bio-samtools 2.3.3 → 2.4.0

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 3741d4320545bb862be52f603e7ac6018eb1601d
+  metadata.gz: 90e15e76b4d1f9b079ab0f3fd6ecca9833a67e99
+  data.tar.gz: 251a8a0a110617d3894cfa6e287bc06bbd24ed89
 SHA512:
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+  data.tar.gz: 6eca1fbf0fcb285c2c4cf7a436eab0b087a697d1e858e8a4b491bd1ec13e2bc90fccec00c1c1d8c12c70b1bcb88ad4663271720c0b6de9fc5121c4b263cb4841

data/.travis.yml

@@ -1,7 +1,11 @@
 language: ruby
-before_install:
-  - sudo apt-get update
-  - sudo apt-get install zlib1g-dev libncurses5-dev libtinfo-dev
+sudo: false
+addons:
+  apt:
+    packages:
+    - zlib1g-dev
+    - libncurses5-dev
+    - libtinfo-dev   
 before_script:
   - cd ext
   - ruby mkrf_conf.rb
@@ -12,3 +16,4 @@ rvm:
   - 2.0.0
   - 2.1.0
   - 2.2.2
+  - 2.2.3

data/Gemfile

@@ -4,11 +4,12 @@ source "http://rubygems.org"
 #   gem "activesupport", ">= 2.3.5"
 gem "bio-svgenes", ">= 0.4.1"
 gem "bio", ">= 1.4.2"
+gem 'open_uri_redirections'
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
 group :development do
-  gem "shoulda", ">= 0"
+  gem "shoulda", "> 2.10"
   gem "shoulda-context"
   gem  "shoulda-matchers"
   gem "bundler", "> 1.0.21"

data/README.md

@@ -485,6 +485,18 @@ The latest I think is the easiest way, cause you are replicating the automatic p
 
 For testing just run `rake test`. Tests must be improved.
 
+####Travis integration###
+If you are integrating this library into another tool and testing it with travis, add the follwing in ```.travis.yml```:
+
+```yml
+addons:
+  apt:
+    packages:
+    - zlib1g-dev
+    - libncurses5-dev
+    - libtinfo-dev
+```
+
 ## Copyright
 
 Copyright (c) 2011 Raoul J.P. Bonnal. See LICENSE.txt for

data/VERSION

@@ -1 +1 @@
-2.3.4
+2.4.0

data/bin/bam_consensus.rb

@@ -63,7 +63,6 @@ fasta_db.load_fai_entries
 
 output = $stdout
 
-
 output = File.open(options[:output_file], "w") if options[:output_file] != "-"
 
 fasta_db.index.entries.each do | r |

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 2.3.3 ruby lib
+# stub: bio-samtools 2.4.0 ruby lib
 # stub: ext/mkrf_conf.rb
 
 Gem::Specification.new do |s|
   s.name = "bio-samtools"
-  s.version = "2.3.3"
+  s.version = "2.4.0"
 
   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 = "2015-06-19"
+  s.date = "2016-05-25"
   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 = "Ricardo.Ramirez-Gonzalez@tgac.ac.uk"
   s.executables = ["bam_consensus.rb"]
@@ -101,6 +101,9 @@ Gem::Specification.new do |s|
     "test/helper.rb",
     "test/sample.vcf",
     "test/samples/.gitignore",
+    "test/samples/LCI/NC_001988.ffn",
+    "test/samples/LCI/test.bam",
+    "test/samples/LCI/test.bam.bai",
     "test/samples/small/dupes.bam",
     "test/samples/small/dupes.sam",
     "test/samples/small/ids2.txt",
@@ -133,7 +136,6 @@ Gem::Specification.new do |s|
     "test/samples/small/test_chr.fasta.sa",
     "test/samples/small/test_cov.svg",
     "test/samples/small/testu.bam",
-    "test/samples/small/testu.bam.bai",
     "test/samples/small/testu.bed",
     "test/test_bio-samtools.rb",
     "test/test_pileup.rb",
@@ -145,7 +147,7 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://github.com/helios/bioruby-samtools"
   s.licenses = ["MIT"]
-  s.rubygems_version = "2.4.6"
+  s.rubygems_version = "2.2.2"
   s.summary = "Binder of samtools for ruby, on the top of FFI."
 
