diff -Nru libbio-samtools-perl-1.31/Build.PL libbio-samtools-perl-1.32/Build.PL --- libbio-samtools-perl-1.31/Build.PL 2011-09-22 13:27:25.000000000 +0000 +++ libbio-samtools-perl-1.32/Build.PL 2011-11-08 22:21:28.000000000 +0000 @@ -32,7 +32,7 @@ }, requires => { 'perl' => '5.008', - 'Bio::Root::Version' => '1.005009001', + 'Bio::Root::Version' => '1.006009001', }, # create_makefile_pl => 'passthrough', ); diff -Nru libbio-samtools-perl-1.31/Changes libbio-samtools-perl-1.32/Changes --- libbio-samtools-perl-1.31/Changes 2011-09-22 13:27:25.000000000 +0000 +++ libbio-samtools-perl-1.32/Changes 2011-11-08 22:21:28.000000000 +0000 @@ -1,3 +1,11 @@ +Version 1.32 + * Fix loss of strand information when joining split alignments. + * Give read_pair objects a primary_id that will allow them to be retrieved intact using get_feature_by_id(). + +Version 1.31 + * Added Bio::DB::Sam->max_pileup_cnt() and Bio::DB::Bam->max_pileup_cnt() method + to allow users to adjust Samtools cap on pileup depth. + Version 1.30 * Apply patch from Jason Walker to return full arrays across 0-depth coverage and to max the count at a certain coverage. diff -Nru libbio-samtools-perl-1.31/debian/changelog libbio-samtools-perl-1.32/debian/changelog --- libbio-samtools-perl-1.31/debian/changelog 2011-11-15 17:16:33.000000000 +0000 +++ libbio-samtools-perl-1.32/debian/changelog 2011-11-23 07:26:39.000000000 +0000 @@ -1,8 +1,9 @@ -libbio-samtools-perl (1.31-1build1) precise; urgency=low +libbio-samtools-perl (1.32-1) unstable; urgency=low - * Rebuild for Perl 5.14. + [36ac64b] New upstream release. + [dfb9312] Depend on BioPerl 1.6.901, following Upstream. - -- Colin Watson Tue, 15 Nov 2011 17:16:33 +0000 + -- Charles Plessy Wed, 23 Nov 2011 16:26:32 +0900 libbio-samtools-perl (1.31-1) unstable; urgency=low diff -Nru libbio-samtools-perl-1.31/debian/control libbio-samtools-perl-1.32/debian/control --- libbio-samtools-perl-1.31/debian/control 2011-06-28 04:36:58.000000000 +0000 +++ libbio-samtools-perl-1.32/debian/control 2011-11-23 07:25:38.000000000 +0000 @@ -5,7 +5,7 @@ perl (>= 5.8), zlib1g-dev, libbam-dev (>= 0.1.16-1~), # needed for the tests: - libbio-perl-perl (>= 1.6) + libbio-perl-perl (>= 1.6.901) Maintainer: Debian Perl Group Uploaders: Charles Plessy Standards-Version: 3.9.2 @@ -15,7 +15,7 @@ Package: libbio-samtools-perl Architecture: any -Depends: ${perl:Depends}, ${shlibs:Depends}, ${misc:Depends}, perl (>= 5.8), libbio-perl-perl (>= 1.6) +Depends: ${perl:Depends}, ${shlibs:Depends}, ${misc:Depends}, perl (>= 5.8), libbio-perl-perl (>= 1.6.901) Enhances: gbrowse, samtools Description: read SAM/BAM nucleotide sequence aligment database files Bio::SamTools provides a Perl interface to the libbam library for indexed and diff -Nru libbio-samtools-perl-1.31/debian/copyright libbio-samtools-perl-1.32/debian/copyright --- libbio-samtools-perl-1.31/debian/copyright 2011-11-01 10:15:10.000000000 +0000 +++ libbio-samtools-perl-1.32/debian/copyright 2011-11-23 07:23:00.000000000 +0000 @@ -1,5 +1,5 @@ Format: http://dep.debian.net/deps/dep5/ -Source: http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-SamTools-1.31.tar.gz +Source: http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-SamTools-1.32.tar.gz Disclaimer: This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See the Artistic License file in the main Perl distribution for specific terms and conditions of diff -Nru libbio-samtools-perl-1.31/lib/Bio/DB/Bam/Alignment.pm libbio-samtools-perl-1.32/lib/Bio/DB/Bam/Alignment.pm --- libbio-samtools-perl-1.31/lib/Bio/DB/Bam/Alignment.pm 2011-09-22 13:27:25.000000000 +0000 +++ libbio-samtools-perl-1.32/lib/Bio/DB/Bam/Alignment.pm 2011-11-08 22:21:28.000000000 +0000 @@ -1,6 +1,6 @@ package Bio::DB::Bam::Alignment; -# $Id: Alignment.pm 23212 2010-05-14 20:56:24Z lstein $ +# $Id$ =head1 NAME diff -Nru libbio-samtools-perl-1.31/lib/Bio/DB/Bam/AlignWrapper.pm libbio-samtools-perl-1.32/lib/Bio/DB/Bam/AlignWrapper.pm --- libbio-samtools-perl-1.31/lib/Bio/DB/Bam/AlignWrapper.pm 2011-09-22 13:27:25.000000000 +0000 +++ libbio-samtools-perl-1.32/lib/Bio/DB/Bam/AlignWrapper.pm 2011-11-08 22:21:28.000000000 +0000 @@ -1,6 +1,6 @@ package Bio::DB::Bam::AlignWrapper; -# $Id: AlignWrapper.pm 24231 2010-11-23 22:20:26Z lstein $ +# $Id$ =head1 NAME @@ -123,7 +123,7 @@ -start => $s, -end => $e, -seq_id => $self->seq_id, - -strand => +1, + -strand => $self->strand, -seq => [$self,$start+$skip,$end-$start], # deferred rendering -type => $self->type); diff -Nru libbio-samtools-perl-1.31/lib/Bio/DB/Bam/Pileup.pm libbio-samtools-perl-1.32/lib/Bio/DB/Bam/Pileup.pm --- libbio-samtools-perl-1.31/lib/Bio/DB/Bam/Pileup.pm 2011-09-22 13:27:25.000000000 +0000 +++ libbio-samtools-perl-1.32/lib/Bio/DB/Bam/Pileup.pm 2011-11-08 22:21:28.000000000 +0000 @@ -1,6 +1,6 @@ package Bio::DB::Bam::Pileup; -# $Id: Pileup.pm 22410 2009-12-15 16:23:24Z lstein $ +# $Id$ # documentation only diff -Nru libbio-samtools-perl-1.31/lib/Bio/DB/Bam/PileupWrapper.pm libbio-samtools-perl-1.32/lib/Bio/DB/Bam/PileupWrapper.pm --- libbio-samtools-perl-1.31/lib/Bio/DB/Bam/PileupWrapper.pm 2011-09-22 13:27:25.000000000 +0000 +++ libbio-samtools-perl-1.32/lib/Bio/DB/Bam/PileupWrapper.pm 2011-11-08 22:21:28.000000000 +0000 @@ -1,5 +1,5 @@ package Bio::DB::Bam::PileupWrapper; -#$Id: PileupWrapper.pm 22410 2009-12-15 16:23:24Z lstein $ +#$Id$ =head1 NAME diff -Nru libbio-samtools-perl-1.31/lib/Bio/DB/Bam/Query.pm libbio-samtools-perl-1.32/lib/Bio/DB/Bam/Query.pm --- libbio-samtools-perl-1.31/lib/Bio/DB/Bam/Query.pm 2011-09-22 13:27:25.000000000 +0000 +++ libbio-samtools-perl-1.32/lib/Bio/DB/Bam/Query.pm 2011-11-08 22:21:28.000000000 +0000 @@ -1,6 +1,6 @@ package Bio::DB::Bam::Query; -# $Id: Query.pm 24242 2010-11-25 21:27:03Z lstein $ +# $Id$ =head1 NAME diff -Nru libbio-samtools-perl-1.31/lib/Bio/DB/Sam/Constants.pm libbio-samtools-perl-1.32/lib/Bio/DB/Sam/Constants.pm --- libbio-samtools-perl-1.31/lib/Bio/DB/Sam/Constants.pm 2011-09-22 13:27:25.000000000 +0000 +++ libbio-samtools-perl-1.32/lib/Bio/DB/Sam/Constants.pm 2011-11-08 22:21:28.000000000 +0000 @@ -1,6 +1,6 @@ package Bio::DB::Sam::Constants; -# $Id: Constants.pm 22410 2009-12-15 16:23:24Z lstein $ +# $Id$ =head1 NAME diff -Nru libbio-samtools-perl-1.31/lib/Bio/DB/Sam.pm libbio-samtools-perl-1.32/lib/Bio/DB/Sam.pm --- libbio-samtools-perl-1.31/lib/Bio/DB/Sam.pm 2011-09-22 13:27:25.000000000 +0000 +++ libbio-samtools-perl-1.32/lib/Bio/DB/Sam.pm 2011-11-08 22:21:28.000000000 +0000 @@ -1,7 +1,7 @@ package Bio::DB::Sam; -# $Id: Sam.pm 25203 2011-09-21 21:22:55Z lstein $ +# $Id$ -our $VERSION = '1.31'; +our $VERSION = '1.32'; =head1 NAME @@ -1672,10 +1672,12 @@ sub get_feature_by_id { my $self = shift; my $id = shift; - my ($name,$tid,$start,$end,$strand) = map {s/%3B/;/ig;$_} split ';',$id; + my ($name,$tid,$start,$end,$strand,$type) = map {s/%3B/;/ig;$_} split ';',$id; return unless $name && defined $tid; + $type ||= 'match'; my $seqid = $self->target_name($tid); my @features = $self->features(-name=>$name, + -type => $type, -seq_id=>$seqid, -start=>$start, -end=>$end, @@ -1965,6 +1967,20 @@ } $read_pairs{$name}->add_SeqFeature($a); } + for my $name (keys %read_pairs) { + my $f = $read_pairs{$name}; + my $primary_id = join(';', + map {s/;/%3B/g; $_} + ($f->display_name, + ($f->get_SeqFeatures)[0]->tid, + $f->start, + $f->end, + $f->strand, + $f->type, + ) + ); + $read_pairs{$name}->primary_id($primary_id); + } push @$dest,values %read_pairs; } diff -Nru libbio-samtools-perl-1.31/META.json libbio-samtools-perl-1.32/META.json --- libbio-samtools-perl-1.31/META.json 2011-09-22 13:27:25.000000000 +0000 +++ libbio-samtools-perl-1.32/META.json 2011-11-08 22:21:28.000000000 +0000 @@ -26,7 +26,7 @@ }, "runtime" : { "requires" : { - "Bio::Root::Version" : "1.005009001", + "Bio::Root::Version" : "1.006009001", "perl" : "5.008" } } @@ -74,7 +74,7 @@ }, "Bio::DB::Sam" : { "file" : "lib/Bio/DB/Sam.pm", - "version" : "1.31" + "version" : "1.32" }, "Bio::DB::Sam::Constants" : { "file" : "lib/Bio/DB/Sam/Constants.pm", @@ -107,5 +107,5 @@ "http://dev.perl.org/licenses/" ] }, - "version" : "1.31" + "version" : "1.32" } diff -Nru libbio-samtools-perl-1.31/META.yml libbio-samtools-perl-1.32/META.yml --- libbio-samtools-perl-1.31/META.yml 2011-09-22 13:27:25.000000000 +0000 +++ libbio-samtools-perl-1.32/META.yml 2011-11-08 22:21:28.000000000 +0000 @@ -46,7 +46,7 @@ version: 0 Bio::DB::Sam: file: lib/Bio/DB/Sam.pm - version: 1.31 + version: 1.32 Bio::DB::Sam::Constants: file: lib/Bio/DB/Sam/Constants.pm version: 0 @@ -66,8 +66,8 @@ file: lib/Bio/DB/Sam.pm version: 0 requires: - Bio::Root::Version: 1.005009001 + Bio::Root::Version: 1.006009001 perl: 5.008 resources: license: http://dev.perl.org/licenses/ -version: 1.31 +version: 1.32