAnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
data/test/vagrant/ubuntu_12.04_64/sample_data/transcripts/GenomeIndex ADDED
@@ -0,0 +1 @@
1
+ 5 0 16384 23399 23 500 4 13697024 1 4
data/transrate.gemspec CHANGED
@@ -18,10 +18,10 @@ Gem::Specification.new do |gem|
18
18
  gem.extensions = ["ext/transrate/extconf.rb"]
19
19
 
20
20
  gem.add_dependency 'yell', '~> 2.0', '>= 2.0.4'
21
- gem.add_dependency 'trollop', '~> 2.0'
22
- gem.add_dependency 'bindeps', '~> 0.1', '>= 0.1.3'
21
+ gem.add_dependency 'trollop', '~> 2.0', '>= 2.0.0'
22
+ gem.add_dependency 'bindeps', '~> 1.0', '>= 1.0.1'
23
23
  gem.add_dependency 'bio', '~> 1.4', '>= 1.4.3'
24
- gem.add_dependency 'crb-blast', '~> 0.4', '>= 0.4.2'
24
+ gem.add_dependency 'crb-blast', '~> 0.5', '>= 0.5.0'
25
25
  gem.add_dependency 'ruby-prof', '~> 0.15', '>= 0.15.1'
26
26
  gem.add_dependency 'fix-trinity-output', '~> 1.0', '>= 1.0'
27
27
 
@@ -31,5 +31,5 @@ Gem::Specification.new do |gem|
31
31
  gem.add_development_dependency 'minitest', '~> 4', '>= 4.7.5'
32
32
  gem.add_development_dependency 'simplecov', '~> 0.8', '>= 0.8.2'
33
33
  gem.add_development_dependency 'shoulda-context', '~> 1.2', '>= 1.2.1'
34
- gem.add_development_dependency 'coveralls', '~> 0.7'
34
+ gem.add_development_dependency 'coveralls', '~> 0.7', '>= 0.7.2'
35
35
  end
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: transrate
3
3
  version: !ruby/object:Gem::Version
4
- version: 1.0.0.alpha.8.bowtie
4
+ version: 1.0.0.beta1
5
5
  platform: ruby
6
6
  authors:
7
7
  - Richard Smith-Unna
@@ -9,278 +9,290 @@ authors:
9
9
  autorequire:
10
10
  bindir: bin
11
11
  cert_chain: []
12
- date: 2014-11-04 00:00:00.000000000 Z
12
+ date: 2014-12-08 00:00:00.000000000 Z
13
13
  dependencies:
14
14
  - !ruby/object:Gem::Dependency
15
15
  name: yell
16
16
  requirement: !ruby/object:Gem::Requirement
17
17
  requirements:
18
- - - ~>
18
+ - - "~>"
19
19
  - !ruby/object:Gem::Version
20
20
  version: '2.0'
21
- - - '>='
21
+ - - ">="
22
22
  - !ruby/object:Gem::Version
23
23
  version: 2.0.4
24
24
  type: :runtime
25
25
  prerelease: false
26
26
  version_requirements: !ruby/object:Gem::Requirement
27
27
  requirements:
28
- - - ~>
28
+ - - "~>"
29
29
  - !ruby/object:Gem::Version
30
30
  version: '2.0'
31
- - - '>='
31
+ - - ">="
32
32
  - !ruby/object:Gem::Version
33
33
  version: 2.0.4
34
34
  - !ruby/object:Gem::Dependency
35
35
  name: trollop
36
36
  requirement: !ruby/object:Gem::Requirement
37
37
  requirements:
38
- - - ~>
38
+ - - "~>"
39
39
  - !ruby/object:Gem::Version
40
40
  version: '2.0'
41
+ - - ">="
42
+ - !ruby/object:Gem::Version
43
+ version: 2.0.0
41
44
  type: :runtime
42
45
  prerelease: false
43
46
  version_requirements: !ruby/object:Gem::Requirement
44
47
  requirements:
45
- - - ~>
48
+ - - "~>"
46
49
  - !ruby/object:Gem::Version
47
50
  version: '2.0'
51
+ - - ">="
52
+ - !ruby/object:Gem::Version
53
+ version: 2.0.0
48
54
  - !ruby/object:Gem::Dependency
49
55
  name: bindeps
50
56
  requirement: !ruby/object:Gem::Requirement
