bio-samtools 2.0.3 → 2.0.4

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: b79cd69ebe66928a53ca9d45f122b1e9538e8c51
+  metadata.gz: f871729e2c0ab8ac18082913e4d6897620e87c32
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data/VERSION

@@ -1 +1 @@
-2.0.3
+2.0.4

data/bio-samtools.gemspec

@@ -2,17 +2,17 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: bio-samtools 2.0.3 ruby lib
+# stub: bio-samtools 2.0.4 ruby lib
 # stub: ext/mkrf_conf.rb
 
 Gem::Specification.new do |s|
   s.name = "bio-samtools"
-  s.version = "2.0.3"
+  s.version = "2.0.4"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib"]
   s.authors = ["Ricardo Ramirez-Gonzalez", "Dan MacLean", "Raoul J.P. Bonnal"]
-  s.date = "2014-04-18"
+  s.date = "2014-04-28"
   s.description = "Binder of samtools for ruby, on the top of FFI. \n\n  This project was born from the need to add support of BAM files to \n  the gee_fu genome browser (http://github.com/danmaclean/gee_fu)."
   s.email = "ilpuccio.febo@gmail.com"
   s.extensions = ["ext/mkrf_conf.rb"]

data/lib/bio-samtools.rb

@@ -1,3 +1,4 @@
+require 'open3'
 require 'bio-svgenes'
 require 'bio'
 require 'bio/db/sam'
@@ -5,5 +6,4 @@ require 'bio/db/pileup'
 require 'bio/db/vcf'
 require 'bio/db/alignment'
 require 'bio/db/fastadb'
-require 'open3'
 require 'bio/BIOExtensions'

data/lib/bio/db/alignment.rb

@@ -18,11 +18,12 @@ module Bio
     class Alignment
       attr_accessor :qname, :flag, :rname,:pos,:mapq,:cigar, :mrnm, :mpos, :isize, :seq, :qual, :tags, :al, :samstr, :calend, :qlen
 
-      attr_accessor :is_paired, :is_mapped, :query_unmapped, :mate_unmapped, :query_strand, :mate_strand, :first_in_pair,:second_in_pair, :primary, :failed_quality, :is_duplicate
+      attr_accessor :sam_string, :is_paired, :is_mapped, :query_unmapped, :mate_unmapped, :query_strand, :mate_strand, :first_in_pair,:second_in_pair, :primary, :failed_quality, :is_duplicate
       
       #parses the SAM string into its constituents and set its attributes
       def initialize(sam_string)
         s = sam_string.chomp.split("\t")
+        @sam_string = sam_string
         @qname = s[0]
         @flag  = s[1].to_i
         @rname = s[2]

data/lib/bio/db/fastadb.rb

@@ -214,7 +214,7 @@ module Bio::DB::Fasta
       query = region.to_s
       query = region.to_region.to_s if region.respond_to?(:to_region) 
       command = "#{@samtools} faidx #{@fasta_path} '#{query}'"
-      puts command
+      puts command  if $VERBOSE
       @last_command = command
       seq = ""
       yield_from_pipe(command, String, :text ) {|line| seq = seq + line unless line =~ /^>/}

data/lib/bio/db/sam.rb

@@ -356,6 +356,26 @@ module Bio
       end
 
       alias_method :idxstats, :index_stats
+      
+      #Retrive a hash with all the regions, with the region id as index or runs the function on each region
+      def each_region
+        stats=index_stats unless @stats
+        if @regions 
+          return @regionss unless block_given? 
+        else
+          @regions = Hash.new
+        end
+        stats.each do |k,v|
+          reg = Bio::DB::Fasta::Region
+          reg.entry = k
+          reg.start = 1
+          reg.end = v[:length]
+          reg.orientation = :forward
+          
+          yield reg if block_given?
+        end
+        @regions
+      end
 
       #Merge multiple sorted alignments
       #* n - sort by read names

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-samtools
 version: !ruby/object:Gem::Version
-  version: 2.0.3
+  version: 2.0.4
 platform: ruby
 authors:
 - Ricardo Ramirez-Gonzalez
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-04-18 00:00:00.000000000 Z
+date: 2014-04-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-svgenes