   if s.respond_to? :specification_version then
@@ -154,7 +156,8 @@ Gem::Specification.new do |s|
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<bio-svgenes>, [">= 0.4.1"])
       s.add_runtime_dependency(%q<bio>, [">= 1.4.2"])
-      s.add_development_dependency(%q<shoulda>, [">= 0"])
+      s.add_runtime_dependency(%q<open_uri_redirections>, [">= 0"])
+      s.add_development_dependency(%q<shoulda>, ["> 2.10"])
       s.add_development_dependency(%q<shoulda-context>, [">= 0"])
       s.add_development_dependency(%q<shoulda-matchers>, [">= 0"])
       s.add_development_dependency(%q<bundler>, ["> 1.0.21"])
@@ -167,7 +170,8 @@ Gem::Specification.new do |s|
     else
       s.add_dependency(%q<bio-svgenes>, [">= 0.4.1"])
       s.add_dependency(%q<bio>, [">= 1.4.2"])
-      s.add_dependency(%q<shoulda>, [">= 0"])
+      s.add_dependency(%q<open_uri_redirections>, [">= 0"])
+      s.add_dependency(%q<shoulda>, ["> 2.10"])
       s.add_dependency(%q<shoulda-context>, [">= 0"])
       s.add_dependency(%q<shoulda-matchers>, [">= 0"])
       s.add_dependency(%q<bundler>, ["> 1.0.21"])
@@ -181,7 +185,8 @@ Gem::Specification.new do |s|
   else
     s.add_dependency(%q<bio-svgenes>, [">= 0.4.1"])
     s.add_dependency(%q<bio>, [">= 1.4.2"])
-    s.add_dependency(%q<shoulda>, [">= 0"])
+    s.add_dependency(%q<open_uri_redirections>, [">= 0"])
+    s.add_dependency(%q<shoulda>, ["> 2.10"])
     s.add_dependency(%q<shoulda-context>, [">= 0"])
     s.add_dependency(%q<shoulda-matchers>, [">= 0"])
     s.add_dependency(%q<bundler>, ["> 1.0.21"])

data/ext/Rakefile

@@ -1,51 +1,50 @@
 require 'rbconfig'
 require 'open-uri'
+#require 'open_uri_redirections'
 require 'fileutils'
 include FileUtils::Verbose
 require 'rake/clean'
 
-URL = "http://sourceforge.net/projects/samtools/files/samtools/1.2/samtools-1.2.tar.bz2/download"
-URL2 = "https://github.com/samtools/bcftools/releases/download/1.2/bcftools-1.2.tar.bz2"
-
+URL = "https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2"
+URL_bcf = "https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2"
 task :download do
   open(URL) do |uri|
-    File.open("samtools-1.2.tar.bz2",'wb') do |fout|
+    File.open("samtools-1.3.1.tar.bz2",'wb') do |fout|
       fout.write(uri.read)
-    end #fout 
+    end #fout
   end #uri
 
-    open(URL2) do |uri|
-    File.open("bcftools-1.2.tar.bz2",'wb') do |fout|
+  open(URL_bcf) do |uri|
+    File.open("bcftools-1.3.1.tar.bz2",'wb') do |fout|
       fout.write(uri.read)
-    end #fout 
+    end #fout
   end #uri
+
 end
-    
+
 task :compile do
-  sh "tar xvfj samtools-1.2.tar.bz2"
-  sh "tar xvfj bcftools-1.2.tar.bz2"
-  cd("samtools-1.2") do
+  sh "tar xvfj samtools-1.3.1.tar.bz2"
+  cd("samtools-1.3.1") do
     sh "make"
-    cp("samtools", "/Users/ramirezr/Documents/public_code/bioruby-samtools/ext/../lib/bio/db/sam/external")
+    cp('samtools', "/Users/ramirezr/Documents/public_code/helios/bioruby-samtools/ext/../lib/bio/db/sam/external")
   end #cd
-  cd("bcftools-1.2") do
+
+  sh "tar xvfj bcftools-1.3.1.tar.bz2"
+  cd("bcftools-1.3.1") do
     sh "make"
-    cp('bcftools', "/Users/ramirezr/Documents/public_code/bioruby-samtools/ext/../lib/bio/db/sam/external")
-  end
+    cp('bcftools', "/Users/ramirezr/Documents/public_code/helios/bioruby-samtools/ext/../lib/bio/db/sam/external")
+  end #cd
 end
-  
+
 task :clean do
-  cd("samtools-1.2") do
+  cd("samtools-1.3.1") do
     sh "make clean"
   end
-  cd("bcftools-1.2") do
-    sh "make clean"
-  end
-  rm("samtools-1.2.tar.bz2")
-  rm_rf("samtools-1.2")
-  rm("bcftools-1.2.tar.bz2")
-  rm_rf("bcftools-1.2")
+  rm("samtools-1.3.1.tar.bz2")
+  rm_rf("samtools-1.3.1")
+  rm("bcftools-1.3.1.tar.bz2")
+  rm_rf("bcftools-1.3.1")
 end
 
