bio-samtools 2.0.5 → 2.1.0

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Files changed (18) hide show
  1. checksums.yaml +4 -4
  2. data/VERSION +1 -1
  3. data/bio-samtools.gemspec +5 -7
  4. data/lib/bio/db/fastadb.rb +21 -12
  5. data/lib/bio/db/pileup.rb +29 -21
  6. data/lib/bio/db/sam.rb +37 -25
  7. data/test/sample.vcf +24 -0
  8. data/test/samples/small/testu.bed +2 -0
  9. data/test/test_pileup.rb +8 -2
  10. data/test/test_sam.rb +34 -14
  11. data/tutorial/tutorial.html +434 -150
  12. data/tutorial/tutorial.md +289 -309
  13. data/tutorial/tutorial.pdf +0 -0
  14. metadata +4 -6
  15. data/lib/bio/.DS_Store +0 -0
  16. data/tutorial/images/out.svg +0 -75
  17. data/tutorial/images/out2.svg +0 -45
  18. data/tutorial/images/out3.svg +0 -275
data/tutorial/tutorial.pdf CHANGED
Binary file
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: bio-samtools
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  version: !ruby/object:Gem::Version
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- version: 2.0.5
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+ version: 2.1.0
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  platform: ruby
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  authors:
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  - Ricardo Ramirez-Gonzalez
@@ -10,7 +10,7 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2014-05-31 00:00:00.000000000 Z
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+ date: 2014-09-03 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: bio-svgenes
@@ -256,7 +256,6 @@ files:
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  - ext/Rakefile
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  - ext/mkrf_conf.rb
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  - lib/bio-samtools.rb
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- - lib/bio/.DS_Store
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  - lib/bio/BIOExtensions.rb
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  - lib/bio/db/alignment.rb
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  - lib/bio/db/fastadb.rb
@@ -268,6 +267,7 @@ files:
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  - lib/bio/db/vcf.rb
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  - test/.gitignore
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  - test/helper.rb
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+ - test/sample.vcf
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  - test/samples/.gitignore
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  - test/samples/small/dupes.bam
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  - test/samples/small/dupes.sam
@@ -302,13 +302,11 @@ files:
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  - test/samples/small/test_cov.svg
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  - test/samples/small/testu.bam
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  - test/samples/small/testu.bam.bai
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+ - test/samples/small/testu.bed
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  - test/test_bio-samtools.rb
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  - test/test_pileup.rb
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  - test/test_sam.rb
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  - test/test_vcf.rb
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- - tutorial/images/out.svg
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- - tutorial/images/out2.svg
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- - tutorial/images/out3.svg
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  - tutorial/tutorial.html
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  - tutorial/tutorial.md
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  - tutorial/tutorial.pdf
data/lib/bio/.DS_Store DELETED
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data/tutorial/images/out.svg DELETED
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