Merge pull request #34 from ICGC-TCGA-PanCancer/dev

v1.0.3 - maintenance release

.gitignore

@@ -5,3 +5,4 @@
 /MANIFEST.bak
 /install_tmp
 /setup.log
+/reports

Changes

@@ -1,3 +1,9 @@
+1.0.3
+  Corrected issue from dynamic de-reference of hash, issue fort pre 5.14 perl
+  and potentially unstable in future.
+  Added missing project code to cv terms.
+  Bug-fixed upgrade path, still needs better solution.
+  Cleaned up messaging in Threaded module.
 1.0.2
   Upgrade install to pull biobambam 0.0.138
    - fastqtobam option 'pairedfile' for where readnames don't have trailing '/1' or '/2'.

MANIFEST

@@ -29,6 +29,36 @@ share/cv_tables/ICGC/dcc_specimen_type.txt
 t/1_pm_compile.t
 t/2_pl_compile.t
 t/3_external_progs.t
+t/data/1.fq
+t/data/1_1.fq
+t/data/1_2.fq
+t/data/2_1.fq
+t/data/3_2.fq
+t/data/data.file
+t/data/empty.bam
+t/data/empty.bam.bas
+t/data/empty.file
+t/data/empty.fq
+t/data/empty_r1_1.fq
+t/data/empty_r1_2.fq
+t/data/empty_r2_1.fq
+t/data/empty_r2_2.fq
+t/data/header.bam
+t/data/header.sam
+t/data/malformed_head.bam
+t/data/malformed_head.sam
+t/data/md5.bam
+t/data/md5.bam.md5
+t/data/multi_sample.bam
+t/data/multi_sample.sam
+t/data/no_readgroups.bam
+t/data/no_readgroups.sam
+t/data/not_really_a.bam
+t/data/paired.bam
+t/data/Stats.bam
+t/data/Stats.bam.bas
+t/data/test.bam.bas
+t/data/unpaired.bam
 t/pcap.t
 t/pcapBam.t
 t/pcapBamBas.t
@@ -38,33 +68,3 @@ t/pcapBwaMeta.t
 t/pcapCli.t
 t/pcapSra.t
 t/pcapThreaded.t
-testData/1.fq
-testData/1_1.fq
-testData/1_2.fq
-testData/2_1.fq
-testData/3_2.fq
-testData/data.file
-testData/empty.bam
-testData/empty.bam.bas
-testData/empty.file
-testData/empty.fq
-testData/empty_r1_1.fq
-testData/empty_r1_2.fq
-testData/empty_r2_1.fq
-testData/empty_r2_2.fq
-testData/header.bam
-testData/header.sam
-testData/malformed_head.bam
-testData/malformed_head.sam
-testData/md5.bam
-testData/md5.bam.md5
-testData/multi_sample.bam
-testData/multi_sample.sam
-testData/no_readgroups.bam
-testData/no_readgroups.sam
-testData/not_really_a.bam
-testData/paired.bam
-testData/Stats.bam
-testData/Stats.bam.bas
-testData/test.bam.bas
-testData/unpaired.bam

MYMETA.json

@@ -54,5 +54,5 @@
       }
    },
    "release_status" : "stable",
-   "version" : "v1.0.1"
+   "version" : "v1.0.3"
 }

MYMETA.yml

@@ -36,4 +36,4 @@ requires:
   Term::UI: 0.42
   Test::Fatal: 0.013
   Try::Tiny: 0.19
-version: v1.0.1
+version: v1.0.3

bin/bwa_aln.pl

@@ -36,6 +36,7 @@ BEGIN
 use Pod::Usage qw(pod2usage);
 use List::Util qw(first);
 use Const::Fast qw(const);
+use File::Copy qw(move);
 
 use PCAP::Cli;
 use PCAP::Threaded;
@@ -75,7 +76,9 @@ BEGIN
 }
 
 sub cleanup {
-  my $tmpdir = shift->{'tmp'};
+  my $options = shift;
+  my $tmpdir = $options->{'tmp'};
+  move(File::Spec->catdir($tmpdir, 'logs'), File::Spec->catdir($options->{'outdir'}, 'logs')) || die $!;
   remove_tree $tmpdir if(-e $tmpdir);
 	return 0;
 }

