bio-samtools 0.4.2 → 0.5.0

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Files changed (45) hide show
  1. data/Gemfile.lock +1 -0
  2. data/README.rdoc +1 -0
  3. data/VERSION +1 -1
  4. data/bio-samtools.gemspec +19 -19
  5. data/doc/Bio.html +71 -4
  6. data/doc/Bio/DB.html +6 -4
  7. data/doc/Bio/DB/Alignment.html +8 -8
  8. data/doc/Bio/DB/Pileup.html +515 -0
  9. data/doc/Bio/DB/SAM.html +37 -37
  10. data/doc/Bio/DB/SAM/Library.html +4 -4
  11. data/doc/Bio/DB/SAM/Tools.html +4 -4
  12. data/doc/Bio/DB/SAM/Tools/Bam1CoreT.html +4 -4
  13. data/doc/Bio/DB/SAM/Tools/Bam1T.html +4 -4
  14. data/doc/Bio/DB/SAM/Tools/BamHeaderT.html +4 -4
  15. data/doc/Bio/DB/SAM/Tools/BamPileup1T.html +4 -4
  16. data/doc/Bio/DB/SAM/Tools/SamfileT.html +4 -4
  17. data/doc/Bio/DB/SAM/Tools/SamfileTX.html +4 -4
  18. data/doc/Bio/DB/SAMException.html +5 -5
  19. data/doc/Bio/DB/Tag.html +5 -5
  20. data/doc/Bio/DB/Vcf.html +467 -0
  21. data/doc/LICENSE_txt.html +57 -60
  22. data/doc/LibC.html +6 -4
  23. data/doc/created.rid +7 -7
  24. data/doc/index.html +4 -4
  25. data/doc/js/search_index.js +1 -1
  26. data/doc/lib/bio-samtools_rb.html +4 -4
  27. data/doc/lib/bio/db/pileup_rb.html +171 -0
  28. data/doc/lib/bio/db/sam/bam_rb.html +4 -4
  29. data/doc/lib/bio/db/sam/faidx_rb.html +4 -4
  30. data/doc/lib/bio/db/sam/library_rb.html +4 -4
  31. data/doc/lib/bio/db/sam/sam_rb.html +4 -4
  32. data/doc/lib/bio/db/sam_rb.html +4 -4
  33. data/doc/lib/bio/db/vcf_rb.html +124 -0
  34. data/doc/table_of_contents.html +16 -26
  35. data/doc/tutorial.html +26 -1
  36. data/doc/tutorial.pdf +0 -0
  37. data/lib/bio/db/{sam/pileup.rb → pileup.rb} +6 -4
  38. data/lib/bio/db/sam.rb +13 -12
  39. data/lib/bio/db/{sam/vcf.rb → vcf.rb} +6 -2
  40. data/test/samples/small/sorted.bam.bai +0 -0
  41. data/test/test_basic.rb +7 -5
  42. data/test/test_vcf.rb +5 -5
  43. metadata +29 -26
  44. data/test/basictest.rb +0 -322
  45. data/test/pileup.rb +0 -68
data/test/pileup.rb DELETED
@@ -1,68 +0,0 @@
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- $: << File.expand_path(File.dirname(__FILE__) + '/../lib')
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- $: << File.expand_path('.')
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-
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- require "bio/db/sam/pileup"
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- require "test/unit"
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-
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- class TestPileup < Test::Unit::TestCase
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-
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- def setup
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- @six_col = Pileup.new("seq1\t272\tT\t24\t,.$.....,,.,.,...,,,.,..^+.\t<<<+;<<<<<<<<<<<=<;<;7<&")
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- @ten_col = Pileup.new("seq2\t151\tG\tG\t36\t0\t99\t12\t...........A\t:9<;;7=<<<<<")
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- @snp = Pileup.new("seq1\t272\tT\t24\t,.$.....,,.gGgGgGgGgGgGg^+.\t<<<+;<<<<<<<<<<<=<;<;7<&")
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- @snp_2 = Pileup.new("seq1\t272\tT\t24\t......aaaaaaggggggcccccc$^+\t<<<+;<<<<<<<<<<<=<;<;7<&")
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- @snp_3 = Pileup.new("seq1\t272\tT\t24\t......aaaaaaaagggggccccc$^+\t<<<+;<<<<<<<<<<<=<;<;7<&")
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- end
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-
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- def test_new_from_6_column
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- assert_equal("seq1", @six_col.ref_name)
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- assert_equal(272, @six_col.pos)
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- assert_equal("T", @six_col.ref_base)
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- assert_equal(24, @six_col.coverage)
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- assert_equal(",.$.....,,.,.,...,,,.,..^+.", @six_col.read_bases)
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- assert_equal("<<<+;<<<<<<<<<<<=<;<;7<&", @six_col.read_quals)
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- end
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-
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- def test_new_from_10_column
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- assert_equal("seq2", @ten_col.ref_name)
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- assert_equal(151, @ten_col.pos)
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- assert_equal("G", @ten_col.ref_base)
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- assert_equal("G", @ten_col.consensus)
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- assert_equal(36, @ten_col.consensus_quality)
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- assert_equal(0, @ten_col.snp_quality)
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- assert_equal(99, @ten_col.rms_mapq)
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- assert_equal(12, @ten_col.coverage)
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- assert_equal("...........A", @ten_col.read_bases)
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- assert_equal(":9<;;7=<<<<<", @ten_col.read_quals)
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- end
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-
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- def test_non_refs
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- assert_equal({:A => 1, :C => 0, :T => 0, :G => 0}, @ten_col.non_refs)
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- assert_equal({:A => 0, :C => 0, :T => 0, :G => 0}, @six_col.non_refs)
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- end
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-
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- def test_consensus
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- assert_equal("G", @snp.consensus)
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- assert_equal("ACGT", @snp_2.consensus)
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- assert_equal("A", @snp_3.consensus)
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- end
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-
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- def test_non_ref_count
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- assert_equal(13,@snp.non_ref_count)
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- assert_equal(18,@snp_2.non_ref_count)
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- assert_equal(18,@snp_3.non_ref_count)
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- end
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-
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- def test_ref_count
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- assert_equal(11,@snp.ref_count)
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- assert_equal(6,@snp_2.ref_count)
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- assert_equal(6,@snp_3.ref_count)
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- end
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-
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- def test_ref_plus_non_ref_equal_to_coverage
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- assert_equal(@snp.coverage,@snp.ref_count + @snp.non_ref_count)
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- assert_equal(@snp_2.coverage,@snp_2.ref_count + @snp_2.non_ref_count)
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- assert_equal(@snp_3.coverage,@snp_3.ref_count + @snp_3.non_ref_count)
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- end
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-
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- end