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BugFix in make_bed_around_RE_site.pl #45

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BugFix in make_bed_around_RE_site.pl #45

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34 changes: 34 additions & 0 deletions src/bin/make_bed_around_RE_site.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
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