dirseq 0.3.0 → 0.4.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA1:
-  metadata.gz: 48124cb9d1c64721dce10b66a4ae9c6d1773ae5c
-  data.tar.gz: 7f7ee356e059956cc204be699d67fab65fa6c41e
+SHA256:
+  metadata.gz: 9ff1307d262c875afd01391fccb60007735127dda4fa1303c17c246fbcc1262c
+  data.tar.gz: 0e040b3e9688aa214da2d2bffc1480b207f8fdc836c75d5bbd9de9199fb67394
 SHA512:
-  metadata.gz: 64263f1b13de9816f978c79961a188f4ab306ff1d7abd0f94d1bfdb6d9c4c807bec7b96b7651afbf1158b2dac38135b6970e273e018bb7f9fdf1fbc9cc736b5e
-  data.tar.gz: 6031c1e7952072c0c379a744bf067ae7f2aa9d7328dfec698ed4af84194ac407eb4b18948a3717ef7538f569cdd787a9f0ad4455025ac8148604834c7bb33988
+  metadata.gz: d6ef576145d863fae37da16dbc6e224572a9928bc5293fd471c7fa4c831e5f69ac8a9eeb272d5dd8b531f48c791476e4a514d63de3be4a17a5f48f21017d9a61
+  data.tar.gz: 49bae83cf0ad60ec57b91e51931cb380369c04921296552024620d9a837b77f4875f1b09e4fd5b69871c5e905423b64da0d974400f3953423f9e4eadacabc61d

data/Gemfile

@@ -11,8 +11,8 @@ gem "bio", "~>1.4", ">=1.4.2"
 group :development do
   #gem "shoulda", "~> 3.5"
   #gem "simplecov", "~> 0.8"
-  gem "jeweler", "~> 2.0"
-  gem "bundler", "~> 1.6"
+  gem "jeweler", "~> 2.3"
+  gem "bundler", "~> 2.1"
   gem "rspec", "~> 3.0"
   gem 'pry', '~>0.10'
 end

data/VERSION

@@ -1 +1 @@
-0.3.0
+0.4.0

data/bin/dirseq

@@ -24,7 +24,11 @@ options = {
   :count_type => COVERAGE_COUNT_TYPE,
   :forward_read_only => false,
   :accepted_feature_types => ['CDS'],
+<<<<<<< HEAD
   :comment_fields_to_print => ['ID'],
+=======
+  :sam_filter_flags => "-F0x100 -F0x800",
+>>>>>>> d6f450a... dirseq: Filter out non-primary and supplementary aligns.
 }
 o = OptionParser.new do |opts|
   opts.banner = "
@@ -57,6 +61,9 @@ o = OptionParser.new do |opts|
           "Print elements from the comments in the GFF file [default #{options[:comment_fields_to_print].join(',')}]") do |arg|
     options[:comment_fields_to_print] = arg
   end
+  opts.on("--sam-filter-flags", "Apply these samtools filters [default: #{options[:sam_filter_flags]}]") do |arg|
+    options[:sam_filter_flags] = arg
+  end
 
   # logger options
   opts.separator "\nVerbosity:\n\n"
@@ -151,7 +158,7 @@ end
 
 chromosome_file = Tempfile.new('bam_contigs')
 log.info "Listing contigs in sorted order .."
-cmd = "samtools idxstats #{bam_file.inspect} |cut -f1,2 >#{chromosome_file.path.inspect}"
+cmd = "samtools idxstats #{bam_file.inspect} |cut -f1,2 |grep -v '^*' >#{chromosome_file.path.inspect}"
 Bio::Commandeer.run(cmd, :log => log)
 
