From 79d2b3c7e006ecc3f2d8ba51842fecfcb0ef4b70 Mon Sep 17 00:00:00 2001
From: Junpeng Fan <schooiboy@qq.com>
Date: Wed, 11 Apr 2018 18:05:26 +0800
Subject: [PATCH] fix bug in make_bed_around_RE_site.pl

skip reading the last fasta recod
---
 src/bin/make_bed_around_RE_site.pl | 34 ++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/src/bin/make_bed_around_RE_site.pl b/src/bin/make_bed_around_RE_site.pl
index 3f64812..c3cc5ba 100755
--- a/src/bin/make_bed_around_RE_site.pl
+++ b/src/bin/make_bed_around_RE_site.pl
@@ -190,6 +190,40 @@
     
 }
 
+# process the last fasta record
+my ( $prev_start, $prev_end ) = (-1,-1);
+foreach my $pos ( @motif_positions ) {
+	if ( $prev_end == -1 ) {
+	$prev_start = $pos;
+	$prev_end   = $pos;
+	}
+	if ( $prev_end + 2*$range < $pos ) {
+	$prev_start =         $range if $prev_start < $range;
+	$prev_end = $offset - $range if $prev_end > $offset - $range; # prevent overflow past the end of the contig/chromosome
+	print BED "$contig_name\t", $prev_start - $range, "\t", $prev_end + $range, "\n";
+	$prev_start = $pos;
+	}
+	#print "pos = $pos\n";
+	$prev_end = $pos;
+}
+	
+# Print the final BED line for this contig/chromosome.
+if (@motif_positions) {
+	$prev_start =         $range if $prev_start < $range;
+	$prev_end = $offset - $range if $prev_end > $offset - $range; # prevent overflow past the end of the contig/chromosome
+	print BED "$contig_name\t", $prev_start - $range, "\t", $prev_end + $range, "\n";
+}
+	
+# Get the new contig's name.
+$contig_name = $1;
+print localtime() . ": $contig_name\n" if $verbose;
+print POS ">$contig_name\n";
+	
+# Reset other contig-related variables.
+$offset = 0;
+$prev_chars = '';
+@motif_positions = ();
+
 close IN;
 close BED;
 close POS;