Module: Minigraph

Defined in:
lib/minigraph.rb,
lib/minigraph/ffi.rb,
lib/minigraph/version.rb,
lib/minigraph/ffi/mappy.rb,
lib/minigraph/ffi/constants.rb,
lib/minigraph/ffi/functions.rb

Overview

Minigraph github.com/lh3/minigraph Li, H., Feng, X. & Chu, C. The design and construction of reference pangenome graphs with minigraph. Genome Biol 21, 265 (2020). doi.org/10.1186

Defined Under Namespace

Modules: FFI Classes: Error

Constant Summary collapse

VERSION = 
"0.0.20.1"

Class Attribute Summary collapse

Class Method Summary collapse

Class Attribute Details

.ffi_lib ⇒ Object

Returns the value of attribute ffi_lib.



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# File 'lib/minigraph.rb', line 18

def ffi_lib
  @ffi_lib
end

Class Method Details

.execute(arg0, arg1, ...) ⇒ Object

Execute minigraph comannd with given options.

Examples:

Get minigraph version

Minigraph.execute('--version')

Parameters:

  • arg (String) —

    minigraph command option.



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

def execute(*rb_argv)
  str_ptrs = []
  # First argument is the program name.
  str_ptrs << ::FFI::MemoryPointer.from_string("minigraph")
  rb_argv.each do |arg|
    arg.to_s.split(/\s+/).each do |s|
      str_ptrs << ::FFI::MemoryPointer.from_string(s)
    end
  end
  str_ptrs << nil

  # Load all the pointers into a native memory block
  argv = ::FFI::MemoryPointer.new(:pointer, str_ptrs.length)
  str_ptrs.each_with_index do |p, i|
    argv[i].put_pointer(0, p)
  end

  FFI.main(str_ptrs.length - 1, argv)
end

.verbose ⇒ Integer

Get verbosity level.

Returns:

  • (Integer) —

    verbosity level.



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

def verbose
  FFI.mg_verbose_level(-1)
end

.verbose=(level) ⇒ Integer

Set verbosity level.

Parameters:

  • verbosity (Integer) —

    level

Returns:

  • (Integer) —

    verbosity level.



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# File 'lib/minigraph.rb', line 69

def verbose=(level)
  FFI.mg_verbose_level(level)
end