From 8ff965cb6cc44f459062492160c503bf45649233 Mon Sep 17 00:00:00 2001
From: maryamghr <maryam.ghareghani@gmail.com>
Date: Thu, 24 May 2018 15:18:05 +0200
Subject: [PATCH] Added the previously existing rule for counting in dynamic
bins
---
Snakefile | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)
diff --git a/Snakefile b/Snakefile
index 88b12a4..f343d64 100644
--- a/Snakefile
+++ b/Snakefile
@@ -253,6 +253,31 @@ rule mosaic_count_fixed:
> {log} 2>&1
"""
+rule mosaic_count_variable:
+ input:
+ bam = lambda wc: expand("bam/" + wc.sample + "/{bam}.bam", bam = BAM_PER_SAMPLE[wc.sample]),
+ bai = lambda wc: expand("bam/" + wc.sample + "/{bam}.bam.bai", bam = BAM_PER_SAMPLE[wc.sample]),
+ bed = lambda wc: config["variable_bins"][str(wc.window)],
+ excl = "log/exclude_file"
+ output:
+ counts = "counts/{sample}/{window}_variable.txt.gz",
+ info = "counts/{sample}/{window}_variable.info"
+ log:
+ "log/{sample}/mosaic_count_variable.{window}.txt"
+ params:
+ mc_command = config["mosaicatcher"]
+ shell:
+ """
+ echo "NOTE: Exclude file not used in variable-width bins"
+ {params.mc_command} count \
+ --verbose \
+ -o {output.counts} \
+ -i {output.info} \
+ -b {input.bed} \
+ {input.bam} \
+ > {log} 2>&1
+ """
+
################################################################################
# Segmentation #
--
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