From 9fe53a1761a67fdbbfd3d70cccdcbdd7a339240c Mon Sep 17 00:00:00 2001
From: Thomas Faraut <Thomas.Faraut@inra.fr>
Date: Thu, 17 Jan 2019 15:58:10 +0100
Subject: [PATCH] bwam in cluster.yaml set to 23h, detect_region_to_exclude
modified
---
cluster.yaml | 3 +++
snakecnv/bin/detect_regions_to_exclude.py | 4 ++--
2 files changed, 5 insertions(+), 2 deletions(-)
diff --git a/cluster.yaml b/cluster.yaml
index 43a7f96..5fcfc7b 100644
--- a/cluster.yaml
+++ b/cluster.yaml
@@ -50,6 +50,9 @@ bed2fasta:
mem: 16
h_vmem: 16
+bwamap:
+ time: "36:00:00"
+
markduplicates:
mem: 32
h_vmem: 32
diff --git a/snakecnv/bin/detect_regions_to_exclude.py b/snakecnv/bin/detect_regions_to_exclude.py
index d0c90f5..ab100d7 100755
--- a/snakecnv/bin/detect_regions_to_exclude.py
+++ b/snakecnv/bin/detect_regions_to_exclude.py
@@ -95,8 +95,8 @@ def dump_overcovered_to_bed(overcovered_regions, fout, window_size):
for chrom, pos in zip(overcovered_regions.chrom,
overcovered_regions.pos):
fout.write("%s\t%d\t%d\n" % (chrom.decode("utf-8"),
- pos - int(window_size/2),
- pos + int(window_size/2)))
+ max(0, pos - int(window_size/2) - 200),
+ pos + int(window_size/2) + 200))
def dump_illcovered_to_bed(overcovered_regions, fout, window_size):
--
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