bio-samtools 0.6.2 → 2.0.3

data/test/test_pileup.rb

@@ -0,0 +1,84 @@
+$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
+$: << File.expand_path('.')
+require 'rubygems'
+require 'bio/db/pileup'
+require "test/unit"
+gem 'test-unit'
+
+
+class TestPileup < Test::Unit::TestCase
+  
+  def setup
+    @pu = Bio::DB::Pileup.new("seq1	279	C	23	A..T,,.,.,...,,,.,.....	;75&<<<<<<<<<=<<<9<<:<<")
+    #a snp...
+    @pu2 = Bio::DB::Pileup.new("seq1	279	C	23	ATTT,,.,.TTTT,,,.,TTTTT	;75&<<<<<<<<<=<<<9<<:<<")
+    #an indel..
+    @pu3 = Bio::DB::Pileup.new("seq2	156	*	+AG/+AG	71	252	99	11	+AG	*	3	8	0")
+  end
+  
+  def test_non_ref_count
+    assert_equal(2, @pu.non_ref_count)
+  end
+  
+  def test_ref_count
+    assert_equal(21, @pu.ref_count)
+  end
+  
+  def test_consensus
+    assert_equal('C', @pu.consensus)
+    assert_equal('T', @pu2.consensus)
+  end
+  
+  def test_non_refs
+    assert_equal(1, @pu.non_refs[:T])
+    assert_equal(1, @pu.non_refs[:A])
+    assert_equal(0, @pu.non_refs[:G])
+    assert_equal(0, @pu.non_refs[:C])
+  end
+  
+   
+  def test_to_vcf
+    @vcf = Bio::DB::Vcf.new(@pu.to_vcf)
+     assert_equal('seq1', @vcf.chrom)
+  end
+  
+  
+  def test_indel_gt
+    indel =  @pu3.send(:indel_gt)
+    assert_equal('IAG', indel[0])
+    assert_equal('1/1', indel[1])
+  end
+  
+  def test_snp_gt
+    snp =  @pu2.send(:snp_gt)
+    assert_equal('T,', snp[0])
+    assert_equal('1/2', snp[1])
+  end
+  
+  def test_genotype_list
+    gt2 = @pu2.genotype_list
+    gt3 = @pu3.genotype_list
+    assert_equal('T,', gt2[0])
+    assert_equal('1/2', gt2[1])
+    assert_equal('IAG', gt3[0])
+    assert_equal('1/1', gt3[1])
+  end
+  
+  def test_iupac_to_base
+    iupac = Bio::DB::Pileup.iupac_to_base('R')
+    iupac.each do |pu|
+      assert_send([['A' , 'G'], :member?, pu])
+    end
+  end
+  
+  def test_parse_indel
+    assert_equal('IAG/+AG', @pu3.parse_indel(@pu3.consensus))
+  end
+  
+  def test_to_s
+    #check whether there are the correct number of tabs in the string (number of columns -1)
+    assert_equal(12, @pu3.to_s.count("\t"))
+    assert_equal(5, @pu.to_s.count("\t"))
+  end
+  
+end

data/test/test_sam.rb

@@ -0,0 +1,331 @@
+$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
+$: << File.expand_path('.')