51
57
  requirements:
52
- - - ~>
58
+ - - "~>"
53
59
  - !ruby/object:Gem::Version
54
- version: '0.1'
55
- - - '>='
60
+ version: '1.0'
61
+ - - ">="
56
62
  - !ruby/object:Gem::Version
57
- version: 0.1.3
63
+ version: 1.0.1
58
64
  type: :runtime
59
65
  prerelease: false
60
66
  version_requirements: !ruby/object:Gem::Requirement
61
67
  requirements:
62
- - - ~>
68
+ - - "~>"
63
69
  - !ruby/object:Gem::Version
64
- version: '0.1'
65
- - - '>='
70
+ version: '1.0'
71
+ - - ">="
66
72
  - !ruby/object:Gem::Version
67
- version: 0.1.3
73
+ version: 1.0.1
68
74
  - !ruby/object:Gem::Dependency
69
75
  name: bio
70
76
  requirement: !ruby/object:Gem::Requirement
71
77
  requirements:
72
- - - ~>
78
+ - - "~>"
73
79
  - !ruby/object:Gem::Version
74
80
  version: '1.4'
75
- - - '>='
81
+ - - ">="
76
82
  - !ruby/object:Gem::Version
77
83
  version: 1.4.3
78
84
  type: :runtime
79
85
  prerelease: false
80
86
  version_requirements: !ruby/object:Gem::Requirement
81
87
  requirements:
82
- - - ~>
88
+ - - "~>"
83
89
  - !ruby/object:Gem::Version
84
90
  version: '1.4'
85
- - - '>='
91
+ - - ">="
86
92
  - !ruby/object:Gem::Version
87
93
  version: 1.4.3
88
94
  - !ruby/object:Gem::Dependency
89
95
  name: crb-blast
90
96
  requirement: !ruby/object:Gem::Requirement
91
97
  requirements:
92
- - - ~>
98
+ - - "~>"
93
99
  - !ruby/object:Gem::Version
94
- version: '0.4'
95
- - - '>='
100
+ version: '0.5'
101
+ - - ">="
96
102
  - !ruby/object:Gem::Version
97
- version: 0.4.2
103
+ version: 0.5.0
98
104
  type: :runtime
99
105
  prerelease: false
100
106
  version_requirements: !ruby/object:Gem::Requirement
101
107
  requirements:
102
- - - ~>
108
+ - - "~>"
103
109
  - !ruby/object:Gem::Version
104
- version: '0.4'
105
- - - '>='
110
+ version: '0.5'
111
+ - - ">="
106
112
  - !ruby/object:Gem::Version
107
- version: 0.4.2
113
+ version: 0.5.0
108
114
  - !ruby/object:Gem::Dependency
109
115
  name: ruby-prof
110
116
  requirement: !ruby/object:Gem::Requirement
111
117
  requirements:
112
- - - ~>
118
+ - - "~>"
113
119
  - !ruby/object:Gem::Version
114
120
  version: '0.15'
115
- - - '>='
121
+ - - ">="
116
122
  - !ruby/object:Gem::Version
117
123
  version: 0.15.1
118
124
  type: :runtime
119
125
  prerelease: false
120
126
  version_requirements: !ruby/object:Gem::Requirement
121
127
  requirements:
122
- - - ~>
128
+ - - "~>"
123
129
  - !ruby/object:Gem::Version
124
130
  version: '0.15'
125
- - - '>='
131
+ - - ">="
126
132
  - !ruby/object:Gem::Version
127
133
  version: 0.15.1
128
134
  - !ruby/object:Gem::Dependency
129
135
  name: fix-trinity-output
130
136
  requirement: !ruby/object:Gem::Requirement
131
137
  requirements:
132
- - - ~>
138
+ - - "~>"
133
139
  - !ruby/object:Gem::Version
134
140
  version: '1.0'
135
- - - '>='
141
+ - - ">="
136
142
  - !ruby/object:Gem::Version
137
143
  version: '1.0'
138
144
  type: :runtime
139
145
  prerelease: false
140
146
  version_requirements: !ruby/object:Gem::Requirement
141
147
  requirements:
142
