396fc7273c589cc83a4107a365fe67aa28b4457e
angie
  Fri Mar 5 15:34:32 2021 -0800
If BioSample date is more complete than GenBank date, use it.

diff --git src/hg/utils/otto/sarscov2phylo/gbMetadataAddBioSample.pl src/hg/utils/otto/sarscov2phylo/gbMetadataAddBioSample.pl
index 037e12b..8e089c7 100755
--- src/hg/utils/otto/sarscov2phylo/gbMetadataAddBioSample.pl
+++ src/hg/utils/otto/sarscov2phylo/gbMetadataAddBioSample.pl
@@ -48,31 +48,31 @@
 while (<$BIOSAMPLE>) {
   my (undef, $bAcc, $name, $date, undef, undef, $country) = split("\t");
   $b2Name{$bAcc} = $name;
   $b2Date{$bAcc} = $date;
   $b2Country{$bAcc} = $country;
 }
 close($BIOSAMPLE);
 
 my $missingCount = 0;
 while (<>) {
   my ($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) {
+      if (! $gbDate || length($bDate) > length($gbDate)) {
         $gbDate = $bDate;
       } elsif ($bDate && $gbDate ne $bDate) {
         print STDERR "CONFLICT: Genbank date ($gbAcc $gbName) = $gbDate, " .
           "BioSample date ($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;
       }