Merge branch 'hotfix/v4.0.12'

README.md

@@ -54,9 +54,10 @@ There are several stages the main component being:
 
 ### Pre-requisites
 
+* The C++ code (within this package) requires the presence of pstreams.h (and associated development libraries).  This is not handled by the `setup.sh` script.
+
 Perl packages:
 
-* The C++ code requires the presence of pstreams.h (and associated development libraries).  This is not handled by the `setup.sh` script.
 * [PCAP-core](https://github.com/ICGC-TCGA-PanCancer/PCAP-core/releases)
 * [cgpVcf](https://github.com/cancerit/cgpVcf/releases)
 * [grass](https://github.com/cancerit/grass/releases)
@@ -68,14 +69,22 @@ R packages (known to work with 3.1.3), recommend install via package manager:
 * [RColorBrewer](https://cran.r-project.org/web/packages/RColorBrewer/index.html)
 * [VGAM](https://cran.r-project.org/web/packages/VGAM/index.html)
 * [stringr](https://cran.r-project.org/web/packages/stringr/index.html)
+* These themselves have further dependancies.
 
 R Bioconductor packages (known to work with 3.1.3)
 * [copynumber](https://www.bioconductor.org/packages/release/bioc/html/copynumber.html)
 
-Please also install the **ssearch36** binary from the FASTA package to your path.
+Other tools that need to be in path
 
 * [FASTA](https://github.com/wrpearson/fasta36/releases)
 
+###  Tools installed by setup.sh
+* Many CPAN hosted libraries, see `perl/Makefile.PL` for the list
+* [BLAT](http://hgwdev.cse.ucsc.edu/~kent/src/)
+* [exonerate](http://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate)
+* [Velvet](https://www.ebi.ac.uk/~zerbino/velvet/)
+* [bedtools2](https://github.com/arq5x/bedtools2/releases)
+
 ###
 
 ## Running BRASS

perl/bin/brass.pl

@@ -173,9 +173,13 @@ sub cleanup {
                     "$basefile.cn_filtered";
 
   for my $to_move(@base_move) {
-    move($to_move, $intdir);
+    move($to_move, $intdir) if(-e $to_move);
   }
 
+  # ascat files may not be in base output folder so copy from inputs:
+  copy($options->{'ascat'}, $intdir);
+  copy($options->{'ascat_summary'}, $intdir);
+
   my $tmplogs = File::Spec->catdir($tmpdir, 'logs');
   if(-e $tmplogs) {
     move($tmplogs, File::Spec->catdir($outdir, 'logs')) or die $!;
@@ -231,6 +235,7 @@ sub setup {
   }
 
   PCAP::Cli::out_dir_check('outdir', $opts{'outdir'});
+  $opts{'outdir'} = File::Spec->rel2abs( $opts{'outdir'} );
   my $intermediates = File::Spec->catdir($opts{'outdir'}, 'intermediates');
   if(-e $intermediates) {
     die "ERROR: Presence of intermediates directory suggests successful complete analysis, please delete to proceed: $intermediates\n";

perl/bin/combineResults.pl

@@ -100,10 +100,12 @@ sub mergeVcf {
       next;
     }
     else {
-      my $old_info = $orig_data{$id}->[7];
+      my $original_info = $orig_data{$id}->[7];
       my ($tsrds) = $bits[7] =~ m/(TSRDS=[^;]+)/;
-
-      $bits[7] = $old_info.';'.$tsrds;
+      $bits[1] = $orig_data{$id}->[1];
+      $bits[3] = $orig_data{$id}->[3];
+      $bits[4] = $orig_data{$id}->[4];
+      $bits[7] = $original_info.';'.$tsrds;
       $bits[7] .= ';BAS='.$orig_data{$id}->[5];
       $bits[5] = q{.};
       $bits[-3] .= ':PS';

perl/lib/Bio/Brass.pm

@@ -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 = '4.0.11';
+our $VERSION = '4.0.12';
 
 =head1 NAME
 

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

@@ -477,13 +477,23 @@ sub split_filtered {
   my $split_dir = File::Spec->catdir($tmp, 'split');
   remove_tree($split_dir) if(-d $split_dir);
   make_path($split_dir);
-  my $command = sprintf q{grep -v "^#" %s | split --suffix-length=7 --numeric-suffixes --verbose --lines=%s - %s/split.},
-                        $groups, $ASSEMBLE_SPLIT, $split_dir;
 
-  PCAP::Threaded::external_process_handler(File::Spec->catdir($tmp, 'logs'), qq{bash -c 'set -o pipefail; $command'}, 0);
-  my $splitOne = $split_dir.'/split.0000000';
-  if(! -e $splitOne){
+  # before running this we need to know if there are any non '#' lines
+  my ($sto, $ste, $exit) = capture { system([0,1], "grep -vc '^#' $groups"); };
+
+	if($exit == 0 && $sto > 0) {
+		my $command = sprintf q{grep -v "^#" %s | split --suffix-length=7 --numeric-suffixes --verbose --lines=%s - %s/split.},
+													$groups, $ASSEMBLE_SPLIT, $split_dir;
+
+		PCAP::Threaded::external_process_handler(File::Spec->catdir($tmp, 'logs'), qq{bash -c 'set -o pipefail; $command'}, 0);
+  }
+  elsif($exit == 1 && $sto == 0) {
+	  my $splitOne = $split_dir.'/split.0000000';
     `touch $splitOne`;
+    warn "No data survived filtering (split_filtered)\n";
+  }
+  else {
+    die "ERROR: Unexpected result when parsing non-header lines from $groups\n";
   }
 
   PCAP::Threaded::touch_success(File::Spec->catdir($tmp, 'progress'), 0);
@@ -632,7 +642,22 @@ sub tabix {
   my $tabix = _which('tabix');
   $tabix .= sprintf ' -p vcf %s', $vcf_gz;
 
-  my @commands = ($header, qq{bash -c 'set -o pipefail; $sort'}, $bgzip, $tabix);
+  # before running this we need to know if there are any non '#' lines
+  my ($sto, $ste, $exit) = capture { system([0,1], "grep -vc '^#' $annotated"); };
+
+  my @commands = ($header);
+
+  if($exit == 0 && $sto > 0) {
+    push @commands, qq{bash -c 'set -o pipefail; $sort'};
+  }
+  elsif($exit == 1 && $sto == 0) {
+    warn "No data survived (tabix)\n";
+  }
+  else {
+    die "ERROR: Unexpected result when parsing non-header lines from $annotated\n";
+  }
+
+  push @commands, $bgzip, $tabix;
 
   PCAP::Threaded::external_process_handler(File::Spec->catdir($tmp, 'logs'), \@commands, 0);
 

setup.sh

@@ -33,6 +33,9 @@
 
 
 SOURCE_BLAT="http://users.soe.ucsc.edu/~kent/src/blatSrc35.zip"
+
+# Warning bedtools 2.24.0 and 2.25.0 have a swapped usage in coverageBed
+# No upgrades until [this ticket](https://github.com/arq5x/bedtools2/issues/319) is resolved
 SOURCE_BEDTOOLS="https://github.com/arq5x/bedtools2/releases/download/v2.21.0/bedtools-2.21.0.tar.gz"
 
 done_message () {
@@ -165,7 +168,7 @@ done
 
 cd $SETUP_DIR
 
-echo -n "Building bedtools ..."
+echo -n "Building bedtools2 ..."
 if [ -e $SETUP_DIR/bedtools.success ]; then
   echo -n " previously installed ...";
 else