 task :default => [:download, :compile, :clean]
-  
+

data/ext/mkrf_conf.rb

@@ -1,4 +1,4 @@
-#(c) Copyright 2011 Raoul Bonnal. All Rights Reserved. 
+#(c) Copyright 2011 Raoul Bonnal. All Rights Reserved.
 
 # create Rakefile for shared library compilation
 
@@ -12,64 +12,64 @@ version = File.open(File.join(path_external,"VERSION"),'r')
 Version = version.read
 version.close
 
-url = "http://sourceforge.net/projects/samtools/files/samtools/#{Version}/samtools-#{Version}.tar.bz2/download"
+#url = "http://sourceforge.net/projects/samtools/files/samtools/#{Version}/samtools-#{Version}.tar.bz2/download"
+url="https://github.com/samtools/samtools/releases/download/#{Version}/samtools-#{Version}.tar.bz2"
 SamToolsFile = "samtools-#{Version}.tar.bz2"
-url2 = "https://github.com/samtools/bcftools/releases/download/#{Version}/bcftools-#{Version}.tar.bz2"
-VcfToolsFile = "bcftools-#{Version}.tar.bz2"
+url_bcftools="https://github.com/samtools/bcftools/releases/download/#{Version}/bcftools-#{Version}.tar.bz2"
+BcfToolsFile = "bcftools-#{Version}.tar.bz2"
 
 File.open(File.join(path,"Rakefile"),"w") do |rakefile|
 rakefile.write <<-RAKE
 require 'rbconfig'
 require 'open-uri'
+#require 'open_uri_redirections'
 require 'fileutils'
 include FileUtils::Verbose
 require 'rake/clean'
 
 URL = "#{url}"
-URL2 = "#{url2}"
-
+URL_bcf = "#{url_bcftools}"
 task :download do
   open(URL) do |uri|
     File.open("#{SamToolsFile}",'wb') do |fout|
       fout.write(uri.read)
-    end #fout 
+    end #fout
   end #uri
 
-    open(URL2) do |uri|
-    File.open("#{VcfToolsFile}",'wb') do |fout|
+  open(URL_bcf) do |uri|
+    File.open("#{BcfToolsFile}",'wb') do |fout|
       fout.write(uri.read)
-    end #fout 
+    end #fout
   end #uri
+
 end
-    
+
 task :compile do
   sh "tar xvfj #{SamToolsFile}"
-  sh "tar xvfj #{VcfToolsFile}"
   cd("samtools-#{Version}") do
     sh "make"
-    cp("samtools", "#{path_external}")
+    cp('samtools', "#{path_external}")
   end #cd
+
+  sh "tar xvfj #{BcfToolsFile}"
   cd("bcftools-#{Version}") do
     sh "make"
     cp('bcftools', "#{path_external}")
-  end
+  end #cd
 end
-  
+
 task :clean do
   cd("samtools-#{Version}") do
     sh "make clean"
   end
-  cd("bcftools-#{Version}") do
-    sh "make clean"
-  end
   rm("#{SamToolsFile}")
   rm_rf("samtools-#{Version}")
-  rm("#{VcfToolsFile}")
+  rm("#{BcfToolsFile}")
   rm_rf("bcftools-#{Version}")
 end
 
 task :default => [:download, :compile, :clean]
-  
+
 RAKE
-  
-end
+
+end

data/lib/bio/db/sam.rb

@@ -1,7 +1,9 @@
-require 'open3'
 module Bio
   class DB
     class Sam
+      
+      class SamException < StandardError; end
+      
       attr_accessor :bam, :fasta, :samtools, :bcftools, :last_command
       attr_accessor :minumum_ratio_for_iup_consensus
       attr_reader :cached_regions
@@ -25,7 +27,7 @@ module Bio
 
