Switch Subfunctions.pm to an exportable module
remodularize assembler functions

assembler returns a hash of contigs, and rename_contigs is now
“write_contig_file.”
make sure output_file is an absolute path
If $save_temp is not on, use a tempdir for the assembler.
now that we've moved system_call to Subfunctions, don't need to close the pipes in the modules.
Assembler->find_bin doesn't ever return "", so these checks are never used.
Assembler is now an exportable package instead of an OO module.
Merge branch 'master' into issue-96
Merge pull request #101 from juliema/issue-96

Fixed Issue #96.