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# Clustered reference method
example_cnn_dir=~/code/cnvkit-examples/targeted
cnr_of_interest=TR_101.clustered.cnr TR_77.clustered.cnr TR_55.clustered.cnr TR_42.clustered.cnr
all: $(cnr_of_interest)
clean:
rm -vf $(cnr_of_interest) ref-clustered.cnn
$(cnr_of_interest): \
TR_%.clustered.cnr: \
$(example_cnn_dir)/TR_%_T.targetcoverage.cnn \
$(example_cnn_dir)/TR_%_T.antitargetcoverage.cnn \
ref-clustered.cnn
cnvkit.py fix $^ --cluster -o $@
ref-clustered.cnn: $(wildcard $(example_cnn_dir)/TR_*targetcoverage.cnn)
cnvkit.py reference $^ --cluster -o $@
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