Class: HTS::Bam::Flag

Inherits:
Object
  • Object
show all
Defined in:
lib/hts/bam/flag.rb

Overview

SAM flags

Constant Summary collapse

PAIRED = 
1
PROPER_PAIR = 
2
UNMAPPED = 
4
MATE_UNMAPPED = 
8
REVERSE = 
16
MATE_REVERSE = 
32
READ1 = 
64
READ2 = 
128
SECONDARY = 
256
QCFAIL = 
512
DUPLICATE = 
1024
SUPPLEMENTARY = 
2048
TABLE = 
{ paired?: PAIRED, proper_pair?: PROPER_PAIR, unmapped?: UNMAPPED,
mate_unmapped?: MATE_UNMAPPED, reverse?: REVERSE,
mate_reverse?: MATE_REVERSE, read1?: READ1, read2?: READ2,
secondary?: SECONDARY, qcfail?: QCFAIL, duplicate?: DUPLICATE,
supplementary?: SUPPLEMENTARY }.freeze

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(flag_value) ⇒ Flag

Returns a new instance of Flag.

Raises:

  • (TypeError) 


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# File 'lib/hts/bam/flag.rb', line 10

def initialize(flag_value)
  raise TypeError unless flag_value.is_a? Integer

  @value = flag_value
end

Instance Attribute Details

#value ⇒ Object

Returns the value of attribute value.



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# File 'lib/hts/bam/flag.rb', line 16

def value
  @value
end

Instance Method Details

#&(other) ⇒ Object 



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# File 'lib/hts/bam/flag.rb', line 64

def &(other)
  self.class.new(@value & other.to_i)
end

#<<(f) ⇒ Object 



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# File 'lib/hts/bam/flag.rb', line 82

def <<(f)
  self.class.new(@value << f.to_i)
end

#>>(other) ⇒ Object 



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# File 'lib/hts/bam/flag.rb', line 86

def >>(other)
  self.class.new(@value >> other.to_i)
end

#^(other) ⇒ Object 



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# File 'lib/hts/bam/flag.rb', line 72

def ^(other)
  self.class.new(@value ^ other.to_i)
end

#duplicate? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/hts/bam/flag.rb', line 57

generate :duplicate?

#has_flag?(f) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/hts/bam/flag.rb', line 60

def has_flag?(f)
  (@value & f) != 0
end

#mate_reverse? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/hts/bam/flag.rb', line 52

generate :mate_reverse?

#mate_unmapped? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/hts/bam/flag.rb', line 50

generate :mate_unmapped?

#paired? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/hts/bam/flag.rb', line 47

generate :paired?

#proper_pair? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/hts/bam/flag.rb', line 48

generate :proper_pair?

#qcfail? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/hts/bam/flag.rb', line 56

generate :qcfail?

#read1? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/hts/bam/flag.rb', line 53

generate :read1?

#read2? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/hts/bam/flag.rb', line 54

generate :read2?

#reverse? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/hts/bam/flag.rb', line 51

generate :reverse?

#secondary? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/hts/bam/flag.rb', line 55

generate :secondary?

#supplementary? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/hts/bam/flag.rb', line 58

generate :supplementary?

#to_i ⇒ Object 



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# File 'lib/hts/bam/flag.rb', line 90

def to_i
  @value
end

#to_s ⇒ Object 



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# File 'lib/hts/bam/flag.rb', line 94

def to_s
  Native.bam_flag_string(@value)
end

#unmapped? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/hts/bam/flag.rb', line 49

generate :unmapped?

#|(other) ⇒ Object 



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# File 'lib/hts/bam/flag.rb', line 68

def |(other)
  self.class.new(@value | other.to_i)
end

#~ ⇒ Object 



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# File 'lib/hts/bam/flag.rb', line 76

def ~
  # FIXME: Only 12bits are used for flags
  # The result is different from the Crystal version.
  self.class.new(~@value)
end