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Fix for rare out of order mpileup failures in genotype qc #389

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merged 1 commit into from
Dec 5, 2016
Merged

Fix for rare out of order mpileup failures in genotype qc #389

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1 change: 1 addition & 0 deletions Changes
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
LIST OF CHANGES FOR NPG-QC PACKAGE

- Fix in npg_qc::utils::bam_genotype for rare out of order mpileup failures
- Travis CI build: when building dependencies, us the same
branch as the one the pull request is made to.
- back to testing with mysql 5.7.13 in travis
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42 changes: 4 additions & 38 deletions lib/npg_qc/utils/bam_genotype.pm
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Expand Up @@ -110,40 +110,6 @@ sub _build_samtools {
return $self->samtools_name;
}

has 'samtools_extract_regions' => (
is => 'ro',
isa => 'NpgCommonResolvedPathExecutable',
lazy_build => 1,
coerce => 1,
);
sub _build_samtools_extract_regions {
my ($self) = @_;
return $self->samtools_name;
}

has 'samtools_mpileup' => (
is => 'ro',
isa => 'NpgCommonResolvedPathExecutable',
lazy_build => 1,
coerce => 1,
);
sub _build_samtools_mpileup {
my ($self) = @_;
return $self->samtools_name;
}

has 'samtools_merge' => (
is => 'ro',
isa => 'NpgCommonResolvedPathExecutable',
lazy_build => 1,
coerce => 1,
);
sub _build_samtools_merge {
my ($self) = @_;
return $self->samtools_name;
}

# you can override the executable name. May be useful for variants like "samtools_irods"
has 'bcftools_name' => (
is => 'ro',
isa => 'Str',
Expand Down Expand Up @@ -334,14 +300,14 @@ sub _build__call_gt_cmd {
my $bam_file_list = $self->bam_file_list;

if(@{$bam_file_list} == 1) {
$cmd = sprintf q{bash -c 'set -o pipefail && %s view -b %s %s 2>/dev/null | %s mpileup -l %s -f %s -g - 2>/dev/null | %s call -c -O v - 2>/dev/null'}, $self->samtools_extract_regions, $bam_file_list->[0], $self->_regions_string, $self->samtools_mpileup, $self->pos_snpname_map_filename, $self->reference, $self->bcftools;
$cmd = sprintf q{bash -c 'set -o pipefail && %s view -b %s %s 2>/dev/null | %s sort -l 0 - 2>/dev/null | %s mpileup -l %s -f %s -g - 2>/dev/null | %s call -c -O v - 2>/dev/null'}, $self->samtools, $bam_file_list->[0], $self->_regions_string, $self->samtools, $self->samtools, $self->pos_snpname_map_filename, $self->reference, $self->bcftools;
}
else {
$cmd = sprintf q{bash -c 'set -o pipefail && %s merge -- - }, $self->samtools_merge;
$cmd = sprintf q{bash -c 'set -o pipefail && %s merge -- - }, $self->samtools;
for my $bam_file (@{$bam_file_list}) {
$cmd .= sprintf q{<(%s view -b %s %s) }, $self->samtools_extract_regions, $bam_file, $self->_regions_string;
$cmd .= sprintf q{<(%s view -b %s %s) }, $self->samtools, $bam_file, $self->_regions_string;
}
$cmd .= sprintf q{ | %s mpileup -l %s -f %s -g - 2>/dev/null | %s call -c -O v - 2>/dev/null'}, $self->samtools_mpileup, $self->pos_snpname_map_filename, $self->reference, $self->bcftools;
$cmd .= sprintf q{ | %s mpileup -l %s -f %s -g - 2>/dev/null | %s call -c -O v - 2>/dev/null'}, $self->samtools, $self->pos_snpname_map_filename, $self->reference, $self->bcftools;
}

return $cmd;
Expand Down