Cleanup and initializations

Author: sammysheep

.vscode/settings.json

@@ -7,6 +7,8 @@
         "ValuesAndExpressions::ProhibitMagicNumbers",
         "InputOutput::RequireBriefOpen",
         "Modules::ProhibitExcessMainComplexity",
-        "Modules::RequireVersionVar"
+        "Modules::RequireVersionVar",
+        "ControlStructures::ProhibitDeepNests",
+        "BuiltinFunctions::ProhibitStringySplit"
     ]
 }

LABEL_RES/scripts/._hmmscore

@@ -78,7 +78,7 @@
     local $RS = "\n";
     while ( my $line = <PL> ) {
         chomp($line);
-        my @pieces = split( '/', $line );
+        my @pieces = split( q{/}, $line );
         my $annot  = pop(@pieces);
         my $junk   = shift(@pieces);
         if ( scalar @pieces > 1 ) {
@@ -116,7 +116,7 @@ ($)
     my $pred = trim( $fields[1] );
     my $anno = 'unknown';
 
-    if ( $fields[0] =~ /{([^{}]*)}\s*$/sxm ) {
+    if ( $fields[0] =~ /{([^{}]*)}\s*$/smx ) {
         $anno = $1;
     }
 

LABEL_RES/scripts/evaluateResults.pl

@@ -43,7 +43,8 @@
 use File::Basename;
 use Getopt::Long;
 
-my ( $numberGroups, $fraction, $fastQ, $byReadPairs, $readZipped, $underscoreHeader, $extension );
+my ( $numberGroups, $fraction, $extension );
+my ( $byReadPairs, $readZipped, $underscoreHeader, $fastQ ) = ( 0, 0, 0, 0 );
 GetOptions(
             'groups|G=i'          => \$numberGroups,
             'fraction|F=i'        => \$fraction,
@@ -54,7 +55,7 @@
             'extension|X:s'       => \$extension
 );
 
-if ( scalar(@ARGV) < 2 ) {
+if ( scalar @ARGV < 2 ) {
     die(   "\n$PROGRAM_NAME <input.fasta> <out_prefix> [-G <#groups>|-F <denom-fraction>] [OPTIONS]\n"
          . "\t-F|--fraction POSITIVE_NUMBER\t\tFraction of dataset, using denominator D: 1/D.\n"
          . "\t-G|--groups POSITIVE_NUMBER\t\tNumber of datasets required.\n"

LABEL_RES/scripts/interleavedSamples.pl

@@ -0,0 +1,6 @@
+
+
+my $s = 'Sam/is/there';
+foreach $x ( split(q{/},$s) ) {
+    print $x,"\n";
+}