GitLab

added immediate loading of PredictionExons option to PredictionTranscript slice fetching; faster than lazy-loading for many use cases

added optimisation: Transcripts and Exons can now be loaded immediately on Gene fetch rather than lazy-loading later

bug fix: Translation start_exon and end_exon for PredictionTranscripts should not have been strand dependant

transcript fetching optimisations, allows optional immediate exon loading as opposed to lazy-loading

applied patch (from March!) from David Craigon to allow fetch_by_name to work w/o start/end/strand values

store each density feature as it is created rather than building a list per seq_region - smaller memory footprint (but repeats still leaking mem)

changed selenocystein implementation to use SeqEdits and be more consistant with Transcript implementatin

for now edits are disabled by default, b/c will slow down dumping, also flush TranscriptMapper when enabling/disabling edits

changed transcript edit implementation to use SeqEdits and made it possible to enable/disable editing

supercontig length should be max(superctg_end) not length because occasionally supercontigs do not start at 1

moved snp typing methods into utility class in an attempt to make very large transcript module more manageable