Class: Bio::Sam::File

Inherits:

Object

• Object
• Bio::Sam::File

Defined in:

lib/bio-sambamba/samfile.rb

Overview

Class providing access to SAM files

Instance Method Summary

• #alignments ⇒ Object

  Returns an AlignmentIterator object for iterating over all alignments in the file.

• #header ⇒ Object

  SAM header.

• #initialize(filename) ⇒ File constructor

  Creates an object for access to SAM file.

Constructor Details

#initialize(filename) ⇒ File

Creates an object for access to SAM file

# File 'lib/bio-sambamba/samfile.rb', line 9

def initialize(filename)
  @filename = filename
end

Instance Method Details

#alignments ⇒ Object

Returns an AlignmentIterator object for iterating over all alignments in the file

# File 'lib/bio-sambamba/samfile.rb', line 19

def alignments
  Bio::Bam::AlignmentIterator.new ['sambamba', '--format=json', '-S', @filename]
end

#header ⇒ Object

SAM header

# File 'lib/bio-sambamba/samfile.rb', line 14

def header
  @header ||= Bio::Bam::SamHeader.new(@filename, ['-S'])
end