From 4ab5c553e2f344dbc76bc2f36d09ad8c57a11335 Mon Sep 17 00:00:00 2001 From: David Kelley Date: Wed, 26 Jul 2023 17:04:30 -0700 Subject: [PATCH] update for new stats --- bin/sonnet_sad.py | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/bin/sonnet_sad.py b/bin/sonnet_sad.py index 6a78de90..1c2ac4bb 100755 --- a/bin/sonnet_sad.py +++ b/bin/sonnet_sad.py @@ -66,9 +66,6 @@ def main(): parser.add_option('-p', dest='processes', default=None, type='int', help='Number of processes, passed by multi script') - parser.add_option('--pseudo', dest='log_pseudo', - default=1, type='float', - help='Log2 pseudocount [Default: %default]') parser.add_option('--rc', dest='rc', default=False, action='store_true', help='Average forward and reverse complement predictions [Default: %default]') @@ -214,8 +211,7 @@ def snp_gen(): pi += 1 # process SNP - write_snp_len(ref_preds, alt_preds, sad_out, si, - options.sad_stats, options.log_pseudo) + write_snp_len(ref_preds, alt_preds, sad_out, si, options.sad_stats) # close genome genome_open.close()