+require 'rubygems'
+require 'bio/db/sam'
+require "test/unit"
+gem 'test-unit'
+
+
+class TestBioDbSam < Test::Unit::TestCase
+  
+  class << self
+    def shutdown
+      File.delete("test/samples/small/different_index.bam.bai")
+      File.delete("test/samples/small/dupes_rmdup.bam")
+      File.delete("test/samples/small/mates_fixed.bam")
+      File.delete("test/samples/small/reheader.bam")
+      File.delete("test/samples/small/test_chr.fasta.fai")
+      File.delete("test/samples/small/test_sorted.bam")
+      File.delete("test/samples/small/maps_merged.bam")
+      File.delete("test/samples/small/maps_cated.bam")
+    end
+  end
+  
+  
+  def setup
+    @test_folder                = "test/samples/small"
+    @testTAMFile                = @test_folder + "/test.tam"
+    @testBAMFile                = @test_folder + "/testu.bam"
+    @testReference              = @test_folder + "/test_chr.fasta"
+    @sam = Bio::DB::Sam.new(
+        :fasta => @testReference, 
+        :bam => @testBAMFile
+    )
+  end
+  
+  
+  
+  def test_new
+    assert_kind_of(Bio::DB::Sam, @sam)
+  end
+  
+  def test_index
+    test_bai_file = @testBAMFile+".bai"
+    #test to see if the index file exists. If so, delete it
+    if File.exist?(test_bai_file) == true
+      puts "bam index exists....deleting..."
+      File.delete(test_bai_file)
+    end
+     #index the bam file
+    @sam.index()
+    
+    #make sure the .bai file exists
+    assert_nothing_thrown do
+      File.open(test_bai_file, "r")
+    end
+    assert(File.size(test_bai_file) > 0, "From test_index: .bai file is empty")
+    #as above, but give the output a different name
+    test_bai_file = @test_folder+"/different_index.bam.bai"
+    @sam.index(:out_index=> test_bai_file)
+    assert_nothing_thrown do
+      File.open(test_bai_file, "r")
+    end
+    assert(File.size(test_bai_file) > 0, "From test_index: .bai file is empty")
+  end
+
+  def test_view
+    #how to get Bio::DB::Alignment objects ..
+    @sam.view() do |sam|
+      #test that all the objects are Bio::DB::Alignment objects and their reference is 'chr_1'
+      assert_equal(sam.class, Bio::DB::Alignment)
+      assert_equal(sam.rname, "chr_1")
+    end
+  end
+  
+  def test_fetch
+    @sam.fetch("chr_1", 10,1000) do |sam|
+      #test that all the objects are Bio::DB::Alignment objects
+      assert_equal(sam.class, Bio::DB::Alignment)
+      assert_equal(sam.rname, "chr_1")
+    end
+  end
+  
+  def test_fetch_with_function
+    #pass the assert to method
+    block = Proc.new {|a| assert_equal(a.class, Bio::DB::Alignment)}
+    @sam.fetch_with_function("chr_1", 10,1000, &block)
+  end
+  
+  def test_chromosome_coverage
+    #the coverage should only be 1.0 or 2.0
+    cov = @sam.chromosome_coverage("chr_1", 33, 19)
+    cov.each do |pu|
+      assert_send([[1.0 , 2.0], :member?, pu])
+    end
+  end
+  
+  def test_average_coverage
+    #there should be 10 positions with cov of 1.0 and 10 with cov of 2.0, so average of 1.5
+    test_bai_file = @testBAMFile+".bai"
+    if File.exist?(test_bai_file) == false
+      @sam.index()
+    end
+    avcov = @sam.average_coverage("chr_1", 33, 19)
+    assert_equal(avcov, 1.5)
+    File.delete(test_bai_file)
+  end
+  
+  def test_faidx
+    @sam.faidx()
+    test_fai_file = @testReference+".fai"
+    #test that the .fai file exists
+    assert_nothing_thrown do
+      File.open(test_fai_file, "r")
+    end
+    #test that the file is not empty
+    assert(File.size(test_fai_file) > 0, "From test_faidx: .fai file is empty")
+  end
+   
+  def test_index_stats
+    @sam.index_stats.each_pair do |seq, stat|
+      assert_send([['chr_1' , '*'], :member?, seq])
+    end
+  end
+  
+  def test_fetch_reference
+    #this is the first 70 nucleotides of the test seqeunce
+    seq_expected = "CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA"
+    #fetch the first 70 nuclotides
+    seq_fetched = @sam.fetch_reference("chr_1", 1, 70, :as_bio => false)
+    #test they're the same
+    assert_equal(seq_fetched, seq_expected)
+  end
+  
+  def test_sort
+    #sort the bam file
+    sortedsam = @test_folder + "/test_sorted.bam"
+    @sam.sort(:prefix=>@test_folder + "/test_sorted")
+    #create a new Bio::DB::Sam from the sorted bam
+    @sortsam = Bio::DB::Sam.new(
+        :fasta => @testReference, 
+        :bam => sortedsam
+    )
+    pos = 0
+    #iterate over the sorted sam file and make sure that the it's sorted by checking the order of the start positions for each read.
