fastq-factory 0.1.9 → 0.1.10

data/VERSION

@@ -1 +1 @@
-0.1.9
+0.1.10

data/fastq-factory.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = "fastq-factory"
-  s.version = "0.1.9"
+  s.version = "0.1.10"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Anthony Underwood"]

data/lib/trim_and_correct.rb

@@ -33,23 +33,23 @@ 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}")
-    File.delete("#{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}")
-    File.delete("orphaned_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_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.#{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}")
     if File.exists?("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}")
-      File.delete("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension}")
-      File.delete("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension}")
-      File.delete("error_model.paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.txt")
-      File.delete("error_model.paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.txt")
-      File.delete("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.stats.txt")
-      File.delete("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor_single.#{forward_reads_file_extension}")
-      File.delete("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.stats.txt")
-      File.delete("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor_single.#{forward_reads_file_extension}")
-      File.delete("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}")
-      File.delete("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}")
-      File.delete("orphaned_paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}")
-      File.delete("orphaned_paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}")
+      File.delete("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension}") if File.exists?("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension}")
+      File.delete("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension}") if File.exists?("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension}")
+      File.delete("error_model.paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.txt") if File.exists?("error_model.paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.txt")
+      File.delete("error_model.paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.txt") if File.exists?("error_model.paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.txt")
+      File.delete("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.stats.txt") if File.exists?("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.stats.txt")
+      File.delete("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor_single.#{forward_reads_file_extension}") if File.exists?("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor_single.#{forward_reads_file_extension}")
+      File.delete("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.stats.txt") if File.exists?("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.stats.txt")
+      File.delete("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor_single.#{forward_reads_file_extension}") if File.exists?("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor_single.#{forward_reads_file_extension}")
+      File.delete("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}") if File.exists?("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}")
+      File.delete("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}") if File.exists?("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}")
+      File.delete("orphaned_paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}") if File.exists?("orphaned_paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}")
+      File.delete("orphaned_paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}") if File.exists?("orphaned_paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}")
       File.rename("paired_paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}", "#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}")
       File.rename("paired_paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}", "#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}")
     else

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: fastq-factory
 version: !ruby/object:Gem::Version
-  version: 0.1.9
+  version: 0.1.10
   prerelease: 
 platform: ruby
 authors:
@@ -165,7 +165,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -2434858303487805098
+      hash: 4493640061867474095
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: