Merge branch 'hotfix/v6.2.1'

Author: keiranmraine

.travis.yml

@@ -28,6 +28,8 @@ addons:
    - time
    - unzip
    - zlib1g-dev
+   - libgd-dev
+   - libdb-dev
 
 install:
  - git clone --depth 1 --single-branch --branch develop https://github.com/cancerit/cgpBigWig.git

CHANGES.md

@@ -1,11 +1,17 @@
 # Changes
 
+## v6.2.1
+
+* Fixes #80 - allow RGID == 0
+* Resolves #84 - use helper threads where possible
+
 ## v6.2.0
+
 * Fixed bug where subset of intervals does not have reads -issue#65
 * Informative error when .bas file is absent - issue#71
 * temp file were now kept after running filter step - issue#73
-* Fixed issue#66 
-* Added script to process centro/telomere data - issue#70  
+* Fixed issue#66
+* Added script to process centro/telomere data - issue#70
 * Fixed bug where intermediate file name matches with one of the sample
 
 ## v6.1.2

perl/bin/brassI_prep_bam.pl

@@ -1,7 +1,7 @@
 #!/usr/bin/perl
 
 ########## LICENCE ##########
-# Copyright (c) 2014-2018 Genome Research Ltd.
+# Copyright (c) 2014-2019 Genome Research Ltd.
 #
 # Author: CASM/Cancer IT <[email protected]>
 #
@@ -143,8 +143,7 @@ sub process_header {
     $rg_id = $1 if($row =~ /\tID:([^\t]+)/);
 
     # die horribly if RG ids don't match
-    unless ($bas_ob->get($rg_id, 'readgroup')) { die "Readgroup $rg_id in bam file but not in bas file $!"; }
-
+    unless (defined $bas_ob->get($rg_id, 'readgroup')) { die "Readgroup $rg_id in bam file but not in bas file $!"; }
 
     # The script needs use the information in the *.bas file to augment the Reagd-group line with the 'MI:' tag.
     #     This holds the 'maximum insert' size, this should be calculated as:

perl/lib/Bio/Brass.pm

@@ -1,7 +1,7 @@
 package Bio::Brass;
 
 ########## LICENCE ##########
-# Copyright (c) 2014-2018 Genome Research Ltd.
+# Copyright (c) 2014-2019 Genome Research Ltd.
 #
 # Author: CASM/Cancer IT <[email protected]>
 #
@@ -46,7 +46,7 @@ our @EXPORT = qw(find_breakpoints find_dusty_vertices
 		 is_dusty get_isolated_bp_alignment get_isolated_bp_surrounding_region
 		 $VERSION);
 
-our $VERSION = '6.2.0';
+our $VERSION = '6.2.1';
 
 =head1 NAME
 

perl/lib/Sanger/CGP/Brass/Implement.pm

@@ -1,7 +1,7 @@
 package Sanger::CGP::Brass::Implement;
 
 ########## LICENCE ##########
-# Copyright (c) 2014-2018 Genome Research Ltd.
+# Copyright (c) 2014-2019 Genome Research Ltd.
 #
 # Author: CASM/Cancer IT <[email protected]>
 #
@@ -63,7 +63,7 @@ const my $BAMCOLLATE => q{ outputformat=sam exclude= classes=F,F2 T=%s/bamcollat
 # tmpdir, iter, file
 const my $PREP_BAM => q{ -b %s -p %s};
 # basfile[ -e exclude chrs]
-const my $BAMSORT => q{ tmpfile=%s/bamsort_%s inputformat=sam verbose=0 index=1 md5=1 md5filename=%s.md5 indexfilename=%s.bai O=%s};
+const my $BAMSORT => q{ tmpfile=%s/bamsort_%s inputformat=sam verbose=0 index=1 md5=1 md5filename=%s.md5 indexfilename=%s.bai O=%s outputthreads=%d sortthreads=%d};
 # out_bamname, out_bamname, out_bamname
 
 #genome.fa.fai gc_windows.bed[.gz] in.bam out_path [chr_idx] sample_type
@@ -124,6 +124,9 @@ sub input {
       $rg_prefix = 'N';
     }
 
+    my $helper_threads = int $options->{'threads'}/2 || 1;
+    $helper_threads = 6 if($helper_threads > 6);
+
     my $command = _which('samtools');
     $command .= ' view -F 3854 -q 6 -u '.$input;
     $command .= ' | ';
@@ -139,7 +142,7 @@ sub input {
     $command .= " -i ".join(',', valid_seqs($options));
     $command .= ' | ';
     $command .= _which('bamsort');
-    $command .= sprintf $BAMSORT, $tmp, $index, $outbam, $outbam, $outbam;
+    $command .= sprintf $BAMSORT, $tmp, $index, $outbam, $outbam, $outbam, $helper_threads, $helper_threads;
 
     PCAP::Threaded::external_process_handler(File::Spec->catdir($tmp, 'logs'), qq{bash -c 'set -o pipefail; $command'}, $index);