Class: HTS::Hts

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

Overview

A base class for hts files.

Direct Known Subclasses

Bam, Bcf, Tabix

Instance Method Summary collapse

Constructor Details

#initialize(*_args) ⇒ Hts

Returns a new instance of Hts.

Raises:

  • (TypeError) 


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# File 'lib/hts/hts.rb', line 34

def initialize(*_args)
  raise TypeError, "Can't make instance of HTS abstract class"
end

Instance Method Details

#close ⇒ Object 



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# File 'lib/hts/hts.rb', line 61

def close
  return if closed?

  LibHTS.hts_close(@hts_file)
  @hts_file = nil
end

#closed? ⇒ Boolean

Returns:

  • (Boolean) 


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

def closed?
  @hts_file.nil? || @hts_file.null?
end

#fai=(fai) ⇒ Object 



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

def fai=(fai)
  check_closed
  LibHTS.hts_set_fai_filename(@hts_file, fai) > 0 || raise
end

#file_format ⇒ Object 



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# File 'lib/hts/hts.rb', line 46

def file_format
  LibHTS.hts_get_format(@hts_file)[:format].to_s
end

#file_format_version ⇒ Object 



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

def file_format_version
  v = LibHTS.hts_get_format(@hts_file)[:version]
  major = v[:major]
  minor = v[:minor]
  if minor == -1
    major.to_s
  else
    "#{major}.#{minor}"
  end
end

#rewind ⇒ Object 



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# File 'lib/hts/hts.rb', line 114

def rewind
  raise "Cannot rewind: no start position" unless @start_position

  r = seek(@start_position)
  raise "Failed to rewind: #{r}" if r < 0

  tell
end

#seek(offset) ⇒ Object 



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# File 'lib/hts/hts.rb', line 92

def seek(offset)
  if @hts_file[:is_cram] == 1
    LibHTS.cram_seek(@hts_file[:fp][:cram], offset, IO::SEEK_SET)
  elsif @hts_file[:is_bgzf] == 1
    LibHTS.bgzf_seek(@hts_file[:fp][:bgzf], offset, IO::SEEK_SET)
  else
    LibHTS.hseek(@hts_file[:fp][:hfile], offset, IO::SEEK_SET)
  end
end

#set_threads(n = nil) ⇒ Object

Raises:

  • (TypeError) 


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# File 'lib/hts/hts.rb', line 77

def set_threads(n = nil)
  if n.nil?
    require "etc"
    n = [Etc.nprocessors - 1, 1].max
  end
  raise TypeError unless n.is_a?(Integer)
  raise ArgumentError, "Number of threads must be positive" if n < 1

  r = LibHTS.hts_set_threads(@hts_file, n)
  raise "Failed to set number of threads: #{threads}" if r < 0

  @nthreads = n
  self
end

#struct ⇒ Object 



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# File 'lib/hts/hts.rb', line 38

def struct
  @hts_file
end

#tell ⇒ Object 



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# File 'lib/hts/hts.rb', line 102

def tell
  if @hts_file[:is_cram] == 1
    # LibHTS.cram_tell(@hts_file[:fp][:cram])
    # warn 'cram_tell is not implemented in c htslib'
    nil
  elsif @hts_file[:is_bgzf] == 1
    LibHTS.bgzf_tell(@hts_file[:fp][:bgzf])
  else
    LibHTS.htell(@hts_file[:fp][:hfile])
  end
end

#to_ptr ⇒ Object 



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# File 'lib/hts/hts.rb', line 42

def to_ptr
  @hts_file.to_ptr
end