fa70926eb39b233849ef2a1f0e36f4ed264dc832
angie
  Fri Aug 26 11:55:24 2022 -0700
Bump up maxMissing, sometimes there are just a ton.

diff --git src/hg/utils/otto/sarscov2phylo/gbMetadataAddBioSample.pl src/hg/utils/otto/sarscov2phylo/gbMetadataAddBioSample.pl
index 4e0fc6a..88dca79 100755
--- src/hg/utils/otto/sarscov2phylo/gbMetadataAddBioSample.pl
+++ src/hg/utils/otto/sarscov2phylo/gbMetadataAddBioSample.pl
@@ -42,54 +42,55 @@
 
 open(my $BIOSAMPLE, "<$biosampleFile") || die "Can't open $biosampleFile: %!\n";
 
 my %b2Name = ();
 my %b2Date = ();
 my %b2Country = ();
 while (<$BIOSAMPLE>) {
   my (undef, $bAcc, $name, $date, undef, undef, $country) = split("\t");
   $b2Name{$bAcc} = $name;
   $b2Date{$bAcc} = $date;
   $b2Country{$bAcc} = $country;
 }
 close($BIOSAMPLE);
 
 my $missingCount = 0;
+my $maxMissing = 1000000;
 while (<>) {
   my ($gbAcc, $bAcc, $gbDate, $gbGeo, $host, $gbName, $completeness, $len) = split("\t");
   if ($bAcc) {
     if (exists $b2Name{$bAcc}) {
       my ($bName, $bDate, $bCountry) = ($b2Name{$bAcc}, normalizeDate($b2Date{$bAcc}),
                                         $b2Country{$bAcc});
       if (! $gbDate || length($bDate) > length($gbDate)) {
         $gbDate = $bDate;
       } elsif ($bDate && $gbDate ne $bDate) {
         print STDERR join("\t", "dateMismatch", $gbAcc, $gbName, $gbDate, $bAcc, $bName, $bDate) .
           "\n";
       }
       if (! $gbName) {
         $gbName = $bName;
       } elsif (($gbName eq '1' || $gbName eq 'NA') && length($bName) > length($gbName)) {
         $gbName = $bName;
       } elsif ($gbName eq 'nasopharyngeal' && $bName =~ m/\d/) {
         $gbName = $bName;
       }
       if (! $gbGeo) {
         $gbGeo = $bCountry;
       }
       print join("\t", $gbAcc, $bAcc, $gbDate, $gbGeo, $host, $gbName, $completeness, $len);
     } else {
       # BioSample file doesn't have info for this BioSample accession
       print STDERR "Missing BioSample info for $bAcc\n";
       $missingCount++;
-      if ($missingCount >= 100000) {
-        die "Too many missing BioSamples, quitting.\n";
+      if ($missingCount > $maxMissing) {
+        die "Too many missing BioSamples (> $maxMissing), quitting.\n";
       }
       # Pass through as-is
       print;
     }
   } else {
     # No associated BioSample, just pass through as-is
     print;
   }
 }