+    @sortsam.view()do |sam|
+      assert(sam.pos > pos, "Not sorted by position")
+      pos = sam.pos
+    end
+  end
+  
+  def test_reheader
+    sam_header = @test_folder + "/map_for_reheader.sam"
+    outfile = @test_folder + "/reheader.bam"
+    
+    @sam.reheader(sam_header, :out=>outfile)
+    reheader_bam = Bio::DB::Sam.new(:fasta => @testReference, :bam => outfile)
+    #check that the reference is 'chr_2'
+    reheader_bam.view()do |sam|
+      assert_equal(sam.rname, "chr_2")
+    end
+  end
+
+  def test_calmd
+    no_md_sam = @test_folder + "/no_md.sam"
+    md = Bio::DB::Sam.new(:fasta => @testReference, :bam => no_md_sam)
+    block = Proc.new {|a| assert(a.tags.has_key?('MD'), "From test_calmd: couldn't find the MD tag")}
+    md.calmd(:S=>true, &block)
+    
+  end
+  
+  def test_mpileup
+    #create an mpileup
+    @sam.mpileup(:g => false) do |pileup|
+      #test that all the objects are Bio::DB::Pileup objects
+      assert_kind_of(Bio::DB::Pileup, pileup)
+      #test that the reference name is 'chr_1' for all objects
+      assert_equal(pileup.ref_name, 'chr_1')
+    end
+    #do the same for Vcf output
+    @sam.mpileup(:u => true) do |pileup|
+      assert_kind_of(Bio::DB::Vcf, pileup)
+      assert_equal(pileup.chrom, 'chr_1')
+    end
+  end
+  
+  def test_mpileup_reg
+    #create an mpileup
+    reg = Bio::DB::Fasta::Region.new
+    reg.entry = "chr_1"
+    reg.start = 1
+    reg.end = 334
+    
+    @sam.mpileup_cached(:r=>reg,:g => false, :min_cov => 1, :min_per =>0.2) do |pileup|
+      #test that all the objects are Bio::DB::Pileup objects
+      assert_kind_of(Bio::DB::Pileup, pileup)
+      #test that the reference name is 'chr_1' for all objects
+      #puts pileup
+      assert_equal(pileup.ref_name, 'chr_1')
+    end
+  
+    region = @sam.cached_regions[reg.to_s]
+    #puts "cahced_region: #{region.inspect}"
+    puts "AVG COV: #{region.average_coverage}"
+    puts "Reference: #{region.reference}"
+    puts "Consensus: #{region.consensus}"
+    puts "called: #{region.called}"
+    #, :snps, :reference, :base_ratios, :consensus, :coverages
+    snps_tot = Bio::Sequence.snps_between(region.reference, region.consensus)
+    assert_equal(snps_tot, 5)
+    assert_equal(region.called, 213)
+  end
+  
+  def test_mpileup_reg_05
+    #create an mpileup
+    reg = Bio::DB::Fasta::Region.new
+    reg.entry = "chr_1"
+    reg.start = 1
+    reg.end = 334
+    @sam.mpileup_cached(:r=>reg,:g => false, :min_cov => 1, :min_per =>0.4) do |pileup|
+      #test that all the objects are Bio::DB::Pileup objects
+      assert_kind_of(Bio::DB::Pileup, pileup)
