From b2cec9d0e931461b1be327733ef4001a01226757 Mon Sep 17 00:00:00 2001
From: Surya Saha <ss2489@cornell.edu>
Date: Mon, 13 Jul 2015 09:03:32 -0400
Subject: [PATCH] record insertion event and modify  if that line was already
 inserted at, issue #53

---
 lib/Bio/GenomeUpdate/TPF.pm | 24 +++++++++++++++++++++++-
 1 file changed, 23 insertions(+), 1 deletion(-)

diff --git a/lib/Bio/GenomeUpdate/TPF.pm b/lib/Bio/GenomeUpdate/TPF.pm
index f4b7068..2e5fd56 100644
--- a/lib/Bio/GenomeUpdate/TPF.pm
+++ b/lib/Bio/GenomeUpdate/TPF.pm
@@ -2011,7 +2011,29 @@ Returns the length of the accession. Added for use in switchover and trim files
 			}
 			$line_key++;
 		}		
-		#print STDERR Dumper \%sequence_accessions_to_remove;
+
+		#record insertion event and modify $insert_line_number if that line was already inserted at, issue #53
+		if ( $insert_before_or_after eq 'before'){
+			if (!exist $before_insertion_counter{$insert_line_number}){
+				$before_insertion_counter{$insert_line_number} = 1 ;
+			}
+			else{
+				my $old_insert_line_number = $insert_line_number;
+				$insert_line_number = $insert_line_number - $before_insertion_counter{$insert_line_number};
+				$before_insertion_counter{$old_insert_line_number}++ ;
+			}
+		}
+		elsif ( $insert_before_or_after eq 'after'){
+			if (!exist $after_insertion_counter{$insert_line_number}){
+				$after_insertion_counter{$insert_line_number} = 1 ;
+			}
+			else{
+				my $old_insert_line_number = $insert_line_number;
+				$insert_line_number = $insert_line_number + $after_insertion_counter{$insert_line_number};
+				$after_insertion_counter{$old_insert_line_number}++ ;
+			}
+		}
+
 		my $accession = $tpfline_accession[$insert_line_number];
 		my $tpf_line_arr_ref = $accession_tpflines{$accession};
 		my @temp_arr = @$tpf_line_arr_ref;