From 195d11a48d2a738f4178232ea3b5162a6aff4984 Mon Sep 17 00:00:00 2001
From: "David Eccles (gringer)" <github@gringer.org>
Date: Sun, 1 May 2016 22:11:39 +1200
Subject: [PATCH] added script to remove identical matches from LAST alignment

---
 last-rmident.pl | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100755 last-rmident.pl

diff --git a/last-rmident.pl b/last-rmident.pl
new file mode 100755
index 0000000..b91d5ef
--- /dev/null
+++ b/last-rmident.pl
@@ -0,0 +1,31 @@
+#!/usr/bin/perl
+
+my @lineBuffer = ();
+my @ids = ();
+
+while(<>){
+  my $line = $_;
+  if(/^([a-z])\s(.*?)\s/){
+    my ($flag, $id) = ($1, $2);
+    if($flag eq "s"){
+        push(@ids, $id);
+    } elsif($flag eq "a"){ # new alignment
+      if((scalar(@ids) != 2) || ($ids[0] ne $ids[1])){
+        print(join("",@lineBuffer));
+      }
+      # if(@ids){
+      #   printf("a '%s' '%s' %d %d\n", $ids[0], $ids[1],
+      #          scalar(@lineBuffer), scalar(@ids));
+      # } else {
+      #   print("a\n");
+      # }
+      @lineBuffer = ();
+      @ids = ();
+    }
+  }
+  push(@lineBuffer, $line);
+}
+
+if((scalar(@ids) != 2) || ($ids[0] ne $ids[1])){
+  print(join("",@lineBuffer));
+}