+      #test that the reference name is 'chr_1' for all objects
+      #puts pileup
+      assert_equal(pileup.ref_name, 'chr_1')
+  
+    end
+  
+    region = @sam.cached_regions[reg.to_s]
+    
+    #, :snps, :reference, :base_ratios, :consensus, :coverages
+    snps_tot = Bio::Sequence.snps_between(region.reference, region.consensus)
+    assert_equal(snps_tot, 1)
+    assert_equal(region.called, 213)
+  end
+
+  def test_depth
+    #the depth of coverage should be '1' at all given positions
+    @sam.depth(:r=>"chr_1:25-42") do |al|
+      assert_equal(al[2].to_i, 1)
+    end
+  end
+
+  def test_fixmate
+    mates_fixed_bam = @test_folder + "/mates_fixed.bam"
+    @sam.fix_mates(:out_bam=>mates_fixed_bam)
+    assert_nothing_thrown do
+      File.open(mates_fixed_bam, "r")
+    end
+    assert(File.size(mates_fixed_bam) > 0, "From test_fixmate: .bam file is empty")
+  end
+
+  def test_flagstats
+    #get the stats
+    stats = @sam.flag_stats()
+    #the number of reads mapped will be the first character on the first line.
+    no_reads_mapped = stats[0][0].to_i
+    #check that it's '9'
+    assert_equal(no_reads_mapped, 9)
+  end
+
+  def test_merge
+    bam1 = @test_folder + "/map_to_merge1.bam"
+    bam2 = @test_folder + "/map_to_merge2.bam"
+    bam_to_merge1 = Bio::DB::Sam.new(:fasta => @testReference, :bam => bam1)
+    bam_to_merge2 = Bio::DB::Sam.new(:fasta => @testReference, :bam => bam2)
+    bam_files = [bam_to_merge1, bam_to_merge2]
+    
+    merged_bam_file = @test_folder + "/maps_merged.bam"
+    
+    @sam.merge(:out=>merged_bam_file, :bams=>bam_files, :n=>true)
+    merged_bam = Bio::DB::Sam.new(:fasta => @testReference, :bam => merged_bam_file)
+    no_reads_mapped = 0;
+    
+    merged_bam.view() do |al|
+      assert_kind_of(Bio::DB::Alignment, al)
+      no_reads_mapped+=1
+    end
+    assert_equal(no_reads_mapped, 10)
+  end
+  
+  def test_cat
+    #same files used for merge, but we'll cat them instead
+    bam1 = @test_folder + "/map_to_merge1.bam"
+    bam2 = @test_folder + "/map_to_merge2.bam"
+    
+    bam_files = [bam1, bam2]
+    
+    cat_bam_file = @test_folder + "/maps_cated.bam"
+    
+    @sam.merge(:out=>cat_bam_file, :bams=>bam_files)
+    cated_bam = Bio::DB::Sam.new(:fasta => @testReference, :bam => cat_bam_file)
+    
+    no_reads_mapped = 0;
+    cated_bam.view() do |al|
+      assert_kind_of(Bio::DB::Alignment, al)
+      no_reads_mapped+=1
+    end
+    #there should be 10 reads in the cat'd maps
+    assert_equal(no_reads_mapped, 10)
+  end
+
+  def test_rmdup
+    #dupes contains 4 reads mapped once and one read mapped to the same place 268 times.
