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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
This commit is contained in:
hanna 2011-06-14 15:22:17 +00:00
parent cde2b409a7
commit 7aec71f0e1
1 changed files with 14 additions and 0 deletions
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14
python/generate_per_sample_metrics.py
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@ -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 <bam.list> > <output_metrics_file.tsv>
#
# 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.lang import *
from java.io import File,FileReader from java.io import File,FileReader
from net.sf.picard.metrics import MetricsFile from net.sf.picard.metrics import MetricsFile