Implement the report for barcodes.

run-trust4

@@ -266,6 +266,10 @@ if ( $stage <= 2 )
 if ( $stage <= 3 )
 {
 	system_call( "perl $WD/trust-simplerep.pl ${prefix}_cdr3.out $simpleRepArgs > ${prefix}_report.tsv" ) ;
+	if ( $hasBarcode == 1 )
+	{
+		system_call( "perl $WD/trust-barcoderep.pl ${prefix}_cdr3.out --noPartial > ${prefix}_barcode_report.tsv" ) ;
+	}
 }
 
 print STDERR "[".localtime()."] TRUST4 finishes.\n" ;

trust-simplerep.pl

@@ -329,6 +329,8 @@ sub InferConstantGene
 {
 	chomp ;
 	my @cols = split ;
+	next if ( $reportPartial == 0 && $cols[9] == 0 ) ;
+
 	my $assemblyId = $cols[0] ;
 	my $vgene = (split /,/, $cols[2])[0] ;
 	my $dgene = (split /,/, $cols[3])[0] ;
@@ -339,8 +341,6 @@ sub InferConstantGene
 	my $key = join( "\t", ( $vgene, $dgene, $jgene, $cgene, $cols[8] ) ) ;
 	my $type = GetChainType( $vgene, $jgene, $cgene ) ;
 
-	next if ( $reportPartial == 0 && $cols[9] == 0 ) ;
-
 	if ($type == 2) # TCR
 	{
 		if ($cols[10] < $assemblyMostReads{$assemblyId} * $tcrErrorFilter )