phase change was removed because it meant that an exon whose sequence
and position had not changed would become a candidate for similarity
mapping.  This caused lots of criss-crossing stable ID history entries
between genes/transcripts/translations in some gene families.

Better version. We now avoid gzipping which should give us a good speed boost and bring us closer to the original speed

Switching the logic around here. It makes sense if we are trying to read from a file which hasn't closed yet then maybe we're not going to get all the data into the file.

sequence.  This means that the translation stable ID version might be
incremented independently of the transcript stable ID version if there
was a phase change in an exon.

Changing markup from Markdown to Textile as it supports table formatting which Markdown can only do via hardcoded HTML tables

ENSCORESW-139, ENSCORESW-126, ENSCORESW-164 and ENSCORESW-132. This commit brings in support for stripping out the Y chromosome from Human for all dumps (if required). We also add support for deleting previous runs going into the same dump location. Softmasked sequence is now created by default; hard masked is generated from this. We also produce an email summary of the results of the pipeline.

All is currently untested

Removed fish from GO terms projections. Also double-checked order of execution code and added some explanatory comments.

ENSCORESW-160. Committed with test cases checked in. Also manually verified the code works with transcripts (live as of v67 of Ensembl) ENST00000330803, ENST00000366472 and ENST00000318244

ENSCORESW-171. Bringing in support for splice site work. We also had to change the intron table SQL as it was out of date.