Tidy.

lib/DETCT/Analysis.pm

@@ -871,8 +871,7 @@ sub get_all_ensembl_db_types {
 
     return [
         sort keys %{ $ensembl_db_type{ id $self}
-              || { $DEFAULT_ENSEMBL_DB_TYPE => 1 } }
-    ];
+              || { $DEFAULT_ENSEMBL_DB_TYPE => 1 } } ];
 }
 
 =method slice_adaptor

lib/DETCT/GeneFinder.pm

@@ -700,7 +700,7 @@ sub add_existing_gene_annotation {
         my $end        = $region->[2];
         my $strand     = $region->[7];    ## no critic (ProhibitMagicNumbers)
         my $annotation = $region->[-1];
-        my $key = join q{:}, $seq_name, $start, $end, $strand;
+        my $key        = join q{:}, $seq_name, $start, $end, $strand;
         $gene_annotation{$key} = $annotation;
     }
 

lib/DETCT/Misc/Output.pm

@@ -194,9 +194,9 @@ sub dump_as_table {    ## no critic (ProhibitExcessComplexity)
                       [ $transcript_stable_id, $transcript_stable_id ];
                     push @transcript_biotype, $transcript_biotype;
                 }
-                push @name, $name;
+                push @name,         $name;
                 push @name_to_link, [ $gene_stable_id, $name ];
-                push @description, $description;
+                push @description,  $description;
             }
         }
         push @row, [ \@distance ];
@@ -338,11 +338,11 @@ sub get_definition {
 
     my @def;
 
-    push @def, [ 'Chr',              $STRING, $loc_link, ];
-    push @def, [ 'Region start',     $INT,    $loc_link, ];
-    push @def, [ 'Region end',       $INT,    $loc_link, ];
-    push @def, [ q{3' end position}, $INT,    $loc_link, ];
-    push @def, [ q{3' end strand},   $INT, ];
+    push @def, [ 'Chr',                 $STRING, $loc_link, ];
+    push @def, [ 'Region start',        $INT,    $loc_link, ];
+    push @def, [ 'Region end',          $INT,    $loc_link, ];
+    push @def, [ q{3' end position},    $INT,    $loc_link, ];
+    push @def, [ q{3' end strand},      $INT, ];
     push @def, [ q{3' end read count},  $INT, ];
     push @def, [ 'p value',             $FLOAT, ];
     push @def, [ 'Adjusted p value',    $FLOAT, ];

lib/DETCT/Misc/R.pm

@@ -172,7 +172,7 @@ sub run_deseq {    ## no critic (ProhibitExcessComplexity)
     }
     open my $samples_fh, '>', $samples_file;
     write_or_die( $samples_fh, ( join "\t", @header ), "\n" );
-    write_or_die( $samples_fh,                         $samples_text );
+    write_or_die( $samples_fh, $samples_text );
     close $samples_fh;
 
     my $control_condition = q{-};

lib/DETCT/Misc/SSAHA2.pm

@@ -276,7 +276,7 @@ sub parse_ssaha2 {
             $alignment_length, $percent_id
         ) = split /\s+/xms, $line;
         my ( $seq_name, $index ) = split /:/xms, $query_id;
-        $strand = $strand eq q{F} ? q{+} : q{-};
+        $strand     = $strand eq q{F} ? q{+} : q{-};
         $percent_id = int $percent_id + 0.5; ## no critic (ProhibitMagicNumbers)
         push @{ $alignments{$seq_name}{$index} },
           [

lib/DETCT/Misc/Tag.pm

@@ -73,7 +73,7 @@ sub detag_trim_fastq {
     my $tag_length = length $arg_ref->{read_tags}[0];
 
     my $min_polyt = q{T} x $arg_ref->{polyt_min_length};
-    my $polyt_re = qr/$min_polyt/xms;    # Regexp for polyT matching
+    my $polyt_re  = qr/$min_polyt/xms;    # Regexp for polyT matching
 
     my $read1_required_length    = $arg_ref->{read1_required_length};
     my $read2_required_length    = $arg_ref->{read2_required_length};

