NAME

Bio::AssemblyImprovement::Scaffold::SSpace::PreprocessInputFiles - Make sure the input files are in the correct format, and paths are resolved.

VERSION

version 1.160490

SYNOPSIS

Make sure the input files are in the correct format, and paths are resolved. This object needs to be kept in scope because it creates temp files which are cleaned up when it goes out of scope.

   use Bio::AssemblyImprovement::Scaffold::SSpace::PreprocessInputFiles;

   my $process_input_files = Bio::AssemblyImprovement::Scaffold::SSpace::PreprocessInputFiles->new(
     input_files => ['abc_1.fastq.gz', 'abc_2.fastq'],
     input_assembly => 'contigs.fa'
   );

   $process_input_files->processed_input_files;
   $process_input_files->processed_input_assembly;

METHODS

processed_input_files

Process the input FASTQ files and return their location.

processed_input_assembly

Process the input FASTA file and return its location.

AUTHOR

Andrew J. Page <ap13@sanger.ac.uk>

COPYRIGHT AND LICENSE

This software is Copyright (c) 2012 by Wellcome Trust Sanger Institute.

This is free software, licensed under:

  The GNU General Public License, Version 3, June 2007