From 3d1e1ae19321a5f19dc7369eca3903369882e1de Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Mon, 1 Feb 2021 22:04:33 +0100
Subject: [PATCH] add 4D pairs format
---
main.nf | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/main.nf b/main.nf
index b6a66d3..3169106 100644
--- a/main.nf
+++ b/main.nf
@@ -869,7 +869,7 @@ process convert_to_pairs {
script:
"""
## chr/pos/strand/chr/pos/strand
- awk '{OFS="\t";print \$2,\$3,\$4,\$5,\$6,\$7}' $vpairs | sed -e 's/+/1/g' -e 's/-/16/g' > contacts.txt
+ awk '{OFS="\t";print \$1,\$2,\$3,\$5,\$6,\$4,\$7}' $vpairs > contacts.txt
gzip contacts.txt
"""
}
@@ -893,7 +893,7 @@ process cooler_raw {
script:
"""
cooler makebins ${chrsize} ${res} > ${sample}_${res}.bed
- cooler cload pairs -c1 1 -p1 2 -c2 4 -p2 5 ${sample}_${res}.bed ${contacts} ${sample}_${res}.cool
+ cooler cload pairs -c1 2 -p1 3 -c2 4 -p2 5 ${sample}_${res}.bed ${contacts} ${sample}_${res}.cool
cooler dump ${sample}_${res}.cool | awk '{OFS="\t"; print \$1+1,\$2+1,\$3}' > ${sample}_${res}.txt
"""
}
@@ -942,7 +942,7 @@ process cooler_zoomify {
script:
"""
cooler makebins ${chrsize} ${params.res_zoomify} > bins.bed
- cooler cload pairs -c1 1 -p1 2 -c2 4 -p2 5 bins.bed ${contacts} ${sample}.cool
+ cooler cload pairs -c1 2 -p1 3 -c2 4 -p2 5 bins.bed ${contacts} ${sample}.cool
cooler zoomify --nproc ${task.cpus} --balance ${sample}.cool
"""
}
--
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