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

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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: