From 47cc8975a02846e0f3edcbc4756dfaab4c38a95a Mon Sep 17 00:00:00 2001
From: Sascha Meiers <meiers@embl.de>
Date: Thu, 18 Jan 2018 23:56:25 +0100
Subject: [PATCH] Paired- or single-end mode for StrandPhasR
---
Snake.config.json | 4 +++-
Snakefile | 5 ++++-
2 files changed, 7 insertions(+), 2 deletions(-)
diff --git a/Snake.config.json b/Snake.config.json
index d6e157c..9bc451a 100644
--- a/Snake.config.json
+++ b/Snake.config.json
@@ -23,7 +23,9 @@
"medium" : 0.33,
"many" : 0.9
},
-
+
+ "paired_end" : false,
+
"simulation_min_vaf" : 0.01,
"simulation_max_vaf" : 1.0,
"simulation_neg_binom_p" : {
diff --git a/Snakefile b/Snakefile
index df48cf0..de74d65 100644
--- a/Snakefile
+++ b/Snakefile
@@ -398,7 +398,10 @@ rule prepare_strandphaser_config_per_chrom:
print("[General]", file = f)
print("numCPU = 1", file = f)
print("chromosomes = '" + wildcards.chrom + "'", file = f)
- print("pairedEndReads = TRUE", file = f)
+ if (config["paired_end"]):
+ print("pairedEndReads = TRUE", file = f)
+ else:
+ print("pairedEndReads = FALSE", file = f)
print("min.mapq = 10", file = f)
print("", file = f)
print("[StrandPhaseR]", file = f)
--
GitLab