fix initial windows

pangenome · Nov 3, 2024 · 0f4b2a7 · 0f4b2a7
1 parent 9c48510
commit 0f4b2a7
Showing 1 changed file with 1 addition and 1 deletion.
diff --git 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