From 5c19a0671014cbc2e5946a64bca2adca2ce976ab Mon Sep 17 00:00:00 2001
From: Sascha Meiers <meiers@embl.de>
Date: Thu, 17 May 2018 16:30:06 +0200
Subject: [PATCH] Preparing caller based on the new NB probs
---
Snakefile | 4 +---
utils/mosaiClassifier_call.snakemake.R | 9 +++++++++
2 files changed, 10 insertions(+), 3 deletions(-)
create mode 100644 utils/mosaiClassifier_call.snakemake.R
diff --git a/Snakefile b/Snakefile
index def2ad7..c61fecf 100644
--- a/Snakefile
+++ b/Snakefile
@@ -304,9 +304,7 @@ rule mosaiClassifier_make_call:
output:
"sv_calls/{sample}/{windows}.{bpdens}/simpleCalls.txt"
shell:
- """
- Rscript utils/mosaiClassifier.makeCall.R {input} {output}
- """
+ "utils/mosaiClassifier_call.snakemake.R"
rule mosaiClassifier_calc_probs:
input:
diff --git a/utils/mosaiClassifier_call.snakemake.R b/utils/mosaiClassifier_call.snakemake.R
new file mode 100644
index 0000000..efc74e2
--- /dev/null
+++ b/utils/mosaiClassifier_call.snakemake.R
@@ -0,0 +1,9 @@
+library(data.table)
+source("utils/mosaiClassifier/makeSVcalls.R")
+
+probs = readRDS(snakemake@input[["probs"]])
+llr = as.numeric(snakemake@params[["llr"]])
+
+tab <- makeSVCallSimple(probs)
+
+write.table(tab, file = snakemake@output[[1]], sep = "\t", quote=F, row.names = F, col.names = T)
--
GitLab