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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| package Sanger::CGP::Pindel; | ||
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| ########## LICENCE ########## | ||
| # Copyright (c) 2014-2018 Genome Research Ltd. | ||
| # Copyright (c) 2014-2019 Genome Research Ltd. | ||
| # | ||
| # Author: CASM/Cancer IT <[email protected]> | ||
| # | ||
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@@ -26,7 +26,7 @@ use strict; | |
| use Const::Fast qw(const); | ||
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| use base 'Exporter'; | ||
| our $VERSION = '3.0.6'; | ||
| our $VERSION = '3.1.0'; | ||
| our @EXPORT = qw($VERSION); | ||
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| 1; | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| package Sanger::CGP::Pindel::InputGen; | ||
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| ########## LICENCE ########## | ||
| # Copyright (c) 2014-2018 Genome Research Ltd. | ||
| # Copyright (c) 2014-2019 Genome Research Ltd. | ||
| # | ||
| # Author: CASM/Cancer IT <[email protected]> | ||
| # | ||
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@@ -51,7 +51,7 @@ use Sanger::CGP::Pindel::InputGen::Pair; | |
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| const my $PAIRS_PER_THREAD => 500_000; | ||
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| const my $BAMCOLLATE => q{%s outputformat=sam colsbs=268435456 collate=1 classes=F,F2 exclude=DUP,SECONDARY,QCFAIL,SUPPLEMENTARY T=%s filename=%s reference=%s inputformat=%s}; | ||
| const my $BAMCOLLATE => q{%s outputformat=sam colsbs=268435456 collate=1 classes=F,F2 exclude=DUP,SECONDARY,SUPPLEMENTARY T=%s filename=%s reference=%s inputformat=%s}; | ||
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| sub new { | ||
| my ($class, $bam, $exclude, $ref) = @_; | ||
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@@ -238,8 +238,7 @@ sub reads_to_pindel { | |
| for(1..$total_pairs) { | ||
| my $pair = Sanger::CGP::Pindel::InputGen::Pair->new(\shift @reads, \shift @reads, $tabix); | ||
| next unless($pair->keep_pair); | ||
| $to_pindel->set_pair($pair); | ||
| push @records, @{$to_pindel->pair_to_pindel}; | ||
| push @records, @{$to_pindel->pair_to_pindel($pair)}; | ||
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| } | ||
| my $retained = scalar @records; | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| package Sanger::CGP::Pindel::InputGen::Pair; | ||
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| ########## LICENCE ########## | ||
| # Copyright (c) 2014-2018 Genome Research Ltd. | ||
| # Copyright (c) 2014-2019 Genome Research Ltd. | ||
| # | ||
| # Author: CASM/Cancer IT <[email protected]> | ||
| # | ||
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@@ -57,6 +57,12 @@ sub unmapped_pair { | |
| return 0; | ||
| } | ||
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| sub qcfailed_pair { | ||
| my $self = shift; | ||
| return 1 if($self->{'r1'}->qc_failed && $self->{'r2'}->qc_failed); | ||
| return 0; | ||
| } | ||
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| sub has_good_anchor { | ||
| my $self = shift; | ||
| my $r2_state = $self->{'r2'}->good_anchor; # to ensure both fully populates | ||
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@@ -73,6 +79,7 @@ sub has_good_query { | |
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| sub keep_pair { | ||
| my $self = shift; | ||
| return 0 if($self->qcfailed_pair); | ||
| return 0 if($self->unmapped_pair); | ||
| return 0 if($self->exact); | ||
| return 0 unless($self->has_good_anchor); | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| package Sanger::CGP::Pindel::InputGen::PairToPindel; | ||
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| ########## LICENCE ########## | ||
| # Copyright (c) 2014-2018 Genome Research Ltd. | ||
| # Copyright (c) 2014-2019 Genome Research Ltd. | ||
| # | ||
| # Author: CASM/Cancer IT <[email protected]> | ||
| # | ||
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@@ -55,14 +55,9 @@ sub setup_rg_inserts { | |
| return 1; | ||
| } | ||
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| sub set_pair { | ||
| my ($self, $pair) = @_; | ||
| croak "No pair provided" unless(defined $pair); | ||
| $self->{'pair'} = $pair; | ||
| } | ||
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| sub pair_to_pindel { | ||
| my $self = shift; | ||
| my ($self, $pair_in) = @_; | ||
| $self->{'pair'} = $pair_in; | ||
| my $r1 = $self->{'pair'}->{'r1'}; | ||
| my $r2 = $self->{'pair'}->{'r2'}; | ||
| my @pindel_records; | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| package Sanger::CGP::Pindel::InputGen::Read; | ||
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| ########## LICENCE ########## | ||
| # Copyright (c) 2014-2018 Genome Research Ltd. | ||
| # Copyright (c) 2014-2019 Genome Research Ltd. | ||
| # | ||
| # Author: CASM/Cancer IT <[email protected]> | ||
| # | ||
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@@ -41,6 +41,7 @@ const my $UNMAPPED => 4; | |
| const my $READ_REVERSED => 16; #0x0010 (set when reverse) | ||
| const my $FIRST_IN_PAIR => 64; | ||
| const my $SECOND_IN_PAIR => 128; | ||
| const my $QC_FAIL => 512; | ||
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| const my $MIN_MAPQ => 0; | ||
| const my $MIN_ANCHOR_MAPQ => 0; | ||
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@@ -102,6 +103,11 @@ sub reversed { | |
| (($self->{'flag'} | $READ_REVERSED) == $self->{'flag'}) ? 1 : 0; | ||
| } | ||
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| sub qc_failed { | ||
| my $self = shift; | ||
| (($self->{'flag'} | $QC_FAIL) == $self->{'flag'}) ? 1 : 0; | ||
| } | ||
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| sub strand { | ||
| my $self = shift; | ||
| $self->reversed ? '-' : '+'; | ||
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@@ -191,6 +197,7 @@ sub good_query { | |
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| sub _good_query { | ||
| my $self = shift; | ||
| return 0 if($self->qc_failed); | ||
| return 0 if(index($self->{'seq'},'NN') >= 0); | ||
| return 0 if($self->frac_pbq_poor > $MAX_POOR_PBQ_FRAC); | ||
| unless($self->unmapped) { | ||
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