From 7cfa8513d8846771d584b4c5eedf8d4cdf0795d4 Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Mon, 25 Jul 2022 17:04:02 +0200
Subject: [PATCH] [LINT] padding
---
bin/hicpro_merge_validpairs.sh | 22 +++++++++++-----------
1 file changed, 11 insertions(+), 11 deletions(-)
diff --git a/bin/hicpro_merge_validpairs.sh b/bin/hicpro_merge_validpairs.sh
index 40b758c..e6c5200 100755
--- a/bin/hicpro_merge_validpairs.sh
+++ b/bin/hicpro_merge_validpairs.sh
@@ -27,23 +27,23 @@ if [[ ${rmDup} == 1 ]]; then
fcounts=0
for vfile in ${vpairs}
do
- echo "Sorting ${vfile} ..."
- fcounts=$((fcounts+1))
- ofile=$(echo ${vfile} | sed -e 's/validPairs/sorted.validPairs/')
- #sort -k2,2V -k3,3n -k5,5V -k6,6n -T ./tmp/ -o ${ofile} ${vfile}
- sort -k2,2 -k5,5 -k3,3n -k6,6n -T ./tmp/ -o ${ofile} ${vfile}
+ echo "Sorting ${vfile} ..."
+ fcounts=$((fcounts+1))
+ ofile=$(echo ${vfile} | sed -e 's/validPairs/sorted.validPairs/')
+ #sort -k2,2V -k3,3n -k5,5V -k6,6n -T ./tmp/ -o ${ofile} ${vfile}
+ sort -k2,2 -k5,5 -k3,3n -k6,6n -T ./tmp/ -o ${ofile} ${vfile}
done
if [[ $fcounts -gt 1 ]]
then
- echo "Merging and removing the duplicates ..."
- ## Sort valid pairs and remove read pairs with same starts (i.e duplicated read pairs)
- #sort -k2,2V -k3,3n -k5,5V -k6,6n -T ./tmp/ -m ${vpairs_sorted} | \
- sort -k2,2 -k5,5 -k3,3n -k6,6n -T ./tmp/ -m ${vpairs_sorted} | \
+ echo "Merging and removing the duplicates ..."
+ ## Sort valid pairs and remove read pairs with same starts (i.e duplicated read pairs)
+ #sort -k2,2V -k3,3n -k5,5V -k6,6n -T ./tmp/ -m ${vpairs_sorted} | \
+ sort -k2,2 -k5,5 -k3,3n -k6,6n -T ./tmp/ -m ${vpairs_sorted} | \
awk -F"\t" 'BEGIN{c1=0;c2=0;s1=0;s2=0}(c1!=$2 || c2!=$5 || s1!=$3 || s2!=$6){print;c1=$2;c2=$5;s1=$3;s2=$6}' > ${prefix}.allValidPairs
else
- echo "Removing the duplicates ..."
- cat ${vpairs_sorted} | awk -F"\t" 'BEGIN{c1=0;c2=0;s1=0;s2=0}(c1!=$2 || c2!=$5 || s1!=$3 || s2!=$6){print;c1=$2;c2=$5;s1=$3;s2=$6}' > ${prefix}.allValidPairs
+ echo "Removing the duplicates ..."
+ cat ${vpairs_sorted} | awk -F"\t" 'BEGIN{c1=0;c2=0;s1=0;s2=0}(c1!=$2 || c2!=$5 || s1!=$3 || s2!=$6){print;c1=$2;c2=$5;s1=$3;s2=$6}' > ${prefix}.allValidPairs
fi
## clean
--
GitLab