From a7c2a85a51bdae2f9a168918c8e3318b8ee6f96f Mon Sep 17 00:00:00 2001
From: Li <mourisl@hotmail.com>
Date: Tue, 21 Jan 2020 16:35:01 -0500
Subject: [PATCH] Implement the report for barcodes.

---
 run-trust4         | 4 ++++
 trust-simplerep.pl | 4 ++--
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/run-trust4 b/run-trust4
index 90cc26b..7ed3504 100755
--- a/run-trust4
+++ b/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" ;
diff --git a/trust-simplerep.pl b/trust-simplerep.pl
index 74ebd78..ff05752 100644
--- a/trust-simplerep.pl
+++ b/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 )