From 0f4b2a73c84287d1cc98d16e8a55c21a65f77e65 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino <andreaguarracino@outlook.com>
Date: Sun, 3 Nov 2024 17:06:12 -0600
Subject: [PATCH] fix initial windows

---
 scripts/partitioning.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/partitioning.sh b/scripts/partitioning.sh
index 18471c8..837206b 100755
--- a/scripts/partitioning.sh
+++ b/scripts/partitioning.sh
@@ -18,7 +18,7 @@ SAMPLE=$4
 
 # Prepare initial windows
 WINDOWS_BED=windows.bed
-grep $SAMPLE "$FASTA_FAI" -w -m 1 | awk -v OFS='\t' '{print($1,"0",$2)}' > "$SAMPLE.bed"
+grep $SAMPLE "$FASTA_FAI" -w | awk -v OFS='\t' '{print($1,"0",$2)}' > "$SAMPLE.bed"
 bedtools makewindows -b "$SAMPLE.bed" -w "$AVG_WINDOW_SIZE" > "$WINDOWS_BED"
 
 # Prepare mask file