         @last_command = nil
         raise ArgumentError, "Need Fasta and at least one BAM or SAM" if not @fasta or not @bam
-        raise IOError, "File not found #{files}" if not files_ok?
+        raise IOError, "File not found #{@files}" if not files_ok?
         @bams = [@bams] if @bams.instance_of? String
 
       end
@@ -65,7 +67,7 @@ module Bio
         region = String.new
         if opts[:chr] and opts[:start] and opts[:stop]
           has_e = self.has_entry? opts[:chr]
-          raise Exception.new(), "[view] The sequence #{opts[:chr]} is not in the bam file" unless self.has_entry? opts[:chr] 
+          raise SamException.new(), "[view] The sequence #{opts[:chr]} is not in the bam file" unless self.has_entry? opts[:chr] 
           region = "#{opts[:chr]}:#{opts[:start]}-#{opts[:stop]}"
           [:chr, :start, :stop].each {|o| opts.delete(o)}
         end
@@ -80,7 +82,7 @@ module Bio
         end
         command = String.new
         command = form_opt_string(@samtools, 'view', opts, [:b, :h, :H, :S, :u, '1', :x, :X, :c, :B]) 
-        commad = command + " '#{region}'" if region.size > 0
+        command = command + " '#{region}'" if region.size > 0
         @last_command = command
         type = (opts[:u] or opts[:b]) ? :binary : :text
         klass = (type == :binary) ? String : Bio::DB::Alignment
@@ -258,7 +260,7 @@ module Bio
         query = opts[:r].to_s
         query = opts[:r].to_region.to_s if opts[:r].respond_to?(:to_region)
         if not query.nil? and query.size > 0
-          raise Exception.new(), "The sequence #{query} is not in the bam file"  unless has_region? query 
+          raise SamException.new(), "The sequence #{query} is not in the bam file"  unless has_region? query 
         end
         opts[:r] = query
         
@@ -268,7 +270,7 @@ module Bio
         end
 
         command = form_opt_string(@samtools, "mpileup", opts, [:R, :B, :E, "6", :A, :g, :u, :I] )
-        puts stderr.read if $VERBOSE
+        puts "Running: #{command}" if $VERBOSE
         if opts[:u]
           command = command + " | #{@bcftools} view -cg -"
         end
@@ -285,13 +287,13 @@ module Bio
       #* stop - [INT] the stop position for the subsequence
       #* as_bio - boolean stating if the returned object should be a Bio::Sequence::NA object
       def fetch_reference(chr,start,stop, opts={:as_bio => false})
-        raise Exception.new(), "The sequence #{chr} is not in the bam file" unless has_entry? chr
+        raise SamException.new(), "The sequence #{chr} is not in the bam file" unless has_entry? chr
         seq = ""
         unless @fasta #We return a string of Ns if we don't know the reference. 
           seq = "n" * (stop-start) 
         else
-          command = "#{@samtools} faidx #{@fasta} '#{chr}:#{start}-#{stop}'"
-          puts stderr.read if $VERBOSE
+          command = "#{@samtools} faidx \"#{@fasta}\" '#{chr}:#{start}-#{stop}'"
+          puts "Running: #{command}" if $VERBOSE
           @last_command = command
           seq = ""
           yield_from_pipe(command, String, :text ) {|line| seq = seq + line unless line =~ /^>/}
@@ -313,19 +315,17 @@ module Bio
           opts={:as_bio => false}
           self.fetch_reference(:chr,:start,:stop,opts)
         else
-          command = "#{@samtools} faidx #{@fasta}"
+          command = "#{@samtools} faidx \"#{@fasta}\""
           @last_command = command
           system(command)
         end
       end
 
