transrate 0.3.1 → 1.0.0.alpha.1
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.
- checksums.yaml +4 -4
- data/.gitignore +7 -0
- data/README.md +7 -6
- data/bin/transrate +21 -9
- data/deps/deps.yaml +49 -14
- data/ext/transrate/transrate.c +200 -166
- data/lib/transrate.rb +2 -3
- data/lib/transrate/assembly.rb +0 -49
- data/lib/transrate/cmd.rb +4 -0
- data/lib/transrate/comparative_metrics.rb +16 -64
- data/lib/transrate/contig.rb +57 -18
- data/lib/transrate/express.rb +79 -0
- data/lib/transrate/read_metrics.rb +196 -185
- data/lib/transrate/samtools.rb +88 -16
- data/lib/transrate/snap.rb +123 -0
- data/lib/transrate/transrater.rb +16 -19
- data/lib/transrate/version.rb +4 -4
- data/test/data/bridging_reads.l.fastq +20 -0
- data/test/data/bridging_reads.r.fastq +20 -0
- data/test/test_bin.rb +50 -21
- data/test/test_comp_metrics.rb +3 -27
- data/test/test_contig.rb +8 -0
- data/test/test_inline.rb +1 -1
- data/test/test_read_metrics.rb +108 -19
- data/test/test_transrater.rb +5 -5
- data/transrate.gemspec +2 -5
- metadata +66 -129
- data/lib/transrate/bowtie2.rb +0 -75
- data/lib/transrate/dimension_reduce.rb +0 -18
- data/lib/transrate/metric.rb +0 -16
- data/test/test_bowtie.rb +0 -66
data/test/test_comp_metrics.rb
CHANGED
@@ -155,36 +155,12 @@ class TestCompMetrics < Test::Unit::TestCase
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@reference["LOC_Os01g11360.1"].seq = "A"*200
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@reference["LOC_Os01g44140.1"].seq = "A"*200
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+
assert_equal true, crb.target_is_prot, "target is prot"
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assert_equal false, crb.query_is_prot, "query is prot"
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# total_length of references should be 4400
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cov = @comp.coverage crb
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assert_equal 3600/
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-
end
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-
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-
should "calculate potential chimera count" do
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-
crb = @comp.reciprocal_best_blast
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-
# # T1 |---------|
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-
# # T2 |---------|
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# # Q1 |----------------------------| # chimera = true
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-
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crb.remove_hit("scaf_Os10g39590.1")
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crb.add_hit("scaf_Os10g39590.1", "LOC_Os03g60760.1",
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1, 150, 51, 100, 400, 60) # 0.25
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crb.add_hit("scaf_Os10g39590.1", "LOC_Os10g39590.1",
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200, 350, 51, 100, 400, 60) # 0.25
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-
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-
# # T3 |---------|
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-
# # T3 |---------|
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# # Q2 |----------------------------|
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# # chimera = true because the reference has the region 1-100 duplicated
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crb.remove_hit("scaf_Os12g21920.1")
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crb.add_hit("scaf_Os12g21920.1", "LOC_Os12g21920.1",
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1, 150, 55, 105, 400, 60) # 0.25
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crb.add_hit("scaf_Os12g21920.1", "LOC_Os12g21920.1",
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200, 350, 51, 100, 400, 60) # 0.25
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-
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@comp.chimeras crb
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assert_equal 2/11.0, @comp.p_chimeras
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assert_equal 3600/13200.0, cov, "reference coverage"
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end
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should "calculate overlap amount" do
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data/test/test_contig.rb
CHANGED
@@ -83,6 +83,14 @@ class TestContig < Test::Unit::TestCase
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assert_equal 7, contig.orf_length, "orf length"
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end
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should "get orf length from ATG to stop" do
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s = "AAATAGATAGATAGAATGAATCAACTAACTAAATAA"
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# seq = Bio::FastaFormat.new ">test\n#{s}\n>test_r\n#{s.reverse}\n"
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seq = Bio::FastaFormat.new ">test\n#{s}\n>test_r"
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contig = Transrate::Contig.new seq
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assert_equal 6, contig.orf_length, "orf length"
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end
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should "not fail on bases that aren't ACGTN" do
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seq = Bio::FastaFormat.new ">test\nATGCGTGTARATACGCGTAG"
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contig = Transrate::Contig.new seq
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data/test/test_inline.rb
CHANGED
data/test/test_read_metrics.rb
CHANGED
@@ -8,8 +8,8 @@ class TestReadMetrics < Test::Unit::TestCase
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setup do
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query = File.join(File.dirname(__FILE__), 'data',
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'sorghum_transcript.fa')
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assembly = Transrate::Assembly.new(query)
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@read_metrics = Transrate::ReadMetrics.new(assembly)
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@assembly = Transrate::Assembly.new(query)
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@read_metrics = Transrate::ReadMetrics.new(@assembly)
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end
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teardown do
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@@ -30,30 +30,87 @@ class TestReadMetrics < Test::Unit::TestCase
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Dir.chdir tmpdir do
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@read_metrics.run(left, right)
