From 54c2cd67558eeaf54f0cdc1bd695c81f4e23c09b Mon Sep 17 00:00:00 2001
From: Sascha Meiers <meiers@embl.de>
Date: Fri, 18 May 2018 16:22:32 +0200
Subject: [PATCH] Changed the density of segmentation
---
Snake.config.json | 1 +
Snakefile | 2 ++
utils/chrom.R | 2 +-
3 files changed, 4 insertions(+), 1 deletion(-)
diff --git a/Snake.config.json b/Snake.config.json
index 843a536..e80de9e 100644
--- a/Snake.config.json
+++ b/Snake.config.json
@@ -22,6 +22,7 @@
"bp_density" : {
"few" : 0.1,
"medium" : 0.25,
+ "more" : 0.33,
"many" : 0.5
},
diff --git a/Snakefile b/Snakefile
index 96ac505..02cfa41 100644
--- a/Snakefile
+++ b/Snakefile
@@ -270,6 +270,8 @@ rule segmentation:
shell:
"""
{params.mc_command} segment \
+ -m 0.33 \
+ -M 50000000 \
-o {output} \
{input} > {log} 2>&1
"""
diff --git a/utils/chrom.R b/utils/chrom.R
index bb4c8f5..25d095c 100644
--- a/utils/chrom.R
+++ b/utils/chrom.R
@@ -42,7 +42,7 @@ manual_colors = c(
simul_false_del = "darkgrey",
simul_inv_dup = "darkgoldenrod2",
idup_h1 = muted("darkgoldenrod2", 80, 70),
- idup_h2 = muted("darkgoldenrod2", 80, 70),
+ idup_h2 = muted("gold", 80, 70),
complex = "darkorchid1",
# background
bg1 = "#ffffff",
--
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