GitLab

pass a new reference to files_to_parse array to make sure of any side effects when calling the run method

Introducing a proxy Feature class to allow custom limitation of the boundaries of the feature. This implementation influences the get_all_ methods while leaving the standard methods unaffected.

removing the adding of species if they are in the force_speices list. unintented side effect of limiting it to just those force species

restriction on assembly or repeat mask changes should be enough, and we can have external groups (wormbase, ensemblgenomes) submitting new gene sets

also added url for zebrafish

this is not always the case, especially for ensembl genomes imported species
now checks for the existence of go_xrefs instead

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.