transrate 0.3.0 → 0.3.1

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data/README.md CHANGED
@@ -18,6 +18,10 @@
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  This software is being actively developed. Please be aware that there may be bugs. If you find any, please report them on the [issue tracker](https://github.com/Blahah/transrate/issues).
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+ ## Citation
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+
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+ Transrate is pre-publication academic software. If you use it, please cite the github repository and the DOI: [![DOI](https://zenodo.org/badge/3687/Blahah/transrate.png)](http://dx.doi.org/10.5281/zenodo.11037).
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+
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  ## Documentation
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  **transrate** is documented [on the website](http://hibberdlab.com/transrate).
data/bin/transrate CHANGED
@@ -211,7 +211,7 @@ opts.assembly.split(',').each do |assembly|
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  end
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  # write contig metrics to file for each contig
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- outfile = "#{opts.outfile}_contigs.csv"
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+ outfile = "#{opts.outfile}_#{File.basename(assembly)}_contigs.csv"
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  logger.info "Writing contig metrics for each contig to #{outfile}"
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  # have option to turn off, default on
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  first=true
@@ -10,7 +10,7 @@ module Transrate
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  module VERSION
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  MAJOR = 0
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  MINOR = 3
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- PATCH = 0
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+ PATCH = 1
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  BUILD = nil
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  STRING = [MAJOR, MINOR, PATCH, BUILD].compact.join('.')
metadata CHANGED
@@ -1,7 +1,7 @@
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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: 0.3.0
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+ version: 0.3.1
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  platform: ruby
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  authors:
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  - Richard Smith-Unna