Class: Bio::Bam::Alignment

Inherits:
Object
  • Object
show all
Defined in:
lib/bio-sambamba/alignment.rb

Overview

Class representing an alignment record

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(json) ⇒ Alignment

Creates a new object from JSON output of sambamba tool



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# File 'lib/bio-sambamba/alignment.rb', line 8

def initialize(json)
  @json = json
end

Instance Attribute Details

#cigar_string ⇒ Object (readonly)

CIGAR string



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# File 'lib/bio-sambamba/alignment.rb', line 34

def cigar_string
  @cigar_string
end

#flag ⇒ Object (readonly)

Bitwise flag



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# File 'lib/bio-sambamba/alignment.rb', line 40

def flag
  @flag
end

#mapping_quality ⇒ Object (readonly)

Mapping quality



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# File 'lib/bio-sambamba/alignment.rb', line 31

def mapping_quality
  @mapping_quality
end

#mate_position ⇒ Object (readonly)

1-based leftmost position of the mate/next segment



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# File 'lib/bio-sambamba/alignment.rb', line 53

def mate_position
  @mate_position
end

#mate_reference ⇒ Object (readonly)

Reference sequence name of the mate/next segment



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# File 'lib/bio-sambamba/alignment.rb', line 50

def mate_reference
  @mate_reference
end

#position ⇒ Object (readonly)

1-based leftmost mapping position



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# File 'lib/bio-sambamba/alignment.rb', line 28

def position
  @position
end

#quality ⇒ Object (readonly)

Phred-scaled base quality, an integer array of the same length as the sequence



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# File 'lib/bio-sambamba/alignment.rb', line 44

def quality
  @quality
end

#read_name ⇒ Object (readonly)

Query template name



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# File 'lib/bio-sambamba/alignment.rb', line 25

def read_name
  @read_name
end

#reference ⇒ Object (readonly)

Name of reference sequence



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# File 'lib/bio-sambamba/alignment.rb', line 22

def reference
  @reference
end

#sequence ⇒ Object (readonly)

Segment sequence



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# File 'lib/bio-sambamba/alignment.rb', line 47

def sequence
  @sequence
end

#tags ⇒ Object (readonly)

Hash of record tags



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

def tags
  @tags
end

#template_length ⇒ Object (readonly)

Observed template length



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# File 'lib/bio-sambamba/alignment.rb', line 37

def template_length
  @template_length
end

Instance Method Details

#[](tag) ⇒ Object

Access a record tag



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# File 'lib/bio-sambamba/alignment.rb', line 13

def [](tag)
  raise 'tag length must be two' unless tag.length == 2
  @json['tags'][tag]
end

#failed_quality_control ⇒ Object

Not passing quality controls



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# File 'lib/bio-sambamba/alignment.rb', line 120

def failed_quality_control   
  (flag & 0x200) != 0
end

#is_duplicate ⇒ Object

PCR or optical duplicate



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# File 'lib/bio-sambamba/alignment.rb', line 125

def is_duplicate             
  (flag & 0x400) != 0
end

#is_first_of_pair ⇒ Object

The first segment in the template



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# File 'lib/bio-sambamba/alignment.rb', line 105

def is_first_of_pair         
  (flag & 0x40) != 0
end

#is_paired ⇒ Object

Template having multiple segments in sequencing



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# File 'lib/bio-sambamba/alignment.rb', line 75

def is_paired                
  (flag & 0x1) != 0
end

#is_reverse_strand ⇒ Object

Sequence being reverse complemented



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# File 'lib/bio-sambamba/alignment.rb', line 95

def is_reverse_strand        
  (flag & 0x10) != 0
end

#is_second_of_pair ⇒ Object

The last segment in the template



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# File 'lib/bio-sambamba/alignment.rb', line 110

def is_second_of_pair        
  (flag & 0x80) != 0
end

#is_secondary_alignment ⇒ Object

Secondary alignment



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# File 'lib/bio-sambamba/alignment.rb', line 115

def is_secondary_alignment   
  (flag & 0x100) != 0
end

#is_unmapped ⇒ Object

Segment unmapped



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# File 'lib/bio-sambamba/alignment.rb', line 85

def is_unmapped              
  (flag & 0x4) != 0
end

#mate_is_reverse_strand ⇒ Object

Sequence of the next segment in the template being reversed



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# File 'lib/bio-sambamba/alignment.rb', line 100

def mate_is_reverse_strand   
  (flag & 0x20) != 0
end

#mate_is_unmapped ⇒ Object

Next segment in the template unmapped



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# File 'lib/bio-sambamba/alignment.rb', line 90

def mate_is_unmapped         
  (flag & 0x8) != 0
end

#proper_pair ⇒ Object

Each segment properly aligned according to the aligner



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# File 'lib/bio-sambamba/alignment.rb', line 80

def proper_pair              
  (flag & 0x2) != 0
end