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stats = @read_metrics.read_stats
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assert @read_metrics.has_run
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assert_equal 223,
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assert_equal
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assert_equal
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'
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assert_equal
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assert_equal
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stats[:pc_good_mapping].round(2),
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assert @read_metrics.has_run, "has run"
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assert_equal 223, stats[:fragments], 'number of read pairs'
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assert_equal 217, stats[:fragments_mapped], 'number mapping'
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assert_equal 0.9731, stats[:p_fragments_mapped].round(4),
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'proportion mapping'
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assert_equal 129, stats[:good_mappings], 'good mapping'
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assert_equal 0.5785, stats[:p_good_mapping].round(4),
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'percent good mapping'
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assert_equal
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assert_equal
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assert_equal
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assert_equal 0
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-
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-
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assert_equal 88, stats[:bad_mappings], 'bad mapping'
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assert_equal 2, stats[:potential_bridges], 'bridges'
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assert_equal 2, stats[:contigs_uncovbase], 'uncovered base contig'
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assert_equal 0, stats[:contigs_uncovered], 'uncovered contig'
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assert_equal 0, stats[:contigs_lowcovered], 'lowcovered contig'
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assert_equal 2, stats[:contigs_good], 'good contigs'
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end
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end
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end
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should "get metrics for individual contigs" do
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left = File.join(File.dirname(__FILE__), 'data', '150uncovered.l.fq')
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right = File.join(File.dirname(__FILE__), 'data', '150uncovered.r.fq')
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Dir.mktmpdir do |tmpdir|
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Dir.chdir tmpdir do
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@read_metrics.run(left, right)
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contigs = []
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@assembly.each do |name, contig|
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contigs << contig
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end
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a = contigs[0].read_metrics
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b = contigs[1].read_metrics
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edit_a = a[:p_seq_true].round(5)
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edit_b = b[:p_seq_true].round(5)
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assert_equal 0.98342, edit_a, "edit distance 1"
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assert_equal 0.96645, edit_b, "edit distance 2"
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assert_equal 0.59524, a[:p_good].round(5), "proportion of good mappings"
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assert_equal 0.59398, b[:p_good].round(5), "proportion of good mappings"
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# uncovered bases
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unc_a = contigs[0].uncovered_bases
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unc_b = contigs[1].uncovered_bases
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assert_equal 11, unc_a, "uncovered bases"
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assert_equal 1, unc_b, "uncovered bases"
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prop_unc_a = a[:p_bases_covered]
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prop_unc_b = b[:p_bases_covered]
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assert_equal 0.98497, prop_unc_a.round(5), "proportion covered bases"
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assert_equal 0.99878, prop_unc_b.round(5), "proportion covered bases"
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end
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end
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end
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should "get segmentation probability for individual contigs" do
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left = File.join(File.dirname(__FILE__), 'data', '150uncovered.l.fq')
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right = File.join(File.dirname(__FILE__), 'data', '150uncovered.r.fq')
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Dir.mktmpdir do |tmpdir|
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Dir.chdir tmpdir do
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@read_metrics.run(left, right)
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contigs = []
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@assembly.each do |name, contig|
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contigs << contig
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end
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a = contigs[0].read_metrics
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b = contigs[1].read_metrics
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edit_a = a[:p_not_segmented].round(5)
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edit_b = b[:p_not_segmented].round(5)
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assert_equal 0.11444, edit_a, "probability not segmented 1"
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assert_equal 0.79629, edit_b, "probability not segmented 2"
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+
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end
