perltidy

bystrogenomics · Feb 21, 2024 · 5e4bde9 · 5e4bde9
1 parent 49def01
commit 5e4bde9
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Showing 3 changed files with 222 additions and 172 deletions.
diff --git a/perl/lib/Seq/Role/IO.pm b/perl/lib/Seq/Role/IO.pm
@@ -1,6 +1,7 @@
 use 5.10.0;
 use strict;
 use warnings;
+
 package Seq::Role::IO;
 
 our $VERSION = '0.001';
@@ -44,25 +45,25 @@ has cat => (
 
 has gzip => (
   is      => 'ro',
-  lazy     => 1,
-  default  => sub {
+  lazy    => 1,
+  default => sub {
     return which('bgzip') || which('pigz') || which('gzip');
   },
 );
 
 has lz4 => (
   is      => 'ro',
-  lazy     => 1,
-  default  => sub {
+  lazy    => 1,
+  default => sub {
     return which('lz4');
   },
 );
 
 has gzipDcmpArgs => (
-  is      => 'ro',
-  lazy    => 1,
+  is       => 'ro',
+  lazy     => 1,
   init_arg => undef,
-  default => sub {
+  default  => sub {
     my $self = shift;
 
     my $gzip = $self->gzip;
@@ -76,10 +77,10 @@ has gzipDcmpArgs => (
 );
 
 has gzipCmpArgs => (
-  is      => 'ro',
-  lazy    => 1,
+  is       => 'ro',
+  lazy     => 1,
   init_arg => undef,
-  default => sub {
+  default  => sub {
     my $self = shift;
     my $gzip = $self->gzip;
 
@@ -119,18 +120,17 @@ has zip => (
   },
 );
 
-
 sub getReadArgs {
   my ( $self, $filePath ) = @_;
 
   my ( $remoteCpCmd, $remoteFileSizeCmd ) = $self->getRemoteProg($filePath);
   my $outerCommand = $self->getDecompressProgWithArgs($filePath);
 
   if ($remoteCpCmd) {
-    if ($outerCommand != $self->cat) {
+    if ( $outerCommand != $self->cat ) {
       # If we're piping to unzip, that won't work with standard unzip
       # For now raise an exception
-      if (index($outerCommand, $self->unzip) != -1) {
+      if ( index( $outerCommand, $self->unzip ) != -1 ) {
         die "Cannot pipe to unzip with remote files";
       }
 
@@ -260,7 +260,7 @@ sub getWriteFh {
 
   my $fh;
 
-  ( $err, my $cmd ) = $self->getCompresssedWriteCmd( $file );
+  ( $err, my $cmd ) = $self->getCompresssedWriteCmd($file);
 
   if ($err) {
     return ( $err, undef );
@@ -280,33 +280,40 @@ sub getCompresssedWriteCmd {
   my ( $self, $file ) = @_;
 
   my $hasGz  = $file =~ /[.]gz$/ || $file =~ /[.]bgz$/;
-  my $hasZip  = $file =~ /[.]zip$/;
+  my $hasZip = $file =~ /[.]zip$/;
   my $hasLz4 = $file =~ /[.]lz4$/;
 
-  if ( $hasLz4 ) {
-    if(!$self->lz4) {
-      return ("lz4 requested but lz4 program not passed to Seq::Role::IO or not found in system", undef)
+  if ($hasLz4) {
+    if ( !$self->lz4 ) {
+      return (
+        "lz4 requested but lz4 program not passed to Seq::Role::IO or not found in system",
+        undef );
     }
-    return (undef, $self->lz4 . " > $file");
+    return ( undef, $self->lz4 . " > $file" );
   }
 
-  if ( $hasGz ) {
-    if(!$self->gzip) {
-      return ("gzip requested but gzip-compatible program not passed to Seq::Role::IO or not found in system", undef)
+  if ($hasGz) {
+    if ( !$self->gzip ) {
+      return (
+        "gzip requested but gzip-compatible program not passed to Seq::Role::IO or not found in system",
+        undef
+      );
     }
 
-    return (undef, $self->gzip . " " . $self->gzipCmpArgs . " > $file");
+    return ( undef, $self->gzip . " " . $self->gzipCmpArgs . " > $file" );
   }
 
-  if ( $hasZip ) {
-    if(!$self->zip) {
-      return ("zip requested but zip program not passed to Seq::Role::IO or not found in system", undef)
+  if ($hasZip) {
+    if ( !$self->zip ) {
+      return (
+        "zip requested but zip program not passed to Seq::Role::IO or not found in system",
+        undef );
     }
 
-    return (undef, $self->zip . " -q > $file");
+    return ( undef, $self->zip . " -q > $file" );
   }
 
-  return (undef, undef);
+  return ( undef, undef );
 }
 
 # Allows user to return an error; dies with logging by default
@@ -464,12 +471,12 @@ sub compressDirIntoTarball {
     return 'Directory is empty';
   }
 
-  my $tar = $self->tar;
+  my $tar  = $self->tar;
   my $gzip = $self->gzip;
-  my $lz4 = $self->lz4;
+  my $lz4  = $self->lz4;
 
   my $tarProg =
-      $tarballName =~ /tar.gz$/
+    $tarballName =~ /tar.gz$/
     ? "$tar --use-compress-program=$gzip"
     : ( $tarballName =~ /tar.lz4$/ ? "$tar --use-compress-program=$lz4" : "tar" );
   my $tarCommand = sprintf(

diff --git a/perl/lib/Seq/Tracks/Vcf/Build.pm b/perl/lib/Seq/Tracks/Vcf/Build.pm
@@ -449,7 +449,7 @@ sub _openVcfPipe {
   my $outputter = Seq::Output::Delimiters->new();
 
   my $delim = $outputter->emptyFieldChar;
-  my $prog = $self->getDecompressProgWithArgs($file);
+  my $prog  = $self->getDecompressProgWithArgs($file);
 
   my $errPath = $file . ".build." . localtime() . ".log";