Merge pull request #2 from wtsi-hgi/develop

pulling develop into feature/runner-checkpointing
run-filter: Extended docs, select training sites by AF
Adds +checkpoint option to Runner.pm to enable checkpointing

This is not yet fully implemented in RunnerLSF.pm, but using +checkpoint will
cause jobs to be submitted with `bsub -k` and using cr_run
Support for single queries, in addition to the batch mode
Do not choke on variants close to chromosome ends
Informative error message to hint on stretches of Ns
moved _all_values_by_field() from Core_obj to parent class Table_obj, so it can be used by Individual
lane_info() now includes individual alias in the output hash
Better documented output
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase into develop
Initial release of run-analyze-annots
run-filter: Added cleaning step
Adds perl5lib_dependencies to .gitignore
run-mpileup: Work with latest rc6 bcftools release
display individual alias instead of name, if defined
Initial release of human-core-exome script
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase into develop
renamed after its primary function
Sanity checks to detect wrong/broken input files
RunnerLSF: Request at least 1GB, mem has to be set explicitly