lib/DETCT/Pipeline.pm

@@ -58,7 +58,7 @@ private sleep_time    => my %sleep_time;       # e.g. 600
 private skip_clean_up => my %skip_clean_up;    # e.g. 1
 private serialiser_format       => my %serialiser_format;          # e.g. json
 private memory_limit_multiplier => my %memory_limit_multiplier;    # e.g. 1000
-private stage_to_run => my %stage_to_run;    # DETCT::Pipeline::Stage object
+private stage_to_run     => my %stage_to_run;    # DETCT::Pipeline::Stage object
 private component_to_run => my %component_to_run;    # e.g. 5
 private all_stages_run   => my %all_stages_run;      # e.g. 1
 private jobs_running     => my %jobs_running;        # e.g. 1
@@ -1813,8 +1813,8 @@ sub num_pending_jobs {
 
     return 0 if $self->scheduler ne 'lsf';
 
-    my @output = capture('busers');
-    my @fields = split /\s+/xms, $output[1];    # Ignore header line
+    my @output           = capture('busers');
+    my @fields           = split /\s+/xms, $output[1];    # Ignore header line
     my $num_pending_jobs = $fields[4];    ## no critic (ProhibitMagicNumbers)
 
     if ( $num_pending_jobs !~ m/\A \d+ \z/xms ) {

lib/DETCT/Pipeline/DiffExpr.pm

@@ -421,9 +421,9 @@ sub run_summarise_read_peaks {
             bin_size          => $self->analysis->bin_size,
             peak_buffer_width => $self->analysis->peak_buffer_width,
             hmm_sig_level     => $self->analysis->hmm_sig_level,
-            total_bp    => $self->analysis->total_bp * 2,    # Two strands
-            read_length => $self->analysis->read2_length,
-            peaks       => \@merged_peaks,
+            total_bp          => $self->analysis->total_bp * 2,    # Two strands
+            read_length       => $self->analysis->read2_length,
+            peaks             => \@merged_peaks,
         }
     );
 

script/dump_ensembl_transcripts.pl

@@ -149,7 +149,7 @@ =head1 EXAMPLES
     foreach my $transcript (
         sort {
                  $a->seq_region_start <=> $b->seq_region_start
-              || $a->seq_region_end <=> $b->seq_region_end
+              || $a->seq_region_end   <=> $b->seq_region_end
         } @{$transcripts}
       )
     {

script/extract_regions_with_multiple_ends.pl

@@ -59,8 +59,8 @@ sub check_regions {
 
         ## no critic (ProhibitMagicNumbers)
         # Get region ID by joining chr, start, end and strand
-        my $region              = join q{:}, @fields[ 0, 1, 2, 4 ];
-        my $genes               = $fields[9];
+        my $region = join q{:}, @fields[ 0, 1, 2, 4 ];
+        my $genes  = $fields[9];
         my @three_prime_end_pos = split /,/xms, $fields[3];
         ## use critic
         next if !$genes;

script/filter_output.pl

@@ -986,10 +986,10 @@ sub write_log {
     push @output, $reason;
     push @output, $end->[$THREE_PRIME_END_READ_COUNT_FIELD];
     push @output, $end->[$IS_POLYA_FIELD];
-    push @output, $end->[$UPSTREAM_14_BP_FIELD] || q{-};
-    push @output, $end->[$DOWNSTREAM_14_BP_FIELD] || q{-};
+    push @output, $end->[$UPSTREAM_14_BP_FIELD]            || q{-};
+    push @output, $end->[$DOWNSTREAM_14_BP_FIELD]          || q{-};
     push @output, $end->[$DISTANCE_HEXAMER_UPSTREAM_FIELD] || q{-};
-    push @output, $end->[$HEXAMER_FIELD] || q{-};
+    push @output, $end->[$HEXAMER_FIELD]                   || q{-};
 
     if ( $end->[$CONTINUOUS_RNASEQ_TRANSCRIPTS_FIELD] ) {
         my @pairs = split /[|]/xms,

