From c8e5c181f55c3475fe0a8a93f1aa4b51f14a01ac Mon Sep 17 00:00:00 2001
From: Tobias Marschall <tobias.marschall@0ohm.net>
Date: Fri, 5 Oct 2018 08:47:14 +0200
Subject: [PATCH] Use whitelist
---
Snakefile | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/Snakefile b/Snakefile
index 9855049..c05f2d8 100644
--- a/Snakefile
+++ b/Snakefile
@@ -447,14 +447,15 @@ rule extract_single_cell_counts:
rule merge_blacklist_bins:
input:
- norm = "utils/normalization/HGSVC.{window}.txt"
+ norm = "utils/normalization/HGSVC.{window}.txt",
+ whitelist = "utils/normalization/inversion-whitelist.tsv",
output:
merged = "normalizations/HGSVC.{window}.merged.tsv"
log:
"log/merge_blacklist_bins/{window}.log"
shell:
"""
- utils/merge-blacklist.py --merge_distance 500000 {input.norm} > {output.merged} 2> {log}
+ utils/merge-blacklist.py --merge_distance 500000 {input.norm} --whitelist {input.whitelist} --min_whitelist_interval_size 400000 > {output.merged} 2> {log}
"""
rule normalize_counts:
--
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