Read ACE format assembly files

These are typically output by sequence assembly tools, like CAP3 or Phrap.

Documented in the section labelled "ACE FILE FORMAT" at http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt

Briefly: each field is a line starting with a two letter code, in some cases followed by data lines termintated by a blank line. -- AS contigs reads -- CO contig_name bases reads segments compl (CAP3: segments=0) -- sequence -- BQ -- base_qualities -- AF read1 compl padded_start_consensus (negatives meaning?) -- AF read2 .. -- BS segments -- RD read1 bases info_items info_tags (latter two set to 0 by CAP3) -- sequence -- QA read1 qual_start qual_end align_start align_end -- DS (phred header? left empty by CAP3) -- RD read2 ...