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Merge pull request #461 from sanger-pathogens/splitfastq-bugfix
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Splitfastq bugfix
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@Oliver-Lorenz-dev
Oliver-Lorenz-dev authored Mar 22, 2022
2 parents a85c4e2 + 7c70ec2 commit 9683e48