+    dupes = @test_folder + "/dupes.bam"
+    unduped = @test_folder + "/dupes_rmdup.bam"
+    bam_with_dupes = Bio::DB::Sam.new(:fasta => @testReference, :bam => dupes)
+    bam_with_dupes.remove_duplicates(:s=>true, :out=>unduped)
+
+    unduped_bam = Bio::DB::Sam.new(:fasta => @testReference, :bam => unduped)
+    #rmdup should remove 267 of the 268 reads mapping to the same place, so producing a bam file with 5 reads
+    readcount = 0
+    unduped_bam.view()do |sam|
+        readcount +=1  
+    end
+    assert_equal(readcount, 5)
+  end
+  
+  def test_targetcut
+    sorted_bam = @test_folder + "/sorted.bam"
+    cut = Bio::DB::Sam.new(:fasta => @testReference, :bam => sorted_bam)
+    assert_nothing_thrown do
+      cut.targetcut
+    end
+  end
+  
+  def test_docs
+    #force an error (use 'samtool' instead of 'samtools')
+    output = Bio::DB::Sam.docs('samtool', 'tview')
+    assert_equal(output, "program must be 'samtools' or 'bcftools'")
+  end   
+end

data/test/test_vcf.rb

@@ -3,6 +3,7 @@ $: << File.expand_path('.')
 require 'rubygems'
 require 'bio/db/vcf'
 require "test/unit"
+gem 'test-unit'
 
 
 class TestVcf < Test::Unit::TestCase
@@ -65,4 +66,14 @@ class TestVcf < Test::Unit::TestCase
                    "3"=>{"DP"=>"5", "GT"=>"1/1", "HQ"=>".,", "GQ"=>"43"}}, @vcf4.samples)
   end
   
+  def test_int_or_raw
+    assert_nothing_raised do
+      @vcf1.int_or_raw(1)
+    end
+    assert_raise do
+      @vcf1.int_or_raw(A)
+    end
+  end
+  
+  
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-samtools
 version: !ruby/object:Gem::Version
-  version: 0.6.2
+  version: 2.0.3
 platform: ruby
 authors:
 - Ricardo Ramirez-Gonzalez
@@ -10,22 +10,22 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-02-25 00:00:00.000000000 Z
+date: 2014-04-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: ffi
+  name: bio-svgenes
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 0.4.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 0.4.1
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement
@@ -40,20 +40,6 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: 1.4.2
-- !ruby/object:Gem::Dependency
-  name: systemu
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 2.5.2
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 2.5.2
 - !ruby/object:Gem::Dependency
   name: shoulda
   requirement: !ruby/object:Gem::Requirement
@@ -166,6 +152,20 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: test-unit
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 description: "Binder of samtools for ruby, on the top of FFI. \n\n  This project was
   born from the need to add support of BAM files to \n  the gee_fu genome browser
   (http://github.com/danmaclean/gee_fu)."
@@ -192,80 +192,19 @@ files:
 - doc/Bio/DB/SAM.html
 - doc/Bio/DB/SAM/Library.html
 - doc/Bio/DB/SAM/Tools.html
-- doc/Bio/DB/SAM/Tools/Bam1CoreT.html
-- doc/Bio/DB/SAM/Tools/Bam1T.html
-- doc/Bio/DB/SAM/Tools/BamHeaderT.html
-- doc/Bio/DB/SAM/Tools/BamPileup1T.html
