Module: Minimap2

Defined in:
lib/minimap2.rb,
lib/minimap2/ffi.rb,
lib/minimap2/aligner.rb,
lib/minimap2/version.rb,
lib/minimap2/alignment.rb,
lib/minimap2/ffi/mappy.rb,
lib/minimap2/ffi/constants.rb,
lib/minimap2/ffi/functions.rb

Overview

github.com/lh3/minimap2/blob/master/python/cmappy.h

Defined Under Namespace

Modules: FFI Classes: Aligner, Alignment, Error

Constant Summary collapse

VERSION = 
"0.2.28.0"

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/minimap2.rb', line 19

def ffi_lib
  @ffi_lib
end

Class Method Details

.execute(arg0, arg1, ...) ⇒ Object

Execute minimap2 comannd with given options.

Examples:

Get minimap2 version

Minimap2.execute('--version')

Parameters:

  • arg (String) —

    minimap2 command option.



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# File 'lib/minimap2.rb', line 40

def execute(*rb_argv)
  str_ptrs = []
  # First argument is the program name.
  str_ptrs << ::FFI::MemoryPointer.from_string("minimap2")
  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

.fastx_read(file_path, comment: false) {|name, seq, qual, comment| ... } ⇒ Enumerator

Read fasta/fastq file. Note: You can BioRuby instead of this method.

Parameters:

  • file_path (String)
  • comment (Boolean) (defaults to: false) —

    If True, the comment will be read.

Yields:

  • (name, seq, qual, comment)

Returns:

  • (Enumerator) —

    enum Return Enumerator if not block given.

Raises:

  • (ArgumentError) 


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# File 'lib/minimap2.rb', line 82

def fastx_read(file_path, comment: false, &block)
  path = File.expand_path(file_path)

  # raise error in Ruby because ks.null? is false even if file not exist.
  raise ArgumentError, "File not found: #{path}" unless File.exist?(path)

  ks = FFI.mm_fastx_open(path)

  if block_given?
    fastx_each(ks, comment, &block)
  else
    Enumerator.new do |y|
      # rewind not work
      fastx_each(ks, comment) { |r| y << r }
    end
  end
end

.revcomp(seq) ⇒ string

Reverse complement sequence.

Parameters:

  • seq (String)

Returns:

  • (string) —

    seq



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# File 'lib/minimap2.rb', line 104

def revcomp(seq)
  l = seq.size
  bseq = ::FFI::MemoryPointer.new(:char, l)
  bseq.put_bytes(0, seq)
  FFI.mappy_revcomp(l, bseq)
end

.verbose ⇒ Integer

Get verbosity level.

Returns:

  • (Integer) —

    verbosity level.



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# File 'lib/minimap2.rb', line 63

def verbose
  FFI.mm_verbose_level(-1)
end

.verbose=(level) ⇒ Integer

Set verbosity level.

Parameters:

  • verbosity (Integer) —

    level

Returns:

  • (Integer) —

    verbosity level.



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# File 'lib/minimap2.rb', line 71

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