fastq-factory 0.1.13 → 0.1.14

data/VERSION

@@ -1 +1 @@
-0.1.13
+0.1.14

data/fastq-factory.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "fastq-factory"
-  s.version = "0.1.13"
+  s.version = "0.1.14"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Anthony Underwood"]
-  s.date = "2012-09-18"
+  s.date = "2012-10-11"
   s.description = "This tool can process fastq files, using fastq_quality_trimmer and quake to correct fastq files and then provide a quality asssessment of the data"
   s.email = "anthony.underwood@hpa.org.uk"
   s.executables = ["fastq-factory"]

data/lib/trim_and_correct.rb

@@ -7,9 +7,10 @@ def trim_and_correct_fastqs(sample_map, directory, forward_reads_suffix, forward
     #determine read length
     read_length = calculate_read_length("#{directory}/#{sample_file_prefix}#{forward_reads_suffix}.#{forward_reads_file_extension}")
     trim_point = (trim_point_fraction * read_length).to_i
-
-    `#{fastq_quality_trimmer_path} -i #{directory}/#{sample_file_prefix}#{forward_reads_suffix}.#{forward_reads_file_extension} -o #{directory}/#{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension} -t #{trim_quality_cutoff} -l #{trim_point} -Q #{quality_scale} -v`
-    `#{fastq_quality_trimmer_path} -i #{directory}/#{sample_file_prefix}#{reverse_reads_suffix}.#{reverse_reads_file_extension} -o #{directory}/#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension} -t #{trim_quality_cutoff} -l #{trim_point} -Q #{quality_scale} -v`
+    unless File.exists?("#{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension}")
+      `#{fastq_quality_trimmer_path} -i #{directory}/#{sample_file_prefix}#{forward_reads_suffix}.#{forward_reads_file_extension} -o #{directory}/#{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension} -t #{trim_quality_cutoff} -l #{trim_point} -Q #{quality_scale} -v`
+      `#{fastq_quality_trimmer_path} -i #{directory}/#{sample_file_prefix}#{reverse_reads_suffix}.#{reverse_reads_file_extension} -o #{directory}/#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension} -t #{trim_quality_cutoff} -l #{trim_point} -Q #{quality_scale} -v`
+    end
     `perl /tmp/fastq-remove-orphans.pl -1 #{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension} -2 #{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension}`
   end
 
@@ -33,7 +34,7 @@ def trim_and_correct_fastqs(sample_map, directory, forward_reads_suffix, forward
   # cleanup and rename files
 
   sample_map.each do |sample_file_prefix, sample_name|
-    File.delete("#{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension}") if File.exists?("#{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension}")
+    File.delete("#{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension}") if File.exists?("#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}")
     File.delete("#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension}") if File.exists?("#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension}")
     File.delete("orphaned_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension}") if File.exists?("orphaned_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension}")
     File.delete("orphaned_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension}") if File.exists?("orphaned_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension}")

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: fastq-factory
 version: !ruby/object:Gem::Version
-  version: 0.1.13
+  version: 0.1.14
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-09-18 00:00:00.000000000 Z
+date: 2012-10-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: trollop
@@ -165,7 +165,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -1919309219181792755
+      hash: 968500425624435397
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: