diff --git a/debian/patches/use_both_hmmsets b/debian/patches/use_both_hmmsets
index 7daf6f0..5c91bc7 100644
--- a/debian/patches/use_both_hmmsets
+++ b/debian/patches/use_both_hmmsets
@@ -1,7 +1,9 @@
 Description: Use_both_hmmsets
---- a/bin/barrnap
-+++ b/bin/barrnap
-@@ -3,6 +3,7 @@
+Index: barrnap/bin/barrnap
+===================================================================
+--- barrnap.orig/bin/barrnap
++++ barrnap/bin/barrnap
+@@ -3,6 +3,7 @@ use strict;
  use warnings;
  use List::Util qw(max);
  use FindBin;
@@ -9,7 +11,7 @@
  use File::Temp;
  
  # . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 
-@@ -64,6 +65,7 @@
+@@ -64,6 +65,7 @@ my $kdom = $KINGDOM{ lc substr($kingdom,
  my $hmmdb = "$DBDIR/$kdom.hmm";
  err("Can't find database: $hmmdb") unless -r $hmmdb;
  msg("Using database: $hmmdb");
@@ -17,7 +19,7 @@
  
  # . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 
  # check if user is piping to STDIN
-@@ -84,6 +86,20 @@
+@@ -84,6 +86,20 @@ $fasta && -r $fasta or err("No input fil
  # . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 
  # run the external command
  
@@ -38,7 +40,7 @@
  msg("Scanning $fasta for $kdom rRNA genes... please wait");
  my $opts = "--cpu $threads -E $evalue --w_length $MAXLEN -o /dev/null --tblout /dev/stdout";
  my $cmd = "nhmmer $opts '$hmmdb' '$fasta'";
-@@ -123,7 +139,7 @@
+@@ -123,7 +139,7 @@ foreach (@hits) {
    # check for incomplete alignments
    my $note = '';
    my $len = $end-$begin+1;
@@ -47,7 +49,7 @@
    if ( $len < int($reject * $LENG{$gene}) ) {
      msg("Rejecting short $len nt predicted $gene. Adjust via --reject option.");
      next HIT;
-@@ -144,7 +160,7 @@
+@@ -144,7 +160,7 @@ foreach (@hits) {
    ];
  }
  
diff --git a/debian/patches/use_debian_dirs b/debian/patches/use_debian_dirs
index 4e42545..72f2722 100644
--- a/debian/patches/use_debian_dirs
+++ b/debian/patches/use_debian_dirs
@@ -1,13 +1,15 @@
 Description: Make sure we use correct paths for Debian policy
---- a/bin/barrnap
-+++ b/bin/barrnap
+Index: barrnap/bin/barrnap
+===================================================================
+--- barrnap.orig/bin/barrnap
++++ barrnap/bin/barrnap
 @@ -1,4 +1,4 @@
 -#!/usr/bin/env perl
 +#!/usr/bin/perl
  use strict;
  use warnings;
  use List::Util qw(max);
-@@ -14,6 +14,9 @@
+@@ -14,6 +14,9 @@ my $DESC = "rapid ribosomal RNA predicti
  my $AUTHOR = 'Torsten Seemann';
  my $URL = 'https://github.com/tseemann/barrnap';
  my $DBDIR = "$FindBin::RealBin/../db";