SciLifeLab/scilifelab — pull request #215 by percyfal (2013-03-16 09:45:15+00:00)
Title: Develop - add function for getting barcode lane stats from Demultiplex_stats. Random halo stuff.

Summary:

- since base quality stats info is present in Demulitplex_stats.htm use this info instead of fastqc. See function statusdb.FlowcellRunMetricsConnection.get_barcode_lane_statistics
- add test for get_barcode_lane_statistics
- modified sample_report template to include pct_q30_bases - should this go somewhere else too?
- add and modify halo templates in experimental. NB: if the ratatosk pipeline works, I suggest we remove these scripts from the repo
- add test data files (runInfo.xml, runParameters.xml)

@b97pla @mayabrandi

I have added a function and a test for getting avg base QV and %bases>Q30. @mayabrandi, I modified your code somewhat. Both: note that I have not verified that the reports look ok!