-- doc/Bio/DB/SAM/Tools/SamfileT.html
-- doc/Bio/DB/SAM/Tools/SamfileTX.html
-- doc/Bio/DB/SAMException.html
 - doc/Bio/DB/Tag.html
 - doc/Bio/DB/Vcf.html
 - doc/LICENSE_txt.html
-- doc/LibC.html
-- doc/Pileup.html
-- doc/Vcf.html
-- doc/basic_styles.css
-- doc/classes/Bio.html
-- doc/classes/Bio/DB.html
-- doc/classes/Bio/DB/Alignment.html
-- doc/classes/Bio/DB/Alignment.src/M000012.html
-- doc/classes/Bio/DB/Alignment.src/M000013.html
-- doc/classes/Bio/DB/Alignment.src/M000014.html
-- doc/classes/Bio/DB/Alignment.src/M000015.html
-- doc/classes/Bio/DB/SAM.html
-- doc/classes/Bio/DB/SAM/Library.html
-- doc/classes/Bio/DB/SAM/Library.src/M000006.html
-- doc/classes/Bio/DB/SAM/Tools.html
-- doc/classes/Bio/DB/SAM/Tools.src/M000007.html
-- doc/classes/Bio/DB/SAM/Tools/Bam1CoreT.html
-- doc/classes/Bio/DB/SAM/Tools/Bam1T.html
-- doc/classes/Bio/DB/SAM/Tools/Bam1T.src/M000010.html
-- doc/classes/Bio/DB/SAM/Tools/BamHeaderT.html
-- doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000008.html
-- doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000009.html
-- doc/classes/Bio/DB/SAM/Tools/BamPileup1T.html
-- doc/classes/Bio/DB/SAM/Tools/SamfileT.html
-- doc/classes/Bio/DB/SAM/Tools/SamfileTX.html
-- doc/classes/Bio/DB/SAMException.html
-- doc/classes/Bio/DB/SAMException.src/M000016.html
-- doc/classes/Bio/DB/Sam.src/M000017.html
-- doc/classes/Bio/DB/Sam.src/M000018.html
-- doc/classes/Bio/DB/Sam.src/M000019.html
-- doc/classes/Bio/DB/Sam.src/M000020.html
-- doc/classes/Bio/DB/Sam.src/M000021.html
-- doc/classes/Bio/DB/Sam.src/M000022.html
-- doc/classes/Bio/DB/Sam.src/M000023.html
-- doc/classes/Bio/DB/Sam.src/M000024.html
-- doc/classes/Bio/DB/Sam.src/M000025.html
-- doc/classes/Bio/DB/Sam.src/M000026.html
-- doc/classes/Bio/DB/Sam.src/M000027.html
-- doc/classes/Bio/DB/Sam.src/M000028.html
-- doc/classes/Bio/DB/Sam.src/M000029.html
-- doc/classes/Bio/DB/Sam.src/M000030.html
-- doc/classes/Bio/DB/Sam.src/M000031.html
-- doc/classes/Bio/DB/Sam.src/M000032.html
-- doc/classes/Bio/DB/Tag.html
-- doc/classes/Bio/DB/Tag.src/M000011.html
-- doc/classes/LibC.html
-- doc/classes/Pileup.html
-- doc/classes/Pileup.src/M000001.html
-- doc/classes/Pileup.src/M000002.html
-- doc/classes/Pileup.src/M000003.html
-- doc/classes/Pileup.src/M000004.html
-- doc/classes/Pileup.src/M000005.html
 - doc/created.rid
-- doc/files/lib/bio-samtools_rb.html
-- doc/files/lib/bio/db/sam/bam_rb.html
-- doc/files/lib/bio/db/sam/faidx_rb.html
-- doc/files/lib/bio/db/sam/library_rb.html
-- doc/files/lib/bio/db/sam/pileup_rb.html
-- doc/files/lib/bio/db/sam/sam_rb.html
-- doc/files/lib/bio/db/sam_rb.html
-- doc/fr_class_index.html
-- doc/fr_file_index.html
-- doc/fr_method_index.html
+- doc/fonts.css
+- doc/fonts/Lato-Light.ttf
+- doc/fonts/Lato-LightItalic.ttf
+- doc/fonts/Lato-Regular.ttf
+- doc/fonts/Lato-RegularItalic.ttf
+- doc/fonts/SourceCodePro-Bold.ttf
+- doc/fonts/SourceCodePro-Regular.ttf
 - doc/images/add.png
+- doc/images/arrow_up.png
 - doc/images/brick.png
