lederhosen 1.6.1 → 1.6.2

data/lederhosen.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = "lederhosen"
-  s.version = "1.6.1"
+  s.version = "1.6.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Austin G. Davis-Richardson"]

data/lib/lederhosen/tasks/trim.rb

@@ -40,7 +40,9 @@ module Lederhosen
         ohno 'glob matches no reads'
       end
 
-      raw_reads.map do |prefix, files|
+      pbar = ProgressBar.new 'trimming', raw_reads.size
+
+      raw_reads.each do |prefix, files|
 
         # get an output handle
         out = File.join(out_dir, "#{File.basename(prefix)}.fasta")
@@ -62,8 +64,11 @@ module Lederhosen
           end
         end # File.open
 
+        pbar.inc
       end
 
+      pbar.finish
+
     end
 
     no_tasks do

data/lib/lederhosen/version.rb

@@ -3,7 +3,7 @@ module Lederhosen
     MAJOR = 1
     MINOR = 6
     CODENAME = 'Sauerkraut' # changes for minor versions
-    PATCH = 1
+    PATCH = 2
 
     STRING = [MAJOR, MINOR, PATCH].join('.')
   end

data/readme.md

@@ -48,6 +48,8 @@ You can also trim interleaved, paired-end FASTQ files:
 
     lederhosen trim --reads_dir=reads/*.fastq --out_dir=trimmed/ read-type='fastq'
 
+(WARNING: by default, Lederhosen trims off the first 11 nucleotides. This was to remain backwards-compatibility with an experiment-specific version. To disable use `--pretrim 0`)
+
 ### Create Database
 
 Create UDB database required by usearch from TaxCollector

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: lederhosen
 version: !ruby/object:Gem::Version
-  version: 1.6.1
+  version: 1.6.2
   prerelease: 
 platform: ruby
 authors:
@@ -162,7 +162,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -3171751151013656560
+      hash: -3699960078851600472
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: