Merge branch 'release/v2.4.0'

Author: keiranmraine

bin/bamToBw.pl

@@ -39,7 +39,7 @@
 use PCAP::Threaded;
 use version;
 
-const my @VALID_PROCESS => qw(bamToBw mergeBw generateBw);
+const my @VALID_PROCESS => qw(bamToBw generateBw);
 const my %INDEX_FACTOR => ( 'bamToBw' => -1,
                             'generateBw' => 1,
                             );
@@ -166,9 +166,8 @@ =head1 SYNOPSIS
 
   Targeted processing:
     -process   -p   Only process this step then exit, optionally set -index
-                      bwamem - only applicable if input is bam
-                        mark - Run duplicate marking (-index N/A)
-                       stats - Generates the *.bas file for the final BAM.
+                         bamToBw - Per chromosome BigWigs
+                      generateBw - Generates merged BigWig
 
     -index     -i   Optionally restrict '-p' to single job
                       bwamem - 1..<lane_count>

docs.tar.gz

@@ -26,7 +26,7 @@ use base 'Exporter';
 use FindBin qw($Bin);
 use File::Which qw(which);
 
-our $VERSION = '2.3.0';
+our $VERSION = '2.4.0';
 our @EXPORT = qw($VERSION _which);
 
 const my $LICENSE =>
@@ -79,6 +79,7 @@ const my %UPGRADE_PATH => ( # all earlier versions need full upgrade
                             '2.2.0' => 'biobambam,samtools',
                             '2.2.1' => '',
                             '2.3.0' => '',
+                            '2.4.0' => '',
                           );
 
 sub license {

lib/PCAP.pm

@@ -46,16 +46,11 @@ sub bamToBw {
     my $outfile = q{'}.File::Spec->catfile($options->{'tmp'}, $seq.'.bw').q{'};
 
     my $command = q{bash -c "set pipefail; };
-    if($options->{'bam'} =~ m/\.bam$/) {
-      $command .= _which('bam2bedgraph');
-      $command .= q{ }.$options->{'bam'}.q{ '}.$seq.q{'};
-    }
-    else {
-      $command .= _which('samtools');
-      $command .= q{ view -T }.$options->{'reference'};
-      $command .= q{ -ub }.$options->{'bam'}.q{ '}.$seq.q{'};
-      $command .= ' | '._which('bam2bedgraph').' - ';
-    }
+    $command .= _which('samtools');
+    $command .= q{ view -T }.$options->{'reference'};
+    $command .= q{ -F 3844}; # don't include data that set these flags
+    $command .= q{ -ub }.$options->{'bam'}.q{ '}.$seq.q{'};
+    $command .= ' | '._which('bam2bedgraph').' - ';
     $command .= ' | ';
     $command .= _which('wigToBigWig');
     $command .= ' -fixedSummaries -keepAllChromosomes stdin '.$options->{'reference'}.'.fai '.$outfile;