script/make_test_fastq.pl

@@ -98,7 +98,7 @@ =head1 EXAMPLES
     write_or_die( $fh2, q{@}, $read_name, '/2', "\n" );
     write_or_die( $fh2, get_read2_seq($read_length), "\n" );
     write_or_die( $fh2, "+\n" );
-    write_or_die( $fh2, q{~} x $read_length,         "\n" );
+    write_or_die( $fh2, q{~} x $read_length, "\n" );
 
     if ( !$has_polyt ) {
         $tag = $read_tags[-1];             # Dummy tag
@@ -157,7 +157,7 @@ sub get_read1_seq {
     # 20% of reads have a single mismatch somewhere in the tag
     if ( int rand 5 ) {              ## no critic (ProhibitMagicNumbers)
         my $mismatch_base = int rand length $tag;
-        my $base          = substr $tag, $mismatch_base, 1;
+        my $base = substr $tag, $mismatch_base, 1;
         $base =~ tr/AGCT/TCGA/;
         substr $tag, $mismatch_base, 1, $base;
     }

script/make_test_sam.pl

@@ -175,7 +175,7 @@ =head1 EXAMPLES
         my $read_tag = $read_tags[ int rand $#read_tags + 1 ];    # Random tag
         my $sequenced_read_tag = get_sequenced_read_tag($read_tag);
         my $read1_qname        = get_qname( $qname_base, $sequenced_read_tag );
-        my $read2_qname = $read1_qname;    # Always the same
+        my $read2_qname        = $read1_qname;    # Always the same
         my ( $read1_pos, $read2_pos ) =
           get_pos( $length_of{$seq_region}, $read1_length, $read2_length );
         my ( $read1_flag, $read2_flag ) = get_flag( $read1_pos, $read2_pos );

script/manipulate_three_prime_ends.pl

@@ -130,7 +130,7 @@ sub output_ends {
                 my @end_data = split /[:\/]/xms, $end, 11;
                 ## use critic
                 splice @end_data, 1, 1;    # Remove redundant strand
-                      # Split last field into transcripts and distances
+                    # Split last field into transcripts and distances
                 my @pairs = split /[|]/xms, pop @end_data;
                 @pairs = map { [ split />/xms ] } @pairs;
                 push @end_data, join q{,}, map { $_->[0] } @pairs;

script/perturb_sam.pl

@@ -100,7 +100,7 @@ =head1 EXAMPLES
     else {
         my @fields     = split /\t/xms, $line;
         my $seq_region = $fields[2];
-        my $pos = $fields[3];    ## no critic (ProhibitMagicNumbers)
+        my $pos        = $fields[3];    ## no critic (ProhibitMagicNumbers)
         my $move =
           ( int rand( $max_move * 2 + 1 ) ) - $max_move;    # e.g. -200 to 200
         $pos += $move;

script/prioritise_regions_with_multiple_ends.pl

@@ -139,8 +139,8 @@ sub get_genes_with_multiple_ends {
 
         ## no critic (ProhibitMagicNumbers)
         # Get region ID by joining chr, start, end and strand
-        my $region              = join q{:}, @fields[ 0, 1, 2, 4 ];
-        my $genes               = $fields[9];
+        my $region = join q{:}, @fields[ 0, 1, 2, 4 ];
+        my $genes  = $fields[9];
         my @three_prime_end_pos = split /,/xms, $fields[3];
         ## use critic
         next if !$genes;
@@ -233,7 +233,7 @@ sub get_significance_matrix {
             my $genes = $fields[9];
 
             # Get region ID by joining chr, start, end and strand
-            my $region          = join q{:}, @fields[ 0, 1, 2, 4 ];
+            my $region = join q{:}, @fields[ 0, 1, 2, 4 ];
             my $adjusted_pvalue = $fields[7];
             ## use critic
 

script/subset_de_output.pl

@@ -84,8 +84,8 @@ sub get_counts_by_region {
 
     open my $fh, '<', $file;          ## no critic (RequireBriefOpen)
                                       # Get range for count columns
-    my $header   = <$fh>;
-    my @headings = DETCT::Misc::Output::parse_line( $header, $extension );
+    my $header       = <$fh>;
+    my @headings     = DETCT::Misc::Output::parse_line( $header, $extension );
     my $counts_start = 15;            ## no critic (ProhibitMagicNumbers)
     my $counts_end;
     my $ordinal = $counts_start;

t/analysis-diffexpr.t

@@ -107,7 +107,7 @@ qr/Invalid peak buffer width/ms, 'Invalid peak buffer width';
 # Test HMM significance level attribute
 is( $analysis->hmm_sig_level,          0.001, 'Get HMM significance level' );
 is( $analysis->set_hmm_sig_level(0.1), undef, 'Set HMM significance level' );
-is( $analysis->hmm_sig_level, 0.1, 'Get new HMM significance level' );
+is( $analysis->hmm_sig_level,          0.1, 'Get new HMM significance level' );
 throws_ok { $analysis->set_hmm_sig_level() }
 qr/No HMM significance level specified/ms, 'No HMM significance level';
 throws_ok { $analysis->set_hmm_sig_level(1) }
@@ -141,7 +141,7 @@ throws_ok { $analysis->set_r_binary() } qr/No R binary specified/ms,
   'No R binary';
 
 # Test DESeq script attribute
-is( $analysis->deseq_script, 'script/run_deseq.R', 'Get DESeq script' );
+is( $analysis->deseq_script, 'script/run_deseq.R',   'Get DESeq script' );
 is( $analysis->set_deseq_script('script'), undef,    'Set DESeq script' );
 is( $analysis->deseq_script,               'script', 'Get new DESeq script' );
 throws_ok { $analysis->set_deseq_script() } qr/No DESeq script specified/ms,
@@ -313,7 +313,7 @@ is( $analysis->ensembl_user, 'anonymous', 'Get new Ensembl username' );
 # Test Ensembl password attribute
 is( $analysis->ensembl_pass,               undef, 'Get Ensembl password' );
 is( $analysis->set_ensembl_pass('secret'), undef, 'Set Ensembl password' );
-is( $analysis->ensembl_pass, 'secret', 'Get new Ensembl password' );
+is( $analysis->ensembl_pass, 'secret',            'Get new Ensembl password' );
 
 # Test Ensembl database name attribute
 is( $analysis->ensembl_name, undef, 'Get Ensembl database name' );
@@ -350,23 +350,23 @@ $sample->set_always( 'bam_file',  't/data/test1.bam' );
 $sample->set_always( 'name',      'zmp_ph1_1m' );
 $sample->set_always( 'tag',       'NNNNBGAGGC' );
 $sample->set_always( 'condition', 'mutant' );
-$sample->set_always( 'groups', [] );
+$sample->set_always( 'groups',    [] );
 
 # Mock sample object with different reference sequence
 my $sample_diff = Test::MockObject->new();
 $sample_diff->set_isa('DETCT::Sample');
 $sample_diff->set_always( 'bam_file', 't/data/test3.bam' );
 $sample_diff->set_always( 'name',     'zmp_ph1_1s' );
 $sample_diff->set_always( 'tag',      'NNNNBCGCAA' );
-$sample_diff->set_always( 'groups', [] );
+$sample_diff->set_always( 'groups',   [] );
 
 my $sample2 = Test::MockObject->new();
 $sample2->set_isa('DETCT::Sample');
 $sample2->set_always( 'bam_file',  't/data/test2.bam' );
 $sample2->set_always( 'name',      'zmp_ph1_2m' );
 $sample2->set_always( 'tag',       'NNNNBCAGAG' );
 $sample2->set_always( 'condition', 'mutant' );
-$sample2->set_always( 'groups', [] );
+$sample2->set_always( 'groups',    [] );
 
 # Test adding and retrieving samples
 my $samples;
@@ -400,7 +400,7 @@ $sample_dupe_name->set_isa('DETCT::Sample');
 $sample_dupe_name->set_always( 'bam_file', 't/data/test1.bam' );
 $sample_dupe_name->set_always( 'name',     'zmp_ph1_1m' );
 $sample_dupe_name->set_always( 'tag',      'NNNNBAGAAG' );
-$sample_dupe_name->set_always( 'groups', [] );
+$sample_dupe_name->set_always( 'groups',   [] );
 
 throws_ok { $analysis->add_sample($sample_dupe_name) } qr/is duplicated/ms,
   'Duplicated sample name';
@@ -419,7 +419,7 @@ $sample_dupe_tag_bam->set_isa('DETCT::Sample');
 $sample_dupe_tag_bam->set_always( 'name',     'zmp_ph1_4s' );
 $sample_dupe_tag_bam->set_always( 'bam_file', 't/data/test1.bam' );
 $sample_dupe_tag_bam->set_always( 'tag',      'NNNNBGAGGC' );
-$sample_dupe_tag_bam->set_always( 'groups', [] );
+$sample_dupe_tag_bam->set_always( 'groups',   [] );
 
 throws_ok { $analysis->add_sample($sample_dupe_tag_bam) }
 qr/Multiple samples have the same tag/ms, 'Duplicated tag and BAM file';
@@ -438,7 +438,7 @@ $sample_diff_groups->set_isa('DETCT::Sample');
 $sample_diff_groups->set_always( 'name',     'zmp_ph1_2m' );
 $sample_diff_groups->set_always( 'bam_file', 't/data/test2.bam' );
 $sample_diff_groups->set_always( 'tag',      'NNNNBCAGAG' );
-$sample_diff_groups->set_always( 'groups', ['1'] );
+$sample_diff_groups->set_always( 'groups',   ['1'] );
 
 throws_ok { $analysis->add_sample($sample_diff_groups) }
 qr/Samples do not all have same number of groups/ms, 'Different groups';
@@ -454,7 +454,7 @@ $sample_dupe_group1->set_isa('DETCT::Sample');
 $sample_dupe_group1->set_always( 'name',     'zmp_ph1_1m' );
 $sample_dupe_group1->set_always( 'bam_file', 't/data/test1.bam' );
 $sample_dupe_group1->set_always( 'tag',      'NNNNBGAGGC' );
-$sample_dupe_group1->set_always( 'groups', [ '1', '2' ] );
+$sample_dupe_group1->set_always( 'groups',   [ '1', '2' ] );
 $analysis->add_sample($sample_dupe_group1);
 
 # Mock sample object with different number of groups
@@ -463,7 +463,7 @@ $sample_dupe_group2->set_isa('DETCT::Sample');
 $sample_dupe_group2->set_always( 'name',     'zmp_ph1_2m' );
 $sample_dupe_group2->set_always( 'bam_file', 't/data/test2.bam' );
 $sample_dupe_group2->set_always( 'tag',      'NNNNBCAGAG' );
-$sample_dupe_group2->set_always( 'groups', [ '2', '3' ] );
+$sample_dupe_group2->set_always( 'groups',   [ '2', '3' ] );
 
 throws_ok { $analysis->add_sample($sample_dupe_group2) }
 qr/is duplicated between groups/ms, 'Duplicate groups';
@@ -481,7 +481,7 @@ $sample_missing_tag->set_isa('DETCT::Sample');
 $sample_missing_tag->set_always( 'bam_file', 't/data/test1.bam' );
 $sample_missing_tag->set_always( 'name',     'zmp_ph1_5s' );
 $sample_missing_tag->set_always( 'tag',      'NNNNBTGAATC' );
-$sample_missing_tag->set_always( 'groups', [] );
+$sample_missing_tag->set_always( 'groups',   [] );
 
 throws_ok { $analysis->add_sample($sample_missing_tag) }
 qr/does not contain tag/ms, 'Tag missing from BAM files';
@@ -492,7 +492,7 @@ $sample_no_index->set_isa('DETCT::Sample');
 $sample_no_index->set_always( 'name',     'zmp_ph1_6s' );
 $sample_no_index->set_always( 'bam_file', 't/data/test4.bam' );
 $sample_no_index->set_always( 'tag',      'NNNNBGAGGC' );
-$sample_no_index->set_always( 'groups', [] );
+$sample_no_index->set_always( 'groups',   [] );
 
 throws_ok { $analysis->add_sample($sample_no_index) } qr/has no index/ms,
   'BAM file with no index file';