Check whether a tax id is in the tree or not.

centrifuge-kreport

@@ -97,6 +97,8 @@ if ($is_cnts_table) {
  my $queryLength = $cols[ $headerMap{ "queryLength" } ] ; 
  my $numMatches = $cols[ $headerMap{ "numMatches" } ] ; 
 
+ $taxID = 1 if ( !isTaxIDInTree( $taxID ) ) ;
+
  if ($no_lca) {
  next if defined $min_length && $hitLength < $min_length;
  next if defined $min_score && $score < $min_score;
@@ -156,6 +158,22 @@ sub dfs_report {
  }
 }
 
+sub isTaxIDInTree {
+ my $a = $_[0] ;
+
+ while ( $a > 1 )
+ {
+ if ( !defined $parent_map{ $a } )
+ {
+ print STDERR "Couldn't find parent of taxID $a - directly assigned to root.\n";
+ return 0 ;
+ }
+ last if ( $a eq $parent_map{$a} ) ;
+ $a = $parent_map{ $a } ;
+ }
+ return 1 ;
+}
+
 sub lca {
  my ($a, $b) = @_;
  return $b if $a eq 0;
@@ -165,7 +183,7 @@ sub lca {
  while ($a ge 1) {
  $a_path{$a} = 1;
  if (!defined $parent_map{$a}) {
- print STDERR "Couldn't find parent of taxID $a - ignoring assignment.";
+ print STDERR "Couldn't find parent of taxID $a - directly assigned to root.\n";
  last;
  }
  last if $a eq $parent_map{$a};
@@ -174,7 +192,7 @@ sub lca {
  while ($b > 1) {
  return $b if (defined $a_path{$b});
  if (!defined $parent_map{$b}) {
- print STDERR "Couldn't find parent of taxID $b - ignoring assignment.";
+ print STDERR "Couldn't find parent of taxID $b - directly assigned to root.\n";
  last;
  }
  last if $b eq $parent_map{$b};