 - doc/images/brick_link.png
 - doc/images/bug.png
@@ -296,64 +235,67 @@ files:
 - doc/js/search.js
 - doc/js/search_index.js
 - doc/js/searcher.js
-- doc/lib/bio-samtools_rb.html
-- doc/lib/bio/db/pileup_rb.html
-- doc/lib/bio/db/sam/bam_rb.html
-- doc/lib/bio/db/sam/faidx_rb.html
-- doc/lib/bio/db/sam/library_rb.html
-- doc/lib/bio/db/sam/pileup_rb.html
-- doc/lib/bio/db/sam/sam_rb.html
-- doc/lib/bio/db/sam/vcf_rb.html
-- doc/lib/bio/db/sam_rb.html
-- doc/lib/bio/db/vcf_rb.html
-- doc/rdoc-style.css
 - doc/rdoc.css
 - doc/table_of_contents.html
-- doc/tutorial.html
-- doc/tutorial.pdf
 - ext/Makefile-bioruby.patch
 - ext/Makefile-suse.patch
+- ext/Rakefile
 - ext/mkrf_conf.rb
 - lib/bio-samtools.rb
 - lib/bio/.DS_Store
+- lib/bio/BIOExtensions.rb
+- lib/bio/db/alignment.rb
+- lib/bio/db/fastadb.rb
 - lib/bio/db/pileup.rb
 - lib/bio/db/sam.rb
-- lib/bio/db/sam/bam.rb
 - lib/bio/db/sam/external/COPYING
 - lib/bio/db/sam/external/VERSION
-- lib/bio/db/sam/faidx.rb
+- lib/bio/db/sam/faidx_old.rb
 - lib/bio/db/sam/library.rb
-- lib/bio/db/sam/sam.rb
 - lib/bio/db/vcf.rb
+- test/.gitignore
 - test/helper.rb
-- test/samples/pipe_char/test.bam
-- test/samples/pipe_char/test.bam.bai
-- test/samples/pipe_char/test.tam
-- test/samples/pipe_char/test_chr.fasta
-- test/samples/pipe_char/test_chr.fasta.fai
+- test/old_test_basic.rb
+- test/samples/small/dupes.bam
+- test/samples/small/dupes.sam
 - test/samples/small/ids2.txt
+- test/samples/small/map_for_reheader.sam
+- test/samples/small/map_to_merge1.bam
+- test/samples/small/map_to_merge1.bam.bai
+- test/samples/small/map_to_merge1.sam
+- test/samples/small/map_to_merge2.bam
+- test/samples/small/map_to_merge2.bam.bai
+- test/samples/small/map_to_merge2.sam
+- test/samples/small/no_md.sam
 - test/samples/small/sorted.bam
 - test/samples/small/sorted.bam.bai
-- test/samples/small/test
-- test/samples/small/test.bam
-- test/samples/small/test.fa
-- test/samples/small/test.fai
 - test/samples/small/test.sai
 - test/samples/small/test.tam
 - test/samples/small/test_chr.fasta
+- test/samples/small/test_chr.fasta.1.bt2
+- test/samples/small/test_chr.fasta.2.bt2
+- test/samples/small/test_chr.fasta.3.bt2
+- test/samples/small/test_chr.fasta.4.bt2
 - test/samples/small/test_chr.fasta.amb
 - test/samples/small/test_chr.fasta.ann
 - test/samples/small/test_chr.fasta.bwt
 - test/samples/small/test_chr.fasta.pac
 - test/samples/small/test_chr.fasta.rbwt
+- test/samples/small/test_chr.fasta.rev.1.bt2
+- test/samples/small/test_chr.fasta.rev.2.bt2
 - test/samples/small/test_chr.fasta.rpac
 - test/samples/small/test_chr.fasta.rsa
 - test/samples/small/test_chr.fasta.sa
+- test/samples/small/test_cov.svg
 - test/samples/small/testu.bam
 - test/samples/small/testu.bam.bai
-- test/test_basic.rb
+- test/svg
 - test/test_bio-samtools.rb
+- test/test_pileup.rb
+- test/test_sam.rb
 - test/test_vcf.rb
+- tutorial/tutorial.html
+- tutorial/tutorial.pdf
 homepage: http://github.com/helios/bioruby-samtools
 licenses:
 - MIT