       #Index sorted alignment for fast random access. Index file <aln.bam>.bai will be created of no out_index is provided.
-      #* out_index - [STRING] name of index Depreciated. It will fail now as
-      #*                      samtools doesn't support it anymore. 
+      #* out_index - [STRING] name of index
       def index(opts={})
-        raise Exception.new "Index can't recieve parameters" if opts.size > 0 
-        command = "#{@samtools} index #{@bam}"
-        puts stderr.read if $VERBOSE
+        command = "#{@samtools} index \"#{@bam}\" #{opts[:out_index]}"
+        puts "Running: #{command}" if $VERBOSE
         @last_command = command
         system(command)
       end
@@ -333,15 +333,14 @@ module Bio
       #Fill in mate coordinates, ISIZE and mate related flags from a name-sorted alignment
       #* out_bam name of outfile
       #* r - remove unmapped reads and secondary alignments
-      #* p -  Disable FR proper pair check.
-      #* o - Add template cigar ct tag.
-      #* O FORMAT Write the final output as sam, bam, or cram.
       def fix_mates(opts={})
-        out_bam = opts[:out_bam]
-        opts.delete(:out_bam)
-        command = form_opt_string(@samtools, "fixmate", opts, [:r,:p,:c])
-        command << " #{out_bam}"
-        puts stderr.read if $VERBOSE
+        #opts.merge!({:out_index=>nil})
+        remove_reads = ""
+        if opts[:r]
+          remove_reads = "-r"
+        end
+        command = "#{@samtools} fixmate #{remove_reads} \"#{@bam}\" #{opts[:out_bam]}"
+        puts "Running: #{command}" if $VERBOSE
         @last_command = command
         system(command)
       end
@@ -351,7 +350,7 @@ module Bio
       #generate simple stats with regard to the number and pairing of reads mapped to a reference
       def flag_stats(opts={})
         command = form_opt_string(@samtools, "flagstat", opts, [])
-        puts stderr.read if $VERBOSE
+        puts "Running: #{command}" if $VERBOSE
         @last_command = command
         strings = []
         yield_from_pipe(command,String) {|line| strings << line.chomp}
@@ -366,7 +365,7 @@ module Bio
         stats = {}   
         command = form_opt_string(@samtools, "idxstats", {}, [])
         @last_command = command
-        puts stderr.read if $VERBOSE
+        puts "Running: #{command}" if $VERBOSE
         yield_from_pipe(command, String, :text, true, "#") do |line|
           info = line.chomp.split(/\t/)
           stats[ info[0] ] = {:length => info[1].to_i, :mapped_reads => info[2].to_i, :unmapped_reads => info[3].to_i }
@@ -447,7 +446,7 @@ module Bio
         command = "#{@samtools} merge #{options} #{out} #{bam_list}"
 
         @last_command = command
-        puts command puts stderr.read if $VERBOSE
+        puts "Running: #{command}" if $VERBOSE
         system(command)
 
       end
@@ -482,10 +481,9 @@ module Bio
       #* S - treat PE reads as SE in rmdup (force -s)
       #* out - [FILE] output bam
       def remove_duplicates(opts={})
-        raise Exception.new(), "Remove duplicates is unsuported in samtools 1.2. This function will come back onece rmdup is available again." 
         out = opts[:out]
         opts.delete(:out)
-        command = "#{form_opt_string(@samtools, "rmdup", opts, [:s, :S])} #{out} #{@bam}"
+        command = "#{form_opt_string(@samtools, "rmdup", opts, [:s, :S])} #{out} \"#{@bam}\""
         @last_command = command
         system(command)
       end
@@ -495,26 +493,28 @@ module Bio
       #Sort alignments by leftmost coordinates
       #* n - sort by read name
       #* f - use <out.prefix> as full file name instead of prefix
-      #* o - final output to stdout returns bio::db::alignment
+      #* o - final output to stdout returns bio::db::alignment depreciated (samtools-1.x saves to a file)
       #* l - [INT]  compression level, from 0 to 9 [-1]
       #* at - [INT] number of sorting and compression threads [1]
       #* m - [INT] max memory per thread; suffix K/M/G recognized [768M]
-      #* prefix - [STRING] prefix for output bamfile
+      #* prefix - [STRING] prefix for output bamfile (for legacy, becomes "o" to use in samtools-1.x)
       def sort(opts={})
         if !opts.has_key?(:prefix)
-          opts.merge!({:prefix => "sorted"})
+          opts.merge!({:o => "sorted"})
+        else
+          opts[:o] = opts[:prefix] += ".bam"
         end
-        prefix = opts[:prefix]
+       
         opts.delete(:prefix)
-        command = form_opt_string(@samtools, "sort", opts, [:n, :f, :o])
-        command = command + " " + prefix
+        command = form_opt_string(@samtools, "sort", opts, [:n, :f])
+        command = command + " " 
         @last_command = command
-        puts stderr.read if $VERBOSE
-        if opts[:o]
-          yield_from_pipe(command, Bio::DB::Alignment)
-        else
-          system(command)
-        end
+        puts "Running: #{command}" if $VERBOSE
+        #if opts[:o]
+        #  yield_from_pipe(command, Bio::DB::Alignment)
+        #else
+        system(command)
+        #end
       end
 
