Merge pull request #9 from martinghunt/master

added script fastaq_scaffolds_to_contigs
Merge pull request #10 from martinghunt/master

Added option to filter file from a file of sequence names
Merge pull request #11 from martinghunt/master

Added option to output numbered contig names instead of using coords
Merge pull request #12 from martinghunt/master

Added option to output numbered contig names instead of using coords
added --fragments option to dump fasta file of fragments