26d45e650717542b662ab602aa4d9a37dda67885
markd
  Wed Nov 9 19:14:57 2022 -0800
generate error if a chromsome in first column of chromAlias is not in chromSizes instead of spew perl warnings

diff --git src/hg/utils/automation/aliasTextToBed.pl src/hg/utils/automation/aliasTextToBed.pl
index ba33a60..7728a02 100755
--- src/hg/utils/automation/aliasTextToBed.pl
+++ src/hg/utils/automation/aliasTextToBed.pl
@@ -98,30 +98,33 @@
 printf AS "    )\n";
 close (AS);
 
 printf STDERR "# indexNames: '%s'\n", $indexNames;
 
 open (BD, "|sort -k1,1 -k2,2n>$opt_aliasBed") or die "can not write to $opt_aliasBed";
 
 while (my $line = <FH>) {
   chomp $line;
   my @a = split('\t', $line, -1); # the -1 keeps all empty fields too
   if (scalar(@a) != $expectFieldCount) {
      printf STDERR "ERROR: expected field count %d =! %d on line %d\n", $expectFieldCount, scalar(@a), $.;
      exit 255;
   }
   my $nameIndex = 0;
+  if (! exists $chromSizes{$a[$nameIndex]}) {
+      die("sequence '$a[$nameIndex]' not found in chromSizes")
+  }
   printf BD "%s\t0\t%d", $a[$nameIndex], $chromSizes{$a[$nameIndex]};
   foreach my $name (@a) {
     printf BD "\t%s", $a[$nameIndex++];
   }
   printf BD "\n";
 }
 close (FH);
 close (BD);
 
 printf STDERR "bedToBigBed -tab -type=bed3+5 -as=$opt_aliasAs -extraIndex=$indexNames $opt_aliasBed $opt_chromSizes $opt_aliasBigBed\n";
 print `bedToBigBed -tab -type=bed3+5 -as=$opt_aliasAs -extraIndex=$indexNames $opt_aliasBed $opt_chromSizes $opt_aliasBigBed`;
 
 __END__
 
 # ucsc	assembly	genbank	ncbi	refseq