Commit 7305d28a authored by Mikaël Salson's avatar Mikaël Salson
Browse files

should-vdj-to-tap: Process at most 50 sequences in a file, with FineSegmenter

parent 1b52f8c5
......@@ -26,7 +26,7 @@ from subprocess import Popen, PIPE, STDOUT
import os
import argparse
VIDJIL_FINE = '{directory}/vidjil -c segment -i -g {directory}/germline %s > %s'
VIDJIL_FINE = '{directory}/vidjil -X 50 -c segment -i -g {directory}/germline %s > %s'
VIDJIL_KMER = '{directory}/vidjil -b out -c windows -uU -2 -i -g {directory}/germline %s > /dev/null ; cat out/out.segmented.vdj.fa out/out.unsegmented.vdj.fa > %s'
parser = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter)
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