8c084018dedc1241e5220ad9b80f83e957368890
hiram
  Fri Jun 24 15:27:06 2022 -0700
handle case of empty input file no redmine

diff --git src/utils/bedInvert.pl src/utils/bedInvert.pl
index 636061f..2e35b68 100755
--- src/utils/bedInvert.pl
+++ src/utils/bedInvert.pl
@@ -70,26 +70,29 @@
                 $chromDone{$chr} = 1;
 		printf "%s\t%d\t%d\t%d\n", $chr, $end, $s,
                    $size if ($size > 0);
 		$chr = $c; $start = $s; $end = $e;
 	    }
 	}
     } else {  # first chromosome, first element
 	$chr = $c; $start = $s; $end = $e;
         $size = $start - 0;
         $chromDone{$chr} = 1;
         # might be the first gap this new chrom
         printf "%s\t0\t%d\t%d\n", $chr, $start, $size if ($size > 0);
     }
 }
 # might be final gap on last chrom mentioned
+# might be an empty input file, no lines read, never set chr
+if (length($chr)) {
  my $chromEnd = $chromSizes{$chr};
  $size = $chromEnd - $end;
  $chromDone{$chr} = 1;
  printf "%s\t%d\t%d\t%d\n", $chr, $end, $chromEnd, $size if ($size > 0);;
+}
 close (FH);
 
 # output gaps on chroms never mentioned yet, they had no elements
 foreach $chr (keys %chromSizes) {
   next if (exists($chromDone{$chr}));
   printf "%s\t0\t%d\t%d\n", $chr, $chromSizes{$chr}, $chromSizes{$chr};
 }