Merge pull request #27 from ICGC-TCGA-PanCancer/dev

Dev - merge 1.0.0 into master ready for release

Author: keiranmraine

.gitignore

@@ -2,8 +2,6 @@
 /blib
 /docs
 /pm_to_blib
-/MYMETA.yml
-/MYMETA.json
 /MANIFEST.bak
 /install_tmp
 /setup.log

Changes

@@ -1,3 +1,8 @@
+1.0.0
+  bam_stats.pl actually installed now.
+  Basic *.bas perl access module.
+  Upgraded libmaus/biobambam to resolve patch and CentOS install issue.
+  Reference implementations ensure unique RG:ID between files.
 0.3.0
   Changes for the re-worked PanCancer submission SOP.
   Patch for libmaus issue as not going to be a release in time.

INSTALL

@@ -14,14 +14,25 @@ OS:
 Other Software
   For installation to proceed you require the following packages:
 
-    zlib1g-dev
-    g++
-    dh-autoreconf
-    libncurses-dev
-    pkg-config
-    libgd2-xpm-dev
-
-    This listing is based on Ubuntu 12.04
+    For Ubuntu (tested with 12.04)
+      apt-get
+        zlib1g-dev
+        g++
+        dh-autoreconf
+        libncurses-dev
+        pkg-config
+        libgd2-xpm-dev
+
+    For CentOS (tested with 6.4)
+      yum install
+        zlib-devel
+        gcc-c++
+        autoconf
+        automake
+        libtool
+        boost-devel.x86_64
+        ncurses-devel.x86_64
+        gd-devel
 
   setup.sh will install
     biobambam

MANIFEST

@@ -10,6 +10,7 @@ docs.tar.gz
 INSTALL
 lib/PCAP.pm
 lib/PCAP/Bam.pm
+lib/PCAP/Bam/Bas.pm
 lib/PCAP/Bam/Stats.pm
 lib/PCAP/Bwa.pm
 lib/PCAP/Bwa/Meta.pm
@@ -20,7 +21,6 @@ LICENSE
 Makefile.PL
 MANIFEST			This list of files
 MANIFEST.SKIP
-patches/fileModeFix.diff
 prerelease.sh
 README.md
 setup.sh
@@ -31,6 +31,7 @@ t/2_pl_compile.t
 t/3_external_progs.t
 t/pcap.t
 t/pcapBam.t
+t/pcapBamBas.t
 t/pcapBamStats.t
 t/pcapBwa.t
 t/pcapBwaMeta.t
@@ -44,6 +45,7 @@ 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
@@ -64,4 +66,5 @@ testData/not_really_a.bam
 testData/paired.bam
 testData/Stats.bam
 testData/Stats.bam.bas
+testData/test.bam.bas
 testData/unpaired.bam

MYMETA.json

@@ -0,0 +1,57 @@
+{
+   "abstract" : "unknown",
+   "author" : [
+      "unknown"
+   ],
+   "dynamic_config" : 0,
+   "generated_by" : "ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.131560",
+   "license" : [
+      "unknown"
+   ],
+   "meta-spec" : {
+      "url" : "http://search.cpan.org/perldoc?CPAN::Meta::Spec",
+      "version" : "2"
+   },
+   "name" : "PCAP",
+   "no_index" : {
+      "directory" : [
+         "t",
+         "inc"
+      ]
+   },
+   "prereqs" : {
+      "build" : {
+         "requires" : {
+            "ExtUtils::MakeMaker" : "0"
+         }
+      },
+      "configure" : {
+         "requires" : {
+            "ExtUtils::MakeMaker" : "0"
+         }
+      },
+      "runtime" : {
+         "requires" : {
+            "Bio::DB::Sam" : "1.39",
+            "Bio::Root::Version" : "1.006923",
+            "Capture::Tiny" : "0.24",
+            "Const::Fast" : "0.014",
+            "Data::UUID" : "1.219",
+            "Devel::Cover" : "1.09",
+            "File::Which" : "0.05",
+            "GD" : "2.52",
+            "IPC::System::Simple" : "1.25",
+            "List::Util" : "1.38",
+            "Math::Gradient" : "0.04",
+            "Module::Build" : "0.42",
+            "Pod::Coverage" : "0.23",
+            "Proc::ProcessTable" : "0.5",
+            "Term::UI" : "0.42",
+            "Test::Fatal" : "0.013",
+            "Try::Tiny" : "0.19"
+         }
+      }
+   },
+   "release_status" : "stable",
+   "version" : "v1.0.0"
+}

