Minor optimisation on fetch_all_by_name
Made open_file safe wrt arg assignment and validation. Also restricted make_path to output files. Tweaked _handle_exit_status $err_string
minor revisions to _get_schema_build. Now uses assert_ref and better pod
removed some spurious warning
Added create_DBConnection_from_options to support DBConnection geenration when connecting to non-Ensembl DB
Added many methods from old pwm mappings scripts
Added randomise bed file and explode_fasta
1st pass at fixing motif mapping pipeline: Lots moved out to MotifTools. Now uses all available pfm files from last 2 releases. Job parallelisation & matrix specific outputs to avoid horrible greping issues. Ad-hoc lsf job management and many other improvements
Added stand alone script to run_moods
Minor changes to PDB_NAME handling
removed usage of pwm_mappings/filtered directory as map_dir
now removes intermediate peaks and olaps files
now expects filtered.bed files
fixed slice cache bug for Y non-PARs
fixed fetch_by_dbID throw
Fixed _get_schema_build usage bug
Extending gitignore to cover config files
ImportMotifFeatures refactoring and optimsation. Now also uses bedtools
SeqTools::filter_pwm_mappings now takes a threshold instead of a perc of max.
pwm_filter_mappings.pl Now stores threshold in DB and passes threshold to filter_pwm_mappings instead of perc of max
run_binding_site_import_pipeline.pl now catches readdir failure properly
sequencing.env now passes DB write args to run_pwm_mapping_pipeline.pl
Merge branch 'master' into tj1/migration
update