- - - ~>
148
+ - - "~>"
143
149
  - !ruby/object:Gem::Version
144
150
  version: '1.0'
145
- - - '>='
151
+ - - ">="
146
152
  - !ruby/object:Gem::Version
147
153
  version: '1.0'
148
154
  - !ruby/object:Gem::Dependency
149
155
  name: rake
150
156
  requirement: !ruby/object:Gem::Requirement
151
157
  requirements:
152
- - - ~>
158
+ - - "~>"
153
159
  - !ruby/object:Gem::Version
154
160
  version: '10.3'
155
- - - '>='
161
+ - - ">="
156
162
  - !ruby/object:Gem::Version
157
163
  version: 10.3.2
158
164
  type: :development
159
165
  prerelease: false
160
166
  version_requirements: !ruby/object:Gem::Requirement
161
167
  requirements:
162
- - - ~>
168
+ - - "~>"
163
169
  - !ruby/object:Gem::Version
164
170
  version: '10.3'
165
- - - '>='
171
+ - - ">="
166
172
  - !ruby/object:Gem::Version
167
173
  version: 10.3.2
168
174
  - !ruby/object:Gem::Dependency
169
175
  name: rake-compiler
170
176
  requirement: !ruby/object:Gem::Requirement
171
177
  requirements:
172
- - - ~>
178
+ - - "~>"
173
179
  - !ruby/object:Gem::Version
174
180
  version: '0.9'
175
- - - '>='
181
+ - - ">="
176
182
  - !ruby/object:Gem::Version
177
183
  version: 0.9.2
178
184
  type: :development
179
185
  prerelease: false
180
186
  version_requirements: !ruby/object:Gem::Requirement
181
187
  requirements:
182
- - - ~>
188
+ - - "~>"
183
189
  - !ruby/object:Gem::Version
184
190
  version: '0.9'
185
- - - '>='
191
+ - - ">="
186
192
  - !ruby/object:Gem::Version
187
193
  version: 0.9.2
188
194
  - !ruby/object:Gem::Dependency
189
195
  name: turn
190
196
  requirement: !ruby/object:Gem::Requirement
191
197
  requirements:
192
- - - ~>
198
+ - - "~>"
193
199
  - !ruby/object:Gem::Version
194
200
  version: '0.9'
195
- - - '>='
201
+ - - ">="
196
202
  - !ruby/object:Gem::Version
197
203
  version: 0.9.7
198
204
  type: :development
199
205
  prerelease: false
200
206
  version_requirements: !ruby/object:Gem::Requirement
201
207
  requirements:
202
- - - ~>
208
+ - - "~>"
203
209
  - !ruby/object:Gem::Version
204
210
  version: '0.9'
205
- - - '>='
211
+ - - ">="
206
212
  - !ruby/object:Gem::Version
207
213
  version: 0.9.7
208
214
  - !ruby/object:Gem::Dependency
209
215
  name: minitest
210
216
  requirement: !ruby/object:Gem::Requirement
211
217
  requirements:
212
- - - ~>
218
+ - - "~>"
213
219
  - !ruby/object:Gem::Version
214
220
  version: '4'
215
- - - '>='
221
+ - - ">="
216
222
  - !ruby/object:Gem::Version
217
223
  version: 4.7.5
218
224
  type: :development
219
225
  prerelease: false
220
226
  version_requirements: !ruby/object:Gem::Requirement
221
227
  requirements:
222
- - - ~>
228
+ - - "~>"
223
229
  - !ruby/object:Gem::Version
224
230
  version: '4'
225
- - - '>='
231
+ - - ">="
226
232
  - !ruby/object:Gem::Version
227
233
  version: 4.7.5
228
234
  - !ruby/object:Gem::Dependency
229
235
  name: simplecov
230
236
  requirement: !ruby/object:Gem::Requirement
231
237
  requirements:
232
- - - ~>
238
+ - - "~>"
233
239
  - !ruby/object:Gem::Version
234
240
  version: '0.8'
