VertebrateResequencing/vr-codebase — pull request #38 by CraigPorter (2011-11-30 17:04:08+00:00)
Title: Mapping to two assemblies + minor changes.

Hi Sendu,

I've added the ability to map and SNP-call for two assemblies at same time - it's needed for one study at the moment but I'm sure there will be others. The modification allows a study to be mapped and SNP-called for two different references at same time rather than completing mapping for one reference then rolling back the lanes and repeating for a new reference. The parameters "ignore_mapped_status" and ''ignore_snp_called_status" were added to the mapping and SNP-calling pipelines. If the parameters are present, run-pipeline will ignore the processed status of the lane and instead check the mapstats table for mappings or the snps.done file for SNP-calling.

Other changes in this pull request are:

A bugfix to the pipeline that pathogens uses to import files from iRODS. If LSF killed the job during the compression step then it couldn't be re-run.

And also a couple of changes from Andrew allowing filters to be set in the import config file and a change to the iRODS wrapper to filter unconsented human data and phix files when getting a list of bam files.

Thanks,

Craig