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

s/n/g/; Copy paste error in wait-state command. Omitted "go projection" implication when previous code referred to "name projection" with an "n"

fix by st3

tweaks to formatting of param list so that they (hopefully) all fit on one line. Don't try to check PATCH seq_region_attribs since it doesn't work with with Ensembl-vega databases

Until now we were checking the gene biotype which is insufficient as a
gene can include both protein coding and polymorphic pseudogene
transcripts.

GenomeRNAi is a fly source, should not be parsed in any other species, just because Uniprot mentioned it exists

will return a list of slices which are part of the karyotype
solves issues with genomes where slices are called chromosomes when they should not be

Tabs converted to spaces.

given the file has custom chosen columns, we decide to refer to them according
to the order in which they are given, rather than through their header name
which might change

when cleaning up left over transcript xrefs extended from gene xrefs which match pattern '-201', make sure these are transcript xrefs, not gene xrefs