235
- - - '>='
241
+ - - ">="
236
242
  - !ruby/object:Gem::Version
237
243
  version: 0.8.2
238
244
  type: :development
239
245
  prerelease: false
240
246
  version_requirements: !ruby/object:Gem::Requirement
241
247
  requirements:
242
- - - ~>
248
+ - - "~>"
243
249
  - !ruby/object:Gem::Version
244
250
  version: '0.8'
245
- - - '>='
251
+ - - ">="
246
252
  - !ruby/object:Gem::Version
247
253
  version: 0.8.2
248
254
  - !ruby/object:Gem::Dependency
249
255
  name: shoulda-context
250
256
  requirement: !ruby/object:Gem::Requirement
251
257
  requirements:
252
- - - ~>
258
+ - - "~>"
253
259
  - !ruby/object:Gem::Version
254
260
  version: '1.2'
255
- - - '>='
261
+ - - ">="
256
262
  - !ruby/object:Gem::Version
257
263
  version: 1.2.1
258
264
  type: :development
259
265
  prerelease: false
260
266
  version_requirements: !ruby/object:Gem::Requirement
261
267
  requirements:
262
- - - ~>
268
+ - - "~>"
263
269
  - !ruby/object:Gem::Version
264
270
  version: '1.2'
265
- - - '>='
271
+ - - ">="
266
272
  - !ruby/object:Gem::Version
267
273
  version: 1.2.1
268
274
  - !ruby/object:Gem::Dependency
269
275
  name: coveralls
270
276
  requirement: !ruby/object:Gem::Requirement
271
277
  requirements:
272
- - - ~>
278
+ - - "~>"
273
279
  - !ruby/object:Gem::Version
274
280
  version: '0.7'
281
+ - - ">="
282
+ - !ruby/object:Gem::Version
283
+ version: 0.7.2
275
284
  type: :development
276
285
  prerelease: false
277
286
  version_requirements: !ruby/object:Gem::Requirement
278
287
  requirements:
279
- - - ~>
288
+ - - "~>"
280
289
  - !ruby/object:Gem::Version
281
290
  version: '0.7'
282
- description: ' a library and command-line tool for quality assessment of de-novo transcriptome
283
- assemblies '
291
+ - - ">="
292
+ - !ruby/object:Gem::Version
293
+ version: 0.7.2
294
+ description: " a library and command-line tool for quality assessment of de-novo transcriptome
295
+ assemblies "
284
296
  email: rds45@cam.ac.uk
285
297
  executables:
286
298
  - transrate
@@ -288,8 +300,8 @@ extensions:
288
300
  - ext/transrate/extconf.rb
289
301
  extra_rdoc_files: []
290
302
  files:
291
- - .gitignore
292
- - .travis.yml
303
+ - ".gitignore"
304
+ - ".travis.yml"
293
305
  - Gemfile
294
306
  - LICENSE
295
307
  - README.md
@@ -301,7 +313,6 @@ files:
301
313
  - ext/transrate/transrate.c
302
314
  - lib/transrate.rb
303
315
  - lib/transrate/assembly.rb
304
- - lib/transrate/bowtie.rb
305
316
  - lib/transrate/cmd.rb
306
317
  - lib/transrate/comparative_metrics.rb
307
318
  - lib/transrate/contig.rb
@@ -310,6 +321,7 @@ files:
310
321
  - lib/transrate/read_metrics.rb
311
322
  - lib/transrate/sam_checker.rb
312
323
  - lib/transrate/samtools.rb
324
+ - lib/transrate/score_optimiser.rb
313
325
  - lib/transrate/snap.rb
314
326
  - lib/transrate/transrater.rb
315
327
  - lib/transrate/version.rb
@@ -322,6 +334,7 @@ files:
322
334
  - test/data/assembly.fasta
323
335
  - test/data/bridging_reads.l.fastq
324
336
  - test/data/bridging_reads.r.fastq
337
