From 7aec71f0e1423763f20a3589a15a95fdd02a94a2 Mon Sep 17 00:00:00 2001 From: hanna Date: Tue, 14 Jun 2011 15:22:17 +0000 Subject: [PATCH] Add some very simple documentation on running and modifying the per-sample metrics generator. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5995 348d0f76-0448-11de-a6fe-93d51630548a --- python/generate_per_sample_metrics.py | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/python/generate_per_sample_metrics.py b/python/generate_per_sample_metrics.py index 8dddf8233..a4e57711c 100644 --- a/python/generate_per_sample_metrics.py +++ b/python/generate_per_sample_metrics.py @@ -1,3 +1,17 @@ +# +# Reads in selected Picard metrics, generating an R-compatible TSV suitable for pre-QC analysis. +# +# To run: +# /humgen/gsa-hpprojects/software/bin/jython2.5.2/jython \ +# -J-classpath $STING_HOME/dist/sam-1.44.794.jar:$STING_HOME/dist/picard-1.44.794.jar:$STING_HOME/dist/picard-private-parts-1859.jar \ +# $STING_HOME/python/generate_per_sample_metrics.py > +# +# To add a new metric: +# - If the metric file is new to Picard, add the relevant parser to the picard-private jar +# (see http://www.broadinstitute.org/gsa/wiki/index.php/Adding_and_updating_dependencies for details). +# - Add the field name to the header array. +# - Add the field data to the statement printing the data array. +# from java.lang import * from java.io import File,FileReader from net.sf.picard.metrics import MetricsFile