From 6e5c73f600613eae3143132c79605d5079b6d024 Mon Sep 17 00:00:00 2001
From: Sascha Meiers <meiers@embl.de>
Date: Tue, 12 Jun 2018 20:50:20 +0200
Subject: [PATCH] Enable new segmentation
---
Snakefile | 1 +
utils/helper.prepare_segments.R | 2 +-
2 files changed, 2 insertions(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index 36d36ea..b79e7e1 100644
--- a/Snakefile
+++ b/Snakefile
@@ -326,6 +326,7 @@ rule segmentation:
shell:
"""
{params.mc_command} segment \
+ --remove-none \
-m 0.33 \
-M 50000000 \
-o {output} \
diff --git a/utils/helper.prepare_segments.R b/utils/helper.prepare_segments.R
index 0ee3ae1..fc92d8c 100755
--- a/utils/helper.prepare_segments.R
+++ b/utils/helper.prepare_segments.R
@@ -5,6 +5,6 @@ qu
d = fread(snakemake@input[[1]])
d
# type = 1 is important to get discrete values!
-d = d[, .SD[k == quantile(1:max(k), qu, type = 1)], by=chrom][,.(k, chrom, bps = breakpoint)]
+d = d[, .SD[k == quantile(1:max(k), qu, type = 1)], by=chrom][,.(k, chrom, bps)]
d
write.table(d, file = snakemake@output[[1]], row.names=F, quote=F, sep="\t")
--
GitLab