Adding better strand support (strands in bed are +/- not 1/-1) and not adding a value if one was not defined

Adding support for NCBI blast DB creation. This is not rolled into the main distro yet but is available as a separate pipeline. Existing indexers have had some functionality moved down the stack to avoid massive code duplication

We do not need proxies for this test. Having them actually causes it to go wrong. Deleted HTTP_PROXY and http_proxy from Perl ENV hash

New method store_batch_on_ for faster bulk storage of attributes. New modules GeneGCBatch and PepStatsBatch use this method. Updated test to include use of this method.

Added some additional documentation to counter cases where Transcripts without Slices were being used, creating garbage mappings. ENSCORESW-208

ENSCORESW-365

[ENSCORESW-377]. Fixing the seq region synonym as mentioned by Steve S. Also added a test case which looks for synonyms with a coordinate system not as before which only worked when we had no coordinate system)

using plain assignment to assigne individual values to a has, rather than the fat comma used in the larger hash declaration

Added constrain_to_seq_region for web rendering reasons, where requested slice->expand were flying off the end of chromosomes.

moving logic for slice projection filtering into sliceadaptor so compara have an easier time using it and getting better patch support in

added havana_ig and ensembl_ig analysis logic names to overall logic
for pig specific overwrite, overwrite if existing display is clone name, or if no display

Job name was truncated to bsub limits, but previous job name was not. Fixed for all three invocations.

we need one separate entry for each db_type

Adding BAM checks which ensure the file is consistent. Can cause issues to the program test run if they are not correct but this means they will not work in production