class Bio::Sam::File
Class providing access to SAM files
Public Class Methods
new(filename)
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Creates an object for access to SAM file
# File lib/bio-sambamba/samfile.rb, line 11 def initialize(filename) @filename = filename check_file_existence filename end
Public Instance Methods
alignments()
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Returns an AlignmentIterator object for iterating over all alignments in the file
# File lib/bio-sambamba/samfile.rb, line 22 def alignments cmdline = ['sambamba', 'view', '--format', 'msgpack', '-S', @filename], Bio::Bam::AlignmentIterator.new(cmdline, reference_sequences) end
header()
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SAM header
# File lib/bio-sambamba/samfile.rb, line 17 def header @header ||= Bio::Bam::SamHeader.new(@filename, ['-S']) end
reference_sequences()
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# File lib/bio-sambamba/samfile.rb, line 27 def reference_sequences @reference_sequences ||= Oj.load(Bio::Command.query_command ['sambamba', 'view', '-I', '-S', @filename]) end
Private Instance Methods
reference_sequence_names()
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# File lib/bio-sambamba/samfile.rb, line 32 def reference_sequence_names @reference_sequence_names ||= reference_sequences.map {|ref| ref['name']} end