       #used to generate a text alignment viewer
@@ -535,7 +535,7 @@ module Bio
           opts.delete(:s)
         end
         command = "#{form_opt_string(@samtools, "tview", opts)}"
-        puts stderr.read if $VERBOSE
+        puts "Running: #{command}" if $VERBOSE
         @last_command = command
         system(command)
       end
@@ -546,11 +546,11 @@ module Bio
       def reheader(header_sam, opts={})
         if opts.has_key?(:out)
           out=opts[:out]
-          command = "#{@samtools} reheader #{header_sam} #{@bam} > #{out}"
+          command = "#{@samtools} reheader #{header_sam} \"#{@bam}\" > #{out}"
         else
-          command = "#{@samtools} reheader #{header_sam} #{@bam}"
+          command = "#{@samtools} reheader #{header_sam} \"#{@bam}\""
         end
-        puts stderr.read if $VERBOSE
+        puts "Running: #{command}" if $VERBOSE
         @last_command = command
         system(command)
       end
@@ -566,7 +566,7 @@ module Bio
       #* E - Extended BAQ calculation. This option trades specificity for sensitivity, though the effect is minor. 
       def calmd(opts={}, &block)
         command = form_opt_string(@samtools, "calmd",  opts, [:E, :e, :u, :b, :S, :r] )+ " " + @fasta
-        puts stderr.read if $VERBOSE
+        puts "Running: #{command}" if $VERBOSE
         @last_command = command
         type = :text 
         klass = Bio::DB::Alignment
@@ -587,7 +587,7 @@ module Bio
         end
 
         command = "#{form_opt_string(@samtools, "targetcut", opts, [] )}"
-        puts stderr.read if $VERBOSE
+        puts "Running: #{command}" if $VERBOSE
         @last_command = command
         system(command)
       end
@@ -601,7 +601,7 @@ module Bio
       #* Q - [INT] Minimum base quality to be used in het calling. [13] 
       def phase(opts={})
         command = "#{form_opt_string(@samtools, "phase", opts, [:A, :F] )}"
-        puts stderr.read if $VERBOSE
+        puts "Running: #{command}" if $VERBOSE
         @last_command = command
         system(command)
       end
@@ -646,7 +646,7 @@ module Bio
       #
       #TODO: It may be good to load partially the pileup
       def mpileup_cached (opts={})      
-        raise Exception.new(), "A region must be provided" unless opts[:r] or opts[:region]
+        raise SamException.new(), "A region must be provided" unless opts[:r] or opts[:region]
         @cached_regions = Hash.new unless @cached_regions
         region = opts[:r] ? opts[:r] : opts[:region]
         @cached_regions[region.to_s] = fetch_region(opts) unless @cached_regions[region.to_s]
@@ -675,11 +675,11 @@ module Bio
         #bam = opts[:bam]
         if opts.has_key?(:out)
           out=opts[:out]
-          command = "#{@samtools} bedcov #{bed} #{@bam} > #{out}"
+          command = "#{@samtools} bedcov \"#{bed}\" \"#{@bam}\" > \"#{out}\""
         else
-          command = "#{@samtools} bedcov #{bed} #{@bam}"
+          command = "#{@samtools} bedcov \"#{bed}\" \"#{@bam}\""
         end
-        #puts stderr.read if $VERBOSE
+         puts "Running: #{command}" if $VERBOSE
         #puts command
         @last_command = command
         system(command)
@@ -739,7 +739,7 @@ module Bio
           end
         end
         exit_status = wait_thr.value  # Process::Status object returned.
-        puts stderr.read if $VERBOSE 
+        puts "Running: #{command}" if $VERBOSE 
         stdin.close
         pipe.close
         stderr.close
@@ -753,7 +753,7 @@ module Bio
       # @param singles `flag` options [Array] the options in `opts` that are single options 
       def form_opt_string(prog, command, opts, singles=[])
         opts_string = commandify(opts, singles)
-        "#{prog} #{command} #{opts_string} #{@bam}"
+        "#{prog} #{command} #{opts_string} \"#{@bam}\""
       end
 
       # turns an opts hash into a string