 log.info "Finding featureless contigs"
@@ -186,7 +193,7 @@ end
 
 covs_fwd = nil
 if options[:ignore_directions]
-  cmd1 = "bedtools coverage -b #{bam_file.inspect} -a #{gff_file.inspect} -hist"
+  cmd1 = "samtools view -u #{options[:sam_filter_flags]} #{bam_file.inspect} |bedtools coverage -b /dev/stdin -a #{gff_file.inspect} -hist"
   cov_lines_fwd = Bio::Commandeer.run cmd1, :log => log
   log.info "Parsing coverage profiles"
   covs_fwd = get_covs.call(cov_lines_fwd)
@@ -199,10 +206,10 @@ else
   if options[:count_type] == COUNT_COUNT_TYPE
     bedtools_type_flag = '-counts'
   end
-  cmdf1 = "samtools view -u #{read1_flag} #{bam_file.inspect} |bedtools coverage -sorted -g #{chromosome_file.path.inspect} -b /dev/stdin -a #{sorted_gff_file.inspect} -s #{bedtools_type_flag}"
-  cmdf2 = "samtools view -u #{read2_flag} #{bam_file.inspect} |bedtools coverage -sorted -g #{chromosome_file.path.inspect} -b /dev/stdin -a #{sorted_gff_file.inspect} -s #{bedtools_type_flag}"
-  cmdr1 = "samtools view -u #{read1_flag} #{bam_file.inspect} |bedtools coverage -sorted -g #{chromosome_file.path.inspect} -b /dev/stdin -a #{sorted_gff_file.inspect} -S #{bedtools_type_flag}"
-  cmdr2 = "samtools view -u #{read2_flag} #{bam_file.inspect} |bedtools coverage -sorted -g #{chromosome_file.path.inspect} -b /dev/stdin -a #{sorted_gff_file.inspect} -S #{bedtools_type_flag}"
+  cmdf1 = "samtools view #{options[:sam_filter_flags]} -u #{read1_flag} #{bam_file.inspect} |bedtools coverage -sorted -g #{chromosome_file.path.inspect} -b /dev/stdin -a #{sorted_gff_file.inspect} -s #{bedtools_type_flag}"
+  cmdf2 = "samtools view #{options[:sam_filter_flags]} -u #{read2_flag} #{bam_file.inspect} |bedtools coverage -sorted -g #{chromosome_file.path.inspect} -b /dev/stdin -a #{sorted_gff_file.inspect} -s #{bedtools_type_flag}"
+  cmdr1 = "samtools view #{options[:sam_filter_flags]} -u #{read1_flag} #{bam_file.inspect} |bedtools coverage -sorted -g #{chromosome_file.path.inspect} -b /dev/stdin -a #{sorted_gff_file.inspect} -S #{bedtools_type_flag}"
+  cmdr2 = "samtools view #{options[:sam_filter_flags]} -u #{read2_flag} #{bam_file.inspect} |bedtools coverage -sorted -g #{chromosome_file.path.inspect} -b /dev/stdin -a #{sorted_gff_file.inspect} -S #{bedtools_type_flag}"
 
   command_to_parsed = lambda do |cmds, name|
     covs_lines_initial = cmds.collect do |cmd|

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: dirseq
 version: !ruby/object:Gem::Version
-  version: 0.3.0
+  version: 0.4.0
 platform: ruby
 authors:
 - Ben J. Woodcroft
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2018-10-01 00:00:00.000000000 Z
+date: 2020-12-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-commandeer
@@ -42,50 +42,50 @@ dependencies:
   name: bio
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 1.4.2
     - - "~>"
       - !ruby/object:Gem::Version
         version: '1.4'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 1.4.2
     - - "~>"
       - !ruby/object:Gem::Version
         version: '1.4'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.2
 - !ruby/object:Gem::Dependency
   name: jeweler
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.0'
+        version: '2.3'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.0'
+        version: '2.3'
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.6'
+        version: '2.1'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.6'
+        version: '2.1'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
@@ -144,7 +144,7 @@ homepage: http://github.com/wwood/dirseq
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -159,9 +159,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.6.14.1
-signing_key: 
+rubygems_version: 3.1.2
+signing_key:
 specification_version: 4
 summary: FPKG calculator for metatranscriptomics
 test_files: []