Introduction of new FASTASerializer to replace SeqDumper's FASTA capability. Other formats remain SeqDumper's responsibility.

has unrelated remark beginning with string "selenocysteine ". Found to be the
case in OTTDART00000030742 for Dec 19th 2011 Havana data-freeze of Zebra fish.

First stage commit only. Partial functionality (detailed below), but works and reduces
chance of missing problems.

1. Made exception data structure richer for check_for_stops to allow a number of different
types of exception to to be expressed.

2. Added a new exception type, that of known TGA-stopping Sec-coding transcript.

3. Added data-structure to add_selcys stop checking to allow specification of known
TGA-stopping Sec-coding transcripts.

1. Fix check_for_stops to cope with multiple adjacent internal stops without a loss of codon to AA sync.
Found when running add_selcys.pl on zebrafish for Vega 47.

2. Fix to existing conditional in vega Sec QC script which tests for an anacode bug before deciding to complain
about missing Sec markup for selenoproteins that also stop with TGA, so that this conditional actually spots
this case in more proteins and so cries wolf less often.

unique genes method (for assembly patches), interactive does have an argument, other binaries default to 1 if nothing specified

merge in changes from ensembl-64 for retrieving non-reference slices. Don't need to supply a value for logappend, verbose, interactive and dry_run parameters

Introduced Utils::IO namespace along with serializer code for GFF3 and human-readable formats. Pre-release, not intended for public use.
Also added Utils::BiotypeMapper that performs ontology mappings.

	formatting

	safe use of @aliases (don't expect registry to make copy of the list)

	quote argument names and values

Check the result of the print and die if we have an error. Bits of flatfiles have been missing so hopefully these will now be caught

Faster version of rearrange which ditches uc() and order modifying in favor of editing the input parameters directly with a tr///d. This is 35% faster than our original implementation. Test case suite has been run before this commit.

Edge case support for hive which allows for non-scheme URIs. We now treat these as if they are DB URIs.

Adding support for SQLite since the URI scheme does not take into account the fact that SQLite is a path and the concept of table does not play well with this