Class: HTS::Bam::PileupEntry

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

Instance Method Summary collapse

Constructor Details

#initialize(pointer) ⇒ PileupEntry

Returns a new instance of PileupEntry.



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# File 'lib/hts/bam/pileup_entry.rb', line 4

def initialize(pointer)
  @entry = LibHTS::BamPileup1.new(pointer)
end

Instance Method Details

#base ⇒ Object 



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# File 'lib/hts/bam/pileup_entry.rb', line 28

def base
  s = LibHTS.bam_get_seq(@entry[:b])
  Bam::Record::SEQ_NT16_STR[LibHTS.bam_seqi(s, qpos)]
end

#indel ⇒ Object 



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# File 'lib/hts/bam/pileup_entry.rb', line 12

def indel
  @entry[:indel]
end

#is_del? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/hts/bam/pileup_entry.rb', line 20

def is_del?
  @entry[:is_del] == 1
end

#is_refskip? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/hts/bam/pileup_entry.rb', line 24

def is_refskip?
  @entry[:is_refskip] == 1
end

#level ⇒ Object 



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

def level
  @entry[:level]
end

#qpos ⇒ Object 



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# File 'lib/hts/bam/pileup_entry.rb', line 8

def qpos
  @entry[:qpos]
end

#to_s ⇒ Object 



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# File 'lib/hts/bam/pileup_entry.rb', line 33

def to_s
  "Position: #{qpos}, Indel: #{indel}, Level: #{level}, Base: #{base}, Is_del: #{is_del?}, Is_refskip: #{is_refskip?}"
end