--- a
+++ b/src/trust-barcoderep-to-10X-v0.2.pl
@@ -0,0 +1,93 @@
+#!/usr/bin/env perl
+
+use strict ;
+use warnings ;
+
+die "Usage: ./trust-barcoderep-to-10X.pl trust_barcode_report.tsv 10X_report_prefix\n" if (@ARGV == 0) ;
+
+sub GetDetailChainType
+{
+	foreach my $g (@_)
+	{
+		if ( $g =~ /^IGH/ )
+		{
+			return 0 ;
+		}
+		elsif ( $g =~ /^IGK/ )
+		{
+			return 1 ;
+		}
+		elsif ( $g =~ /^IGL/ )
+		{
+			return 2 ;
+		}
+		elsif ( $g =~ /^TRA/ )
+		{
+			return 3 ;
+		}
+		elsif ( $g =~ /^TRB/ )
+		{
+			return 4 ;
+		}
+		elsif ( $g =~ /^TRG/ )
+		{
+			return 5 ;
+		}
+		elsif ( $g =~ /^TRD/ )
+		{
+			return 6 ;
+		}
+	}
+	return 7 ;	
+}
+
+sub IsProductive
+{
+	my $aa = $_[0] ;
+	return 0 if ($aa eq "partial" || $aa =~ /_/ || $aa =~ /\?/) ;
+	return 1 ;
+}
+
+my @chainName = ("IGH", "IGK", "IGL", "TRA", "TRB", "TRG", "TRD", "None") ;
+open FP, $ARGV[0] ;
+my $prefix = $ARGV[1] ;
+open FPoutT, ">".$prefix."_t.csv" ;
+open FPoutB, ">".$prefix."_b.csv" ;
+
+print FPoutT "barcode,is_cell,contig_id,high_confidence,length,chain,v_gene,d_gene,j_gene,c_gene,full_length,productive,cdr3,cdr3_nt,reads,umis,raw_clonotype_id,raw_consensus_id\n" ;
+print FPoutB "barcode,is_cell,contig_id,high_confidence,length,chain,v_gene,d_gene,j_gene,c_gene,full_length,productive,cdr3,cdr3_nt,reads,umis,raw_clonotype_id,raw_consensus_id\n" ;
+
+my $header = <FP> ;
+while (<FP>)
+{
+	chomp ;
+	my @cols = split ;
+        #AACTCTTGTTATCCGA-1	abT	*	TRAV6*01,*,TRAJ43*01,*,TGTGCTCTAGCCGGGGAGGGCATGCGCTTT,CALAGEGMRF,2.80,AACTCTTGTTATCCGA-1_26095,100.00	*	*
+	for (my $i = 2 ; $i <= 3 ; ++$i)
+	{
+		next if ($cols[$i] eq "*") ;
+		my @chainCols = split /,/, $cols[$i] ;
+		#barcode,is_cell,contig_id,high_confidence,length,chain,v_gene,d_gene,j_gene,c_gene,full_length,productive,cdr3,cdr3_nt,reads,umis,raw_clonotype_id,raw_consensus_id
+		#AAACCTGAGTCGATAA-1,True,AAACCTGAGTCGATAA-1_contig_1,True,551,IGK,IGKV1-5,None,IGKJ1,IGKC,True,True,CQQYNSYSRTF,TGCCAACAGTATAATAGTTATTCTCGAACGTTC,1197,22,clonotype77,clonotype77_consensus_2
+		my @outputCols = ($cols[0], "True", "None", "True", "None", 
+			$chainName[GetDetailChainType($chainCols[0], $chainCols[2],$chainCols[3])],
+			$chainCols[0] eq "*" ? "None": $chainCols[0],
+			$chainCols[1] eq "*" ? "None": $chainCols[1],
+			$chainCols[2] eq "*" ? "None": $chainCols[2],
+			$chainCols[3] eq "*" ? "None": $chainCols[3],
+			"None", IsProductive($cols[5]) ? "True" : "False", 
+			$chainCols[5], $chainCols[4], $chainCols[6], $chainCols[6], "None", "None"
+			) ;
+		if (substr($cols[1], -1) eq "T")
+		{
+			print FPoutT join(",", @outputCols), "\n" ;
+		}
+		else
+		{
+			print FPoutB join(",", @outputCols), "\n" ;
+		}
+	}
+}
+close FPoutT ;
+close FPoutB ;
+close FP ;