bin/bwa_mem.pl

@@ -36,7 +36,7 @@ BEGIN
 use Pod::Usage qw(pod2usage);
 use List::Util qw(first);
 use Const::Fast qw(const);
-use File::Copy qw(copy);
+use File::Copy qw(copy move);
 
 use PCAP::Cli;
 use PCAP::Bam;
@@ -79,7 +79,9 @@ BEGIN
 }
 
 sub cleanup {
-  my $tmpdir = shift->{'tmp'};
+  my $options = shift;
+  my $tmpdir = $options->{'tmp'};
+  move(File::Spec->catdir($tmpdir, 'logs'), File::Spec->catdir($options->{'outdir'}, 'logs')) || die $!;
   remove_tree $tmpdir if(-e $tmpdir);
 	return 0;
 }

lib/PCAP.pm

@@ -23,7 +23,7 @@ package PCAP;
 use strict;
 use Const::Fast qw(const);
 
-our $VERSION = '1.0.1';
+our $VERSION = '1.0.3';
 
 const my $LICENSE =>
 "#################
@@ -35,13 +35,14 @@ const my $LICENSE =>
 const my $DEFAULT_PATH => 'biobambam,samtools,bwa';
 const my %UPGRADE_PATH => ( '0.1.0'  => 'biobambam,samtools,bwa',
                             '0.1.1'  => 'biobambam,bwa',
-                            '0.1.2'  => 'biobambam',
-                            '0.2.0'  => 'biobambam',
-                            '0.2.99' => 'biobambam',
-                            '0.3.0'  => 'biobambam',
-                            '1.0.0'  => 'biobambam',
+                            '0.1.2'  => 'biobambam,bwa',
+                            '0.2.0'  => 'biobambam,bwa',
+                            '0.2.99' => 'biobambam,bwa',
+                            '0.3.0'  => 'biobambam,bwa',
+                            '1.0.0'  => 'biobambam,bwa',
                             '1.0.1'  => 'biobambam,bwa',
-                            '1.0.2'  => '',
+                            '1.0.2'  => 'biobambam,bwa',
+                            '1.0.3'  => '',
                           );
 
 sub license {

lib/PCAP/Bam/Bas.pm

@@ -81,7 +81,7 @@ sub bas_keys {
 }
 
 sub read_groups {
-  return (sort keys shift->{'_data'});
+  return (sort keys %{shift->{'_data'}});
 }
 
 sub get {

lib/PCAP/Threaded.pm

@@ -172,14 +172,24 @@ sub touch_success {
 }
 
 sub external_process_handler {
-  my ($tmp, $command, @indexes) = @_;
+  my ($tmp, $command_in, @indexes) = @_;
+
+  my @commands;
+  if(ref $command_in eq 'ARRAY') {
+    @commands = @{$command_in}
+  }
+  else {
+    @commands = ($command_in);
+  }
 
   if(&use_out_err == 0) {
     # these may be marshalled to different files so output both
-    warn "Errors from command: $command\n";
-    print "Output from command: $command\n";
     try {
-      system($command);
+      for my $c(@commands) {
+        warn "\nErrors from command: $c\n\n";
+        print "\nOutput from command: $c\n\n";
+        system($c);
+      }
     }
     catch { die $_; };
   }
@@ -191,10 +201,12 @@ sub external_process_handler {
 
     my $out_fh = IO::File->new($out, "w+");
     my $err_fh = IO::File->new($err, "w+");
-    print $err_fh "Errors from command: $command\n";
-    print $out_fh "Output from command: $command\n";
     try {
-      capture { system($command); } stdout => $out_fh, stderr => $err_fh;
+      for my $c(@commands) {
+        print $err_fh "\nErrors from command: $c\n\n";
+        print $out_fh "\nOutput from command: $c\n\n";
+        capture { system($c); } stdout => $out_fh, stderr => $err_fh;
+      }
     } catch {
       die $_ if($_);
     };
@@ -313,11 +325,17 @@ Requires implementation of L<success_exists()|PCAP::Threaded/touch_success>.
 
 =item external_process_handler
 
-  PCAP::Threaded::external_process_handler(File::Spec->catdir($tmp, 'logs'), $command, $index[, $index_2...]);
+  PCAP::Threaded::external_process_handler($logdir, $commands, $index[, $index_2...]);
+
+  @params logdir   - Path to pre-existing log directory
+  @params commands - Scalar command or arr-ref of commands
+  @params index    - Which index this is, specifically for log/err files.
 
