From 56e577730fea4cf0636cfa842bd60302953d5798 Mon Sep 17 00:00:00 2001
From: Tobias Marschall <tobias.marschall@0ohm.net>
Date: Fri, 12 Oct 2018 14:16:42 +0200
Subject: [PATCH] Update summary_statistics to use --merged-file option
---
Snakefile | 12 ++++++++----
1 file changed, 8 insertions(+), 4 deletions(-)
diff --git a/Snakefile b/Snakefile
index 325e316..8b6e3d6 100644
--- a/Snakefile
+++ b/Snakefile
@@ -1046,12 +1046,13 @@ rule summary_statistics:
input:
segmentation = 'segmentation2/{sample}/{windows}.{bpdens}.txt',
strandstates = 'strand_states/{sample}/{windows}.{bpdens}/intitial_strand_state',
- sv_calls = 'sv_calls/{sample}/{windows}.{bpdens}/{method}.txt',
- complex = "sv_calls/{sample}/{windows}.{bpdens}/{method}.complex.tsv",
+ sv_calls = 'sv_calls/{sample}/{windows}.{bpdens}/{method}_filter{filter}.txt',
+ complex = "sv_calls/{sample}/{windows}.{bpdens}/{method}_filter{filter}.complex.tsv",
+ merged = "postprocessing/merge/{sample}/{windows}.{bpdens}/{method}.txt",
output:
- tsv = 'stats/{sample}/{windows}.{bpdens,selected_j[0-9\\.]+_s[0-9\\.]+_scedist[0-9\\.]+}/{method}.tsv',
+ tsv = 'stats/{sample}/{windows}.{bpdens,selected_j[0-9\\.]+_s[0-9\\.]+_scedist[0-9\\.]+}/{method}_filter{filter,(TRUE|FALSE)}.tsv',
log:
- 'log/summary_statistics/{sample}/{windows}.{bpdens}/{method}.log'
+ 'log/summary_statistics/{sample}/{windows}.{bpdens}/{method}_filter{filter}.log'
run:
p = []
try:
@@ -1068,6 +1069,9 @@ rule summary_statistics:
p.append(f)
except KeyError:
pass
+ if wildcards.filter == 'TRUE':
+ p.append('--merged-file')
+ p.append(input.merged)
additional_params = ' '.join(p)
shell('utils/callset_summary_stats.py --segmentation {input.segmentation} --strandstates {input.strandstates} --complex-regions {input.complex} {additional_params} {input.sv_calls} > {output.tsv} 2> {log}')
--
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