MYMETA.yml

@@ -0,0 +1,38 @@
+---
+abstract: unknown
+author:
+  - unknown
+build_requires:
+  ExtUtils::MakeMaker: 0
+configure_requires:
+  ExtUtils::MakeMaker: 0
+dynamic_config: 0
+generated_by: 'ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.131560'
+license: unknown
+meta-spec:
+  url: http://module-build.sourceforge.net/META-spec-v1.4.html
+  version: 1.4
+name: PCAP
+no_index:
+  directory:
+    - t
+    - inc
+requires:
+  Bio::DB::Sam: 1.39
+  Bio::Root::Version: 1.006923
+  Capture::Tiny: 0.24
+  Const::Fast: 0.014
+  Data::UUID: 1.219
+  Devel::Cover: 1.09
+  File::Which: 0.05
+  GD: 2.52
+  IPC::System::Simple: 1.25
+  List::Util: 1.38
+  Math::Gradient: 0.04
+  Module::Build: 0.42
+  Pod::Coverage: 0.23
+  Proc::ProcessTable: 0.5
+  Term::UI: 0.42
+  Test::Fatal: 0.013
+  Try::Tiny: 0.19
+version: v1.0.0

Makefile.PL

@@ -31,6 +31,7 @@ WriteMakefile(
   EXE_FILES     => [qw( bin/bam_to_sra_sub.pl
                         bin/bwa_aln.pl
                         bin/bwa_mem.pl
+                        bin/bam_stats.pl
                         bin/diff_bams.pl
                         bin/monitor.pl)],
   PREREQ_PM     => {

bin/bwa_aln.pl

@@ -43,9 +43,6 @@ BEGIN
 use PCAP::Bwa;
 use PCAP::Bwa::Meta;
 
-my @mod_list = keys %INC;
-exit 0 if(first {$_ =~ m|^Devel/Cover| } @mod_list);
-
 const my @VALID_PROCESS => qw(bam2fq aln sampe mark);
 const my %INDEX_FACTOR => ( 'bam2fq' => 1,
                             'aln'    => 2,

bin/bwa_mem.pl

@@ -43,9 +43,6 @@ BEGIN
 use PCAP::Bwa::Meta;
 use version;
 
-my @mod_list = keys %INC;
-exit 0 if(first {$_ =~ m|^Devel/Cover| } @mod_list);
-
 const my @VALID_PROCESS => qw(bwamem mark);
 const my %INDEX_FACTOR => ( 'bwamem' => 1,
                             'mark'   => 1,);

docs.tar.gz

@@ -23,7 +23,7 @@ package PCAP;
 use strict;
 use Const::Fast qw(const);
 
-our $VERSION = '0.3.0';
+our $VERSION = '1.0.0';
 
 const my $LICENSE =>
 "#################
@@ -33,11 +33,13 @@ 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',
-                            '0.3.0' => '',
+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'  => '',
                           );
 
 sub license {

lib/PCAP.pm

@@ -33,6 +33,7 @@ use File::Which qw(which);
 use Bio::DB::Sam;
 use Carp qw(croak);
 use List::Util qw(first);
+use Data::UUID;
 
 use PCAP::Threaded;
 
@@ -51,14 +52,18 @@ sub new {
 }
 
 sub rg_line_for_output {
-  my $bam = shift;
+  my ($bam, $uniq_id) = @_;
   my $sam = sam_ob($bam);
   my $header = $sam->header->text;
   my $rg_line;
   while($header =~ m/^(\@RG\t[^\n]+)/xmsg) {
     my $new_rg = $1;
     die "BAM file appears to contain data for multiple readgroups, not supported: \n\n$header\n" if(defined $rg_line);
     $rg_line = $new_rg;
+    if($uniq_id) {
+      my $uuid = lc Data::UUID->new->create_str;
+      $rg_line =~ s/\tID:[^\t]+/\tID:$uuid/;
+    }
     $rg_line =~ s/\t/\\t/g;
   }
   return ($rg_line, $sam); # also return the SAM object
@@ -359,6 +364,8 @@ The SAM object is also returned should it be useful for other calls
 Takes BAM or Bio::DB::Sam object as input and returns the string representation for the RG line.
 Intended for use when adding RG to BWA MEM output and is only useful in single RG BAMs
 
+Optional second boolean arg causes ID to be replaced with a UUID.
+
 The SAM object is also returned should it be useful for other calls
 
 =item sam_ob

lib/PCAP/Bam.pm

@@ -0,0 +1,119 @@
+package PCAP::Bam::Bas;
+
+##########LICENCE##########
+# PCAP - NGS reference implementations and helper code for the ICGC/TCGA Pan-Cancer Analysis Project
+# Copyright (C) 2014 ICGC PanCancer Project
+#
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not see:
+#   http://www.gnu.org/licenses/gpl-2.0.html
+##########LICENCE##########
+
+use PCAP;
+our $VERSION = PCAP->VERSION;
+
+use strict;
+use English qw( -no_match_vars );
+use warnings FATAL=>'all';
+use autodie qw( :all );
+use Carp qw(croak carp);
+
+sub new {
+  my ($class, $bas) = @_;
+  my $self = { };
+  bless $self, $class;
+  $self->_init($bas);
+  return $self;
+}
+
+sub _init {
+  my ($self, $bas) = @_;
+  croak "No bas file defined" if(!defined $bas);
+  die "*.bas file: $bas does not exist" unless(-e $bas);
+  die "*.bas file: $bas is empty" unless(-s $bas);
+  open my $IN, '<', $bas;
+  $self->bas_keys($IN);
+  $self->_import_data($IN);
+  close $IN;
+  return 1;
+}
+
+sub _import_data {
+  my ($self, $fh) = @_;
+  while(my $line = <$fh>) {
+    chomp $line;
+    my @bits = split /\t/, $line;
+    my %rg;
+    for my $key(@{$self->bas_keys}) {
+      $rg{$key} = $bits[$self->{'key_pos_map'}->{$key}];
+    }
+    $self->{'_data'}->{$rg{'readgroup'}} = \%rg;
+  }
+  return 1;
+}
+
+sub bas_keys {
+  my ($self, $key_fh) = @_;
+  croak "bas_keys should only be initialised once\n" if(exists $self->{'keys'} && defined $key_fh);
+  if(defined $key_fh) {
+    my $line = <$key_fh>;
+    chomp $line;
+    my @head = split /\t/, $line;
+    my %key_pos_map;
+    my $pos=0;
+    for my $key(@head) {
+      $key_pos_map{$key} = $pos++;
+    }
+    $self->{'keys'} = \@head;
+    $self->{'key_pos_map'} = \%key_pos_map;
+  }
+  return $self->{'keys'};
+}
+
+sub get {
+  my ($self, $rg, $key) = @_;
+  die qq{Readgroup '$rg' does not exist\n} unless(exists $self->{'_data'}->{$rg});
+  return exists $self->{'_data'}->{$rg}->{$key} ? $self->{'_data'}->{$rg}->{$key} : undef;
+}
+
+1;
+
+__END__
+
+=head1 PCAP::Bam::Bas
+
+Convenience class for accessing data in a *.bas file.
+
+=head2 METHODS
+
+=over 2
+
+=item new
+
+Construct an access object for BAM statistics file.
+
+ my $bas_ob = PCAP::Bam::Bas->new($bas);
+
+=item bas_keys
+
+Returns the list of available keys for this BAS file.
+
+=item get
+
+Retrieve a value by its readgroup and key:
+
+ $bas->($rg, 'median_insert_size');
+
+NOTE: Returns undef if a key is not available.
+
+=back