Change encoding for scripts in repeatmasker (#14358)

This PR converts ISO-8859 encoding to UTF-8 encoding for three scripts in
repeatmasker.

- the main RepeatMasker script
- SimpleBatcher.pm
- wublastToCrossmatch.pl

The ISO-8859 encoding prevented the sbang replacement of long paths when
spack uses python3.

2 files changed, 200 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/repeatmasker/package.py b/var/spack/repos/builtin/packages/repeatmasker/package.py
index c9b7d52875..15aa062b35 100644
--- a/var/spack/repos/builtin/packages/repeatmasker/package.py
+++ b/var/spack/repos/builtin/packages/repeatmasker/package.py
@@ -29,6 +29,8 @@ class Repeatmasker(Package):
     depends_on('phrap-crossmatch-swat', type=('build', 'run'),
                when='+crossmatch')
 
+    patch('utf8.patch')
+
     def url_for_version(self, version):
         url = 'http://www.repeatmasker.org/RepeatMasker-open-{0}.tar.gz'
         return url.format(version.dashed)
diff --git a/var/spack/repos/builtin/packages/repeatmasker/utf8.patch b/var/spack/repos/builtin/packages/repeatmasker/utf8.patch
new file mode 100644
index 0000000000..529b8809d5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/repeatmasker/utf8.patch
@@ -0,0 +1,198 @@
+diff -ru a/RepeatMasker b/RepeatMasker
+--- a/RepeatMasker	2020-01-01 16:16:26.201675025 -0600
++++ b/RepeatMasker	2020-01-01 16:18:02.059526821 -0600
+@@ -1347,7 +1347,7 @@
+ ##
+ ##    Globals Used: None
+ ##
+-##-------------------------------------------------------------------------##·
++##-------------------------------------------------------------------------##·
+ sub adjustFragmentPositions {
+   my $batcher = shift;
+   my $catfile = shift;
+@@ -1456,7 +1456,7 @@
+ ##         to decypher this subroutine.
+ ##
+ ##   Globals Used: none
+-##-------------------------------------------------------------------------##·
++##-------------------------------------------------------------------------##·
+ sub locateISElements {
+   my %options        = %{ shift() };
+   my $batcher        = shift;
+@@ -2951,7 +2951,7 @@
+ ##
+ ##    Globals Used: None
+ ##    Globals Modified: None
+-##-------------------------------------------------------------------------##·
++##-------------------------------------------------------------------------##·
+ sub runLowComplexTests {
+   my %options   = %{ shift() };    # The RepeatMasker option hashtable
+   my $DIRECTORY = shift;
+@@ -3988,7 +3988,7 @@
+ ##
+ ##    Globals Used: None
+ ##    Globals Modified: None
+-##-------------------------------------------------------------------------##·
++##-------------------------------------------------------------------------##·
+ sub runSearchStages {
+   my %options   = %{ shift() };    # The RepeatMasker option hashtable
+   my $DIRECTORY = shift;
+@@ -4707,7 +4707,7 @@
+ ##  Returns
+ ##
+ ##   Globals Used: None
+-##-------------------------------------------------------------------------##·
++##-------------------------------------------------------------------------##·
+ sub chooseMatrices {
+   my $GC_frac = shift;
+ 
+@@ -4910,7 +4910,7 @@
+ ##
+ ##    Globals Used: None
+ ##
+-##-------------------------------------------------------------------------##·
++##-------------------------------------------------------------------------##·
+ sub preMaskLevelFilter {
+   my $searchResults = shift;
+ 
+@@ -4999,7 +4999,7 @@
+ ##
+ ##    Globals Used: None
+ ##
+-##-------------------------------------------------------------------------##·
++##-------------------------------------------------------------------------##·
+ sub filterResults {
+   my %options       = %{ shift() };
+   my $chooseClass   = shift;
+@@ -5860,7 +5860,7 @@
+ ##  Returns
+ ##
+ ##  Globals Used: None
+-##-------------------------------------------------------------------------##·
++##-------------------------------------------------------------------------##·
+ sub calcSimpleRepeatComplexityFromName {
+   my %num = ( "A", 0, "C", 0, "G", 0, "T", 0 );
+   my %log = ( "A", 0, "C", 0, "G", 0, "T", 0 );
+@@ -5902,7 +5902,7 @@
+ ##     revamped to use a SearchResultCollection.
+ ##
+ ##  NO Globals Used
+-##-------------------------------------------------------------------------##·
++##-------------------------------------------------------------------------##·
+ sub getSegments {
+   my $resultsCollection = shift;
+ 
+@@ -6661,7 +6661,7 @@
+ ##  Returns
+ ##
+ ##  Globals Used: None
+-##-------------------------------------------------------------------------##·
++##-------------------------------------------------------------------------##·
+ sub saveOldFiles {
+   my $fijl        = shift;
+   my $fileend     = shift;
+@@ -6708,7 +6708,7 @@
+ ##  Returns
+ ##
+ ##  Globals Used: None
+-##-------------------------------------------------------------------------##·
++##-------------------------------------------------------------------------##·
+ sub SkipFile {
+   my $file = shift;
+ 
+@@ -6734,7 +6734,7 @@
+ ##         about how files are passed to repeatmasker etc..
+ ##
+ ##   Globals Used: ARGV[0]
+-##-------------------------------------------------------------------------##·
++##-------------------------------------------------------------------------##·
+ sub createTempDir {
+   my %options = %{ shift() };
+   my $date    = shift;
+@@ -6792,7 +6792,7 @@
+ ##  Returns
+ ##
+ ##  Globals Used: None
+-##-------------------------------------------------------------------------##·
++##-------------------------------------------------------------------------##·
+ ###  Interrupt handler used by systemint() ###
+ sub handler {
+   my ( $sig ) = @_;
+@@ -6808,7 +6808,7 @@
+ ##  Returns
+ ##
+ ##  Globals Used: None
+-##-------------------------------------------------------------------------##·
++##-------------------------------------------------------------------------##·
+ ###  systemint -- Interruptible system call routine.  ###
+ sub systemint {
+   my ( $cmd ) = @_;
+@@ -6869,7 +6869,7 @@
+ ##       Expects $options{'dir'} ( if set ) to already exist.
+ ##
+ ##  Globals Used: None
+-##-------------------------------------------------------------------------##·
++##-------------------------------------------------------------------------##·
+ sub cleanUp {
+   my %options     = %{ shift() };
+   my $runnumber   = shift;
+@@ -6987,7 +6987,7 @@
+ ##     matching sequences.
+ ##
+ ##  Globals Used: None
+-##-------------------------------------------------------------------------##·
++##-------------------------------------------------------------------------##·
+ sub createLib {
+   my $options      = %{ shift() };
+   my $db           = shift;
+@@ -7322,7 +7322,7 @@
+ ##     will create the frozen databases for WUBlast.
+ ##
+ ##  Globals Used: None
+-##-------------------------------------------------------------------------##·
++##-------------------------------------------------------------------------##·
+ sub processCustomLib {
+   my $options      = %{ shift() };
+   my $tempdir      = shift;
+@@ -7416,7 +7416,7 @@
+ ##            refined.
+ ##
+ ##  Globals Used: None
+-##-------------------------------------------------------------------------##·
++##-------------------------------------------------------------------------##·
+ sub buildRefineableHash {
+   my $db = shift;
+ 
+@@ -7447,7 +7447,7 @@
+ ##  Returns
+ ##
+ ##  Globals Used: None
+-##-------------------------------------------------------------------------##·
++##-------------------------------------------------------------------------##·
+ sub initLibraries {
+   my %options      = %{ shift() };
+   my $rmLibDir     = shift;
+diff -ru a/SimpleBatcher.pm b/SimpleBatcher.pm
+--- a/SimpleBatcher.pm	2020-01-01 16:16:26.203675022 -0600
++++ b/SimpleBatcher.pm	2020-01-01 16:17:24.464585016 -0600
+@@ -559,7 +559,7 @@
+ ##                                  }
+ ##                };
+ ##
+-##------------------------------------------------------------------------##·
++##------------------------------------------------------------------------##·
+ sub _packBatches {
+   my $this        = shift;
+   my $seqDBObj    = shift;
+diff -ru a/util/wublastToCrossmatch.pl b/util/wublastToCrossmatch.pl
+--- a/util/wublastToCrossmatch.pl	2020-01-01 16:16:26.202675024 -0600
++++ b/util/wublastToCrossmatch.pl	2020-01-01 16:17:38.181563793 -0600
+@@ -244,7 +244,7 @@
+ 
+ =cut
+ 
+-##-------------------------------------------------------------------------##·
++##-------------------------------------------------------------------------##·
+ sub publicMethod {
+   my %parameters = @_;
+