 Wraps up command with stdout and stderr catchalls to keep the output of each threaded process
 separated from the script itself.  Added to simplify interpretation of any issues that may occur.
 
+If you don't want to capture stdout/stderr see <disable_out_err>.
+
 ($index_2... may be useful for some other implementation, see L<bwa_aln()|PCAP::Bwa/bwa_aln>).
 
 =back

share/cv_tables/ICGC/dcc_project_code.txt

@@ -1,72 +1,73 @@
 dcc_project_code
+ALL-US
+BLCA-CN
 BLCA-US
-LAML-US
-LAML-KR
-CLLE-ES
-CMDI-UK
-MALY-DE
-NHLY-MX
 BOCA-UK
-GBM-US
-LGG-US
-PBCA-DE
-PEME-CA
+BRCA-CN
+BRCA-EU
 BRCA-FR
 BRCA-KR
-BRCA-US
-BRCA-EU
-BRCA-UK
 BRCA-MX
+BRCA-UK
+BRCA-US
+BTCA-SG
 CESC-US
+CLLE-ES
+CMDI-UK
 COAD-US
 COCA-CN
-READ-US
+EOPC-DE
 ESAD-UK
 ESCA-CN
-HNSC-US
-THCA-US
-ORCA-IN
-THCA-SA
+GACA-CN
+GBM-CN
+GBM-US
 HNCA-MX
+HNSC-US
 KIRC-US
 KIRP-US
-RECA-EU
+LAML-CN
+LAML-KR
+LAML-US
+LGG-US
 LICA-CN
 LICA-FR
+LIHC-US
 LINC-JP
 LIRI-JP
-LIHC-US
 LUAD-US
+LUCA-DE
+LUSC-CN
+LUSC-KR
 LUSC-US
+MALY-DE
 NACA-CN
+NBL-US
+NHLY-MX
+ORCA-IN
 OV-AU
+OV-CN
 OV-US
+PAAD-US
 PACA-AU
 PACA-CA
+PACA-CN
 PACA-IT
-PAAD-US
-EOPC-DE
+PAEN-AU
+PBCA-DE
+PEME-CA
 PRAD-CA
-PRAD-US
+PRAD-CN
 PRAD-UK
-SKCM-US
-STAD-US
-GACA-CN
-UCEC-US
-ALL-US
-PAEN-AU
-LUCA-DE
+PRAD-US
 PRCA-FR
-SKCA-BR
-BLCA-CN
-LAML-CN
-GBM-CN
-BRCA-CN
-LUSC-CN
-OV-CN
-PACA-CN
-PRAD-CN
+READ-US
 RECA-CN
+RECA-EU
+SKCA-BR
+SKCM-US
+STAD-US
 THCA-CN
-LUSC-KR
-NBL-US
+THCA-SA
+THCA-US
+UCEC-US

t/pcapBam.t

@@ -40,7 +40,7 @@ const my $EXPECTED_MULTI_RG => [ {'CN' => 'SANGER',
                                 } ];
 
 use FindBin qw($Bin);
-my $test_data = "$Bin/../testData";
+my $test_data = "$Bin/data";
 
 # if you need to change the header.bam
 # edit header.sam then:

t/pcapBamBas.t

@@ -11,7 +11,7 @@ const my $EXP_MEDIAN => '462.000';
 const my $RG_ORDER => [qw(1 2 3 4 5 6)];
 
 use FindBin qw($Bin);
-my $test_data = "$Bin/../testData";
+my $test_data = "$Bin/data";
 
 my $bas = File::Spec->catfile($test_data, 'test.bam.bas');
 my $empty_bas = File::Spec->catfile($test_data, 'empty.bam.bas');

t/pcapBamStats.t

@@ -30,7 +30,7 @@ use Bio::DB::Sam;
 
 const my $MODULE => 'PCAP::Bam::Stats';
 
-my $test_data = "$Bin/../testData";
+my $test_data = "$Bin/data";
 my $test_bam_file = join('/',$test_data,'Stats.bam');
 my $test_bas_file = join('/',$test_data,'Stats.bam.bas');