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end
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end
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should "find read pairs that support scaffolding" do
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-
left = File.join(File.dirname(__FILE__),
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left = File.join(File.dirname(__FILE__),
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'data', 'bridging_reads.l.fastq')
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right = File.join(File.dirname(__FILE__),
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'data',
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'bridging_reads.r.fastq')
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'data', 'bridging_reads.r.fastq')
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Dir.mktmpdir do |tmpdir|
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Dir.chdir tmpdir do
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@read_metrics.run(left, right)
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@@ -63,6 +120,38 @@ class TestReadMetrics < Test::Unit::TestCase
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end
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end
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should "run on a list of input fastq files" do
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left = []
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right = []
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left << File.join(File.dirname(__FILE__), 'data', '150uncovered.l.fq')
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right << File.join(File.dirname(__FILE__), 'data', '150uncovered.r.fq')
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left << File.join(File.dirname(__FILE__),
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'data', 'bridging_reads.l.fastq')
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right << File.join(File.dirname(__FILE__),
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'data', 'bridging_reads.r.fastq')
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Dir.mktmpdir do |tmpdir|
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Dir.chdir tmpdir do
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@read_metrics.run(left.join(","), right.join(","))
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stats = @read_metrics.read_stats
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assert_equal 233, stats[:fragments], 'number of read pairs'
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end
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end
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end
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should "calculate read length by scanning fastq files" do
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left = []
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right = []
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left << File.join(File.dirname(__FILE__), 'data', '150uncovered.l.fq')
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right << File.join(File.dirname(__FILE__), 'data', '150uncovered.r.fq')
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left << File.join(File.dirname(__FILE__),
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'data', 'bridging_reads.l.fastq')
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right << File.join(File.dirname(__FILE__),
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'data', 'bridging_reads.r.fastq')
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@read_metrics.get_read_length(left.join(","), right.join(","))
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assert_equal 100, @read_metrics.read_length
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end
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+
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end
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end
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data/test/test_transrater.rb
CHANGED
@@ -8,7 +8,7 @@ class TestTransrater < Test::Unit::TestCase
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context "transrater" do
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setup do
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@assembly = File.join(File.dirname(__FILE__), 'data', '
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@assembly = File.join(File.dirname(__FILE__), 'data', 'sorghum_transcript.fa')
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@reference = File.join(File.dirname(__FILE__), 'data', 'Os.protein.2.fa')
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@rater = Transrate::Transrater.new(@assembly, @reference)
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@left = File.join(File.dirname(__FILE__), 'data', '150uncovered.l.fq')
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@@ -39,8 +39,8 @@ class TestTransrater < Test::Unit::TestCase
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Dir.mktmpdir do |tmpdir|
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Dir.chdir tmpdir do
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stats = @rater.assembly_metrics
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assert_equal
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assert_equal
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assert_equal 823, stats.n50
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assert_equal 1555, stats.n_bases
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end
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end
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end
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@@ -49,7 +49,7 @@ class TestTransrater < Test::Unit::TestCase
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Dir.mktmpdir do |tmpdir|
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Dir.chdir tmpdir do
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stats = @rater.read_metrics(@left, @right)
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-
assert_equal 223, stats.read_stats[:
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assert_equal 223, stats.read_stats[:fragments]
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end
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end
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end
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@@ -59,7 +59,7 @@ class TestTransrater < Test::Unit::TestCase
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Dir.chdir tmpdir do
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all = @rater.all_metrics(@left, @right)
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score = @rater.assembly_score
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assert_equal 0.
