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.
This commit is contained in:
Glenn Johnson
Adam J. Stewart
parent
b69cf08cfb
commit
726a662c2c
2 changed files with 200 additions and 0 deletions
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@ -29,6 +29,8 @@ class Repeatmasker(Package):
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depends_on('phrap-crossmatch-swat', type=('build', 'run'),
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when='+crossmatch')
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patch('utf8.patch')
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def url_for_version(self, version):
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url = 'http://www.repeatmasker.org/RepeatMasker-open-{0}.tar.gz'
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return url.format(version.dashed)
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198
var/spack/repos/builtin/packages/repeatmasker/utf8.patch
Normal file
198
var/spack/repos/builtin/packages/repeatmasker/utf8.patch
Normal file
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@ -0,0 +1,198 @@
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diff -ru a/RepeatMasker b/RepeatMasker
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--- a/RepeatMasker 2020-01-01 16:16:26.201675025 -0600
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+++ b/RepeatMasker 2020-01-01 16:18:02.059526821 -0600
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@@ -1347,7 +1347,7 @@
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##
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## Globals Used: None
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##
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-##-------------------------------------------------------------------------##·
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+##-------------------------------------------------------------------------##·
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sub adjustFragmentPositions {
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my $batcher = shift;
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my $catfile = shift;
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@@ -1456,7 +1456,7 @@
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## to decypher this subroutine.
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##
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## Globals Used: none
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-##-------------------------------------------------------------------------##·
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+##-------------------------------------------------------------------------##·
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sub locateISElements {
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my %options = %{ shift() };
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my $batcher = shift;
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@@ -2951,7 +2951,7 @@
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##
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## Globals Used: None
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## Globals Modified: None
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-##-------------------------------------------------------------------------##·
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+##-------------------------------------------------------------------------##·
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sub runLowComplexTests {
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my %options = %{ shift() }; # The RepeatMasker option hashtable
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my $DIRECTORY = shift;
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@@ -3988,7 +3988,7 @@
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##
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## Globals Used: None
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## Globals Modified: None
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-##-------------------------------------------------------------------------##·
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+##-------------------------------------------------------------------------##·
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sub runSearchStages {
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my %options = %{ shift() }; # The RepeatMasker option hashtable
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my $DIRECTORY = shift;
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@@ -4707,7 +4707,7 @@
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## Returns
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##
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## Globals Used: None
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-##-------------------------------------------------------------------------##·
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+##-------------------------------------------------------------------------##·
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sub chooseMatrices {
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my $GC_frac = shift;
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@@ -4910,7 +4910,7 @@
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##
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## Globals Used: None
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##
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-##-------------------------------------------------------------------------##·
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+##-------------------------------------------------------------------------##·
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sub preMaskLevelFilter {
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my $searchResults = shift;
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@@ -4999,7 +4999,7 @@
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##
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## Globals Used: None
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##
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-##-------------------------------------------------------------------------##·
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+##-------------------------------------------------------------------------##·
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sub filterResults {
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my %options = %{ shift() };
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my $chooseClass = shift;
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@@ -5860,7 +5860,7 @@
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## Returns
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##
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## Globals Used: None
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-##-------------------------------------------------------------------------##·
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+##-------------------------------------------------------------------------##·
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sub calcSimpleRepeatComplexityFromName {
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my %num = ( "A", 0, "C", 0, "G", 0, "T", 0 );
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my %log = ( "A", 0, "C", 0, "G", 0, "T", 0 );
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@@ -5902,7 +5902,7 @@
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## revamped to use a SearchResultCollection.
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##
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## NO Globals Used
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-##-------------------------------------------------------------------------##·
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+##-------------------------------------------------------------------------##·
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sub getSegments {
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my $resultsCollection = shift;
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@@ -6661,7 +6661,7 @@
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## Returns
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##
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## Globals Used: None
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-##-------------------------------------------------------------------------##·
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+##-------------------------------------------------------------------------##·
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sub saveOldFiles {
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my $fijl = shift;
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my $fileend = shift;
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@@ -6708,7 +6708,7 @@
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## Returns
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##
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## Globals Used: None
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-##-------------------------------------------------------------------------##·
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+##-------------------------------------------------------------------------##·
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sub SkipFile {
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my $file = shift;
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@@ -6734,7 +6734,7 @@
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## about how files are passed to repeatmasker etc..
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##
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## Globals Used: ARGV[0]
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-##-------------------------------------------------------------------------##·
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+##-------------------------------------------------------------------------##·
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sub createTempDir {
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my %options = %{ shift() };
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my $date = shift;
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@@ -6792,7 +6792,7 @@
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## Returns
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##
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## Globals Used: None
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-##-------------------------------------------------------------------------##·
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+##-------------------------------------------------------------------------##·
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### Interrupt handler used by systemint() ###
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sub handler {
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my ( $sig ) = @_;
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@@ -6808,7 +6808,7 @@
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## Returns
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##
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## Globals Used: None
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-##-------------------------------------------------------------------------##·
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+##-------------------------------------------------------------------------##·
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### systemint -- Interruptible system call routine. ###
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sub systemint {
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my ( $cmd ) = @_;
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@@ -6869,7 +6869,7 @@
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## Expects $options{'dir'} ( if set ) to already exist.
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##
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## Globals Used: None
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-##-------------------------------------------------------------------------##·
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+##-------------------------------------------------------------------------##·
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sub cleanUp {
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my %options = %{ shift() };
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my $runnumber = shift;
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@@ -6987,7 +6987,7 @@
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## matching sequences.
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##
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## Globals Used: None
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-##-------------------------------------------------------------------------##·
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+##-------------------------------------------------------------------------##·
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sub createLib {
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my $options = %{ shift() };
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my $db = shift;
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@@ -7322,7 +7322,7 @@
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## will create the frozen databases for WUBlast.
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##
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## Globals Used: None
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-##-------------------------------------------------------------------------##·
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+##-------------------------------------------------------------------------##·
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sub processCustomLib {
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my $options = %{ shift() };
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my $tempdir = shift;
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@@ -7416,7 +7416,7 @@
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## refined.
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##
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## Globals Used: None
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-##-------------------------------------------------------------------------##·
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+##-------------------------------------------------------------------------##·
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sub buildRefineableHash {
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my $db = shift;
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@@ -7447,7 +7447,7 @@
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## Returns
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##
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## Globals Used: None
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-##-------------------------------------------------------------------------##·
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+##-------------------------------------------------------------------------##·
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sub initLibraries {
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my %options = %{ shift() };
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my $rmLibDir = shift;
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diff -ru a/SimpleBatcher.pm b/SimpleBatcher.pm
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--- a/SimpleBatcher.pm 2020-01-01 16:16:26.203675022 -0600
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+++ b/SimpleBatcher.pm 2020-01-01 16:17:24.464585016 -0600
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@@ -559,7 +559,7 @@
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## }
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## };
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##
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-##------------------------------------------------------------------------##·
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+##------------------------------------------------------------------------##·
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sub _packBatches {
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my $this = shift;
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my $seqDBObj = shift;
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diff -ru a/util/wublastToCrossmatch.pl b/util/wublastToCrossmatch.pl
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--- a/util/wublastToCrossmatch.pl 2020-01-01 16:16:26.202675024 -0600
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+++ b/util/wublastToCrossmatch.pl 2020-01-01 16:17:38.181563793 -0600
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@@ -244,7 +244,7 @@
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=cut
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-##-------------------------------------------------------------------------##·
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+##-------------------------------------------------------------------------##·
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sub publicMethod {
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my %parameters = @_;
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