From d2e366a7425c7fe1746de4f125bae1397ac1785b Mon Sep 17 00:00:00 2001
From: Kevin Lewis <kl2@sanger.ac.uk>
Date: Mon, 11 Mar 2024 16:11:59 +0000
Subject: [PATCH] - when processing splice/prune directives, unique port names
 now only required within the set of replacement edges (generated by splicing)

- only remove ports (when pruning) if the port does not appear in the replacement edges (generated by splicing)
---
 bin/vtfp.pl | 28 +++++++++++++++++++++++-----
 1 file changed, 23 insertions(+), 5 deletions(-)

diff --git a/bin/vtfp.pl b/bin/vtfp.pl
index d7c7ea44d..bb53bb82a 100755
--- a/bin/vtfp.pl
+++ b/bin/vtfp.pl
@@ -1412,9 +1412,9 @@ sub validate_splice_candidates {
 		}
 	}
 
-	#  all edge termini must be unique (over replacement and pruning edges) except for STDIN/STDOUT
+	#  all edge termini must be unique (over replacement edges) except for STDIN/STDOUT
 	my %endpoints;
-	for my $edge (@{$splice_candidates->{replacement_edges}}, @{$prune_edges}) {
+	for my $edge (@{$splice_candidates->{replacement_edges}}) {
 		my $from_end = $edge->{from};
 		if($from_end and $from_end !~ /:/) { $from_end .= q[:STDOUT] };
 
@@ -1472,15 +1472,33 @@ sub final_splice {
 	# add new edges
 	push @{$flat_graph->{edges}}, @{$splice_candidates->{replacement_edges}};
 
-	# remove pruned ports - prune edges are not required to be two-ended; just disregard undefined to/from attributes
+	# remove pruned ports - prune edges are not required to be two-ended; just disregard undefined to/from attributes; only remove ports
+	#   that do not appear in splice edges (aka replacement edges)
 	for my $prune_edge (@{$splice_candidates->{prune_edges}}) {
-		if($prune_edge->{from}) { remove_port($prune_edge->{from}, $SRC, $flat_graph); }
-		if($prune_edge->{to}) { remove_port($prune_edge->{to}, $DST, $flat_graph); }
+		if($prune_edge->{from} and not _in_replacement_edges($prune_edge->{from}, $splice_candidates, $SRC)) { remove_port($prune_edge->{from}, $SRC, $flat_graph); }
+		if($prune_edge->{to} and not _in_replacement_edges($prune_edge->{to}, $splice_candidates, $DST)) { remove_port($prune_edge->{to}, $DST, $flat_graph); }
 	}
 
 	return $flat_graph;
 }
 
+sub _in_replacement_edges {
+	my ($port_spec, $splice_candidates, $type) = @_;
+
+	my $direction = ($type == $SRC)? q[from]: q[to];
+	my $std_port = ($type == $SRC)? q[STDIN]: q[STDOUT];
+
+	for my $edge (@{$splice_candidates->{replacement_edges}}) {
+		my $end = $edge->{$direction};
+		if($end and $end !~ /:/) { $end .= qq[:$std_port] };
+
+		if($end eq $port_spec) { return 1; }
+	}
+
+	return 0;
+
+}
+
 ################################################################################################
 # resolve_ports:
 #  given a splice_pair specification, fully determine the [set of] source and destination ports