+ - test/data/express_results.xprs
325
338
  - test/data/sorghum_transcript.fa
326
339
  - test/data/tiny.sam
327
340
  - test/helper.rb
@@ -330,11 +343,39 @@ files:
330
343
  - test/test_comp_metrics.rb
331
344
  - test/test_contig.rb
332
345
  - test/test_contig_metrics.rb
346
+ - test/test_express.rb
333
347
  - test/test_inline.rb
334
348
  - test/test_read_metrics.rb
335
349
  - test/test_samtools.rb
336
350
  - test/test_transrate.rb
337
351
  - test/test_transrater.rb
352
+ - test/vagrant/centos_6.5_64/Vagrantfile
353
+ - test/vagrant/debian_7.4_64/Vagrantfile
354
+ - test/vagrant/debian_7.4_64/provision.sh
355
+ - test/vagrant/fedora_20_64/Vagrantfile
356
+ - test/vagrant/fedora_20_64/provision.sh
357
+ - test/vagrant/fedora_20_64/sample_data/params.xprs
358
+ - test/vagrant/fedora_20_64/sample_data/reads_1.fastq
359
+ - test/vagrant/fedora_20_64/sample_data/reads_1.fastq-reads_2.fastq-read_count.txt
360
+ - test/vagrant/fedora_20_64/sample_data/reads_2.fastq
361
+ - test/vagrant/fedora_20_64/sample_data/transcripts.fasta
362
+ - test/vagrant/fedora_20_64/sample_data/transcripts.fasta_results.xprs
363
+ - test/vagrant/fedora_20_64/sample_data/transcripts/Genome
364
+ - test/vagrant/fedora_20_64/sample_data/transcripts/GenomeIndex
365
+ - test/vagrant/fedora_20_64/sample_data/transcripts/GenomeIndexHash
366
+ - test/vagrant/fedora_20_64/sample_data/transcripts/OverflowTable
367
+ - test/vagrant/ubuntu_12.04_64/Vagrantfile
368
+ - test/vagrant/ubuntu_12.04_64/provision.sh
369
+ - test/vagrant/ubuntu_12.04_64/sample_data/params.xprs
370
+ - test/vagrant/ubuntu_12.04_64/sample_data/reads_1.fastq
371
+ - test/vagrant/ubuntu_12.04_64/sample_data/reads_1.fastq-reads_2.fastq-read_count.txt
372
+ - test/vagrant/ubuntu_12.04_64/sample_data/reads_2.fastq
373
+ - test/vagrant/ubuntu_12.04_64/sample_data/transcripts.fasta
374
+ - test/vagrant/ubuntu_12.04_64/sample_data/transcripts.fasta_results.xprs
375
+ - test/vagrant/ubuntu_12.04_64/sample_data/transcripts/Genome
376
+ - test/vagrant/ubuntu_12.04_64/sample_data/transcripts/GenomeIndex
377
+ - test/vagrant/ubuntu_12.04_64/sample_data/transcripts/GenomeIndexHash
378
+ - test/vagrant/ubuntu_12.04_64/sample_data/transcripts/OverflowTable
338
379
  - transrate.gemspec
339
380
  homepage: https://github.com/Blahah/transrate
340
381
  licenses:
@@ -347,19 +388,18 @@ require_paths:
347
388
  - ext
348
389
  required_ruby_version: !ruby/object:Gem::Requirement
349
390
  requirements:
350
- - - '>='
391
+ - - ">="
351
392
  - !ruby/object:Gem::Version
352
393
  version: '0'
353
394
  required_rubygems_version: !ruby/object:Gem::Requirement
354
395
  requirements:
355
- - - '>'
396
+ - - ">"
356
397
  - !ruby/object:Gem::Version
357
398
  version: 1.3.1
358
399
  requirements: []
359
400
  rubyforge_project:
360
- rubygems_version: 2.1.4
401
+ rubygems_version: 2.2.2
361
402
  signing_key:
362
403
  specification_version: 4
363
404
  summary: quality assessment of de-novo transcriptome assemblies
364
405
  test_files: []
365
- has_rdoc: