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

Sign up to get free protection for your applications and to get access to all the features.
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

There are too many changes on this page to be displayed.

The amount of changes on this page would crash your brower.

You can still verify the content by downloading the gem file manually.