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assert_equal 0.40755, score.round(5) # regression test
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end
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end
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end
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data/transrate.gemspec
CHANGED
@@ -19,12 +19,9 @@ Gem::Specification.new do |gem|
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gem.add_dependency 'yell', '~> 2.0', '>= 2.0.4'
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gem.add_dependency 'trollop', '~> 2.0'
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gem.add_dependency 'bindeps', '~> 0.
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gem.add_dependency 'which', '~> 0.0', '>= 0.0.2'
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gem.add_dependency 'bindeps', '~> 0.1', '>= 0.1.0'
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gem.add_dependency 'bio', '~> 1.4', '>= 1.4.3'
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gem.add_dependency '
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gem.add_dependency 'crb-blast', '~> 0.4', '>= 0.4.0'
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gem.add_dependency 'bettersam', '~> 0.0', '>= 0.0.3'
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gem.add_dependency 'crb-blast', '~> 0.4', '>= 0.4.2'
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gem.add_dependency 'ruby-prof', '~> 0.15', '>= 0.15.1'
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gem.add_development_dependency 'rake', '~> 10.3', '>= 10.3.2'
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metadata
CHANGED
@@ -1,7 +1,7 @@
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1
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--- !ruby/object:Gem::Specification
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name: transrate
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version: !ruby/object:Gem::Version
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-
version: 0.
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version: 1.0.0.alpha.1
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platform: ruby
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authors:
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- Richard Smith-Unna
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@@ -9,318 +9,258 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2014-
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+
date: 2014-10-15 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: yell
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requirement: !ruby/object:Gem::Requirement
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requirements:
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-
- - ~>
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+
- - "~>"
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- !ruby/object:Gem::Version
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version: '2.0'
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-
- -
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- - ">="
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- !ruby/object:Gem::Version
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version: 2.0.4
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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-
- - ~>
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+
- - "~>"
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- !ruby/object:Gem::Version
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version: '2.0'
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-
- -
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+
- - ">="
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- !ruby/object:Gem::Version
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version: 2.0.4
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- !ruby/object:Gem::Dependency
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name: trollop
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requirement: !ruby/object:Gem::Requirement
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requirements:
|
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-
- - ~>
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+
- - "~>"
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- !ruby/object:Gem::Version
|
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version: '2.0'
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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45
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-
- - ~>
|
45
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- - "~>"
|
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|
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|
47
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|
version: '2.0'
|
48
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|
49
49
|
name: bindeps
|
50
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requirement: !ruby/object:Gem::Requirement
|
51
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|
requirements:
|
52
|
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- - ~>
|
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|
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- - "~>"
|
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|
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|
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version: '0.
|
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|
-
- -
|
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|
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version: '0.1'
|
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- - ">="
|
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|
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|
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version: 0.0
|
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version: 0.1.0
|
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type: :runtime
|
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prerelease: false
|
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version_requirements: !ruby/object:Gem::Requirement
|
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requirements:
|
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|
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|
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version: '0.
|
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|
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- -
|
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|
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version: '0.1'
|
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- - ">="
|
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|
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version: 0.0
|
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|
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name: which
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version: '0.0'
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version: 0.0.2
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type: :runtime
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
|
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version: '0.0'
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version: 0.0.2
|
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|
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version: 0.1.0
|
88
68
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- !ruby/object:Gem::Dependency
|
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69
|
name: bio
|
90
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|
requirement: !ruby/object:Gem::Requirement
|
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requirements:
|
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|
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version: '1.4'
|
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|
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- -
|
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- - ">="
|
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|
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version: 1.4.3
|
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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version: '1.4'
|
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- -
|
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- - ">="
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version: 1.4.3
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name: bio-samtools
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requirement: !ruby/object:Gem::Requirement
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requirements:
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version: '2.0'
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version: 2.0.5
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type: :runtime
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requirements:
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version: '2.0'
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version: 2.0.5
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name: crb-blast
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version: '0.4'
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version: 0.4.
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version: 0.4.2
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|
type: :runtime
|
139
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prerelease: false
|
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
|
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version: '0.4'
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- -
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version: 0.4.0
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name: bettersam
|
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requirement: !ruby/object:Gem::Requirement
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requirements:
|
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version: '0.0'
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version: 0.
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
|
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version: '0.0'
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version: 0.0.3
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version: 0.4.2
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|
name: ruby-prof
|
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|
requirement: !ruby/object:Gem::Requirement
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requirements:
|
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version: '0.15'
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prerelease: false
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requirements:
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version: '0.15'
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version: 0.15.1
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name: rake
|
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requirements:
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version: '10.3'
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version: 10.3.2
|
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|
type: :development
|
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|
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requirements:
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|
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|
version: '10.3'
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|
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version: 10.3.2
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name: rake-compiler
|
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requirement: !ruby/object:Gem::Requirement
|
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|
requirements:
|
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version: '0.9'
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|
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|
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|
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version: 0.9.2
|
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|
type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
|
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|
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|
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|
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version: '0.9'
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|
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- -
|
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|
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|
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|
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|
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|
version: 0.9.2
|
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|
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|
name: turn
|
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|
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|
requirements:
|
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|
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|
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|
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- - "~>"
|
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|
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|
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|
version: '0.9'
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|
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- -
|
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|
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|
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|
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|
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|
version: 0.9.7
|
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|
type: :development
|
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|
prerelease: false
|
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|
version_requirements: !ruby/object:Gem::Requirement
|
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|
requirements:
|
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- - ~>
|
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|
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- - "~>"
|
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|
- !ruby/object:Gem::Version
|
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|
version: '0.9'
|
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|
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- -
|
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|
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- - ">="
|
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|
- !ruby/object:Gem::Version
|
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|
version: 0.9.7
|
248
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|
- !ruby/object:Gem::Dependency
|
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|
name: minitest
|
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|
requirement: !ruby/object:Gem::Requirement
|
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requirements:
|
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|
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|
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|
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|
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|
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|
version: '4'
|
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- -
|
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|
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- - ">="
|
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|
- !ruby/object:Gem::Version
|
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|
version: 4.7.5
|
258
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|
type: :development
|
259
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|
prerelease: false
|
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|
version_requirements: !ruby/object:Gem::Requirement
|
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|
requirements:
|
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|
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|
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- - "~>"
|
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|
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|
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|
version: '4'
|
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- -
|
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|
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- - ">="
|
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|
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|
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|
version: 4.7.5
|
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|
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|
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|
name: simplecov
|
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|
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|
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|
requirements:
|
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|
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|
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- - "~>"
|
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|
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|
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|
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|
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- -
|
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|
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|
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|
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|
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|
version: 0.8.2
|
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|
type: :development
|
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|
prerelease: false
|
280
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|
version_requirements: !ruby/object:Gem::Requirement
|
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|
requirements:
|
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|
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- - ~>
|
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|
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- - "~>"
|
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|
- !ruby/object:Gem::Version
|
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|
version: '0.8'
|
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|
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- -
|
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|
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|
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|
- !ruby/object:Gem::Version
|
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|
version: 0.8.2
|
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|
- !ruby/object:Gem::Dependency
|
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|
name: shoulda-context
|
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|
requirement: !ruby/object:Gem::Requirement
|
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|
requirements:
|
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|
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- - ~>
|
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|
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- - "~>"
|
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|
- !ruby/object:Gem::Version
|
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|
version: '1.2'
|
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|
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- -
|
235
|
+
- - ">="
|
296
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|
- !ruby/object:Gem::Version
|
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|
version: 1.2.1
|
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|
type: :development
|
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239
|
prerelease: false
|
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|
version_requirements: !ruby/object:Gem::Requirement
|
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|
requirements:
|
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|
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- - ~>
|
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|
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- - "~>"
|
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243
|
- !ruby/object:Gem::Version
|
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244
|
version: '1.2'
|
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|
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- -
|
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|
+
- - ">="
|
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|
- !ruby/object:Gem::Version
|
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|
version: 1.2.1
|
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|
- !ruby/object:Gem::Dependency
|
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|
name: coveralls
|
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|
requirement: !ruby/object:Gem::Requirement
|
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|
requirements:
|
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- - ~>
|
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|
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|
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|
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|
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|
version: '0.7'
|
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|
type: :development
|
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|
prerelease: false
|
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|
version_requirements: !ruby/object:Gem::Requirement
|
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|
requirements:
|
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|
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- - ~>
|
259
|
+
- - "~>"
|
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|
- !ruby/object:Gem::Version
|
321
261
|
version: '0.7'
|
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|
-
description:
|
323
|
-
assemblies
|
262
|
+
description: " a library and command-line tool for quality assessment of de-novo transcriptome
|
263
|
+
assemblies "
|
324
264
|
email: rds45@cam.ac.uk
|
325
265
|
executables:
|
326
266
|
- transrate
|
@@ -328,8 +268,8 @@ extensions:
|
|
328
268
|
- ext/transrate/extconf.rb
|
329
269
|
extra_rdoc_files: []
|
330
270
|
files:
|
331
|
-
- .gitignore
|
332
|
-
- .travis.yml
|
271
|
+
- ".gitignore"
|
272
|
+
- ".travis.yml"
|
333
273
|
- Gemfile
|
334
274
|
- LICENSE
|
335
275
|
- README.md
|
@@ -341,15 +281,14 @@ files:
|
|
341
281
|
- ext/transrate/transrate.c
|
342
282
|
- lib/transrate.rb
|
343
283
|
- lib/transrate/assembly.rb
|
344
|
-
- lib/transrate/bowtie2.rb
|
345
284
|
- lib/transrate/cmd.rb
|
346
285
|
- lib/transrate/comparative_metrics.rb
|
347
286
|
- lib/transrate/contig.rb
|
348
287
|
- lib/transrate/contig_metrics.rb
|
349
|
-
- lib/transrate/
|
350
|
-
- lib/transrate/metric.rb
|
288
|
+
- lib/transrate/express.rb
|
351
289
|
- lib/transrate/read_metrics.rb
|
352
290
|
- lib/transrate/samtools.rb
|
291
|
+
- lib/transrate/snap.rb
|
353
292
|
- lib/transrate/transrater.rb
|
354
293
|
- lib/transrate/version.rb
|
355
294
|
- lib/transrate/writer.rb
|
@@ -365,7 +304,6 @@ files:
|
|
365
304
|
- test/data/tiny.sam
|
366
305
|
- test/helper.rb
|
367
306
|
- test/test_bin.rb
|
368
|
-
- test/test_bowtie.rb
|
369
307
|
- test/test_cmd.rb
|
370
308
|
- test/test_comp_metrics.rb
|
371
309
|
- test/test_contig.rb
|
@@ -387,19 +325,18 @@ require_paths:
|
|
387
325
|
- ext
|
388
326
|
required_ruby_version: !ruby/object:Gem::Requirement
|
389
327
|
requirements:
|
390
|
-
- -
|
328
|
+
- - ">="
|
391
329
|
- !ruby/object:Gem::Version
|
392
330
|
version: '0'
|
393
331
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
394
332
|
requirements:
|
395
|
-
- -
|
333
|
+
- - ">"
|
396
334
|
- !ruby/object:Gem::Version
|
397
|
-
version:
|
335
|
+
version: 1.3.1
|
398
336
|
requirements: []
|
399
337
|
rubyforge_project:
|
400
|
-
rubygems_version: 2.
|
338
|
+
rubygems_version: 2.2.2
|
401
339
|
signing_key:
|
402
340
|
specification_version: 4
|
403
341
|
summary: quality assessment of de-novo transcriptome assemblies
|
404
342
|
test_files: []
|
405
|
-
has_rdoc:
|