sanger-pathogens/vr-codebase — pull request #37 by CraigPorter (2011-11-23 13:34:10+00:00)
Title: Allow mapping and SNP-calling for two assemblies at same time.

Added the parameters "ignore_mapped_status" and ''ignore_snp_called_status" for the mapping and SNP-calling pipelines. If the parameters are present, run-pipeline will ignore the processed status of the lane and instead check if jobs have been mapped by checking the mapstats table for mappings or SNP-called by checking for the snps.done file.

The modification allows a study to be mapped and SNP-called for two different references (optionally using different mappers) at same time rather than completing mapping for one reference then rolling back lanes and repeating for a new reference. For mapping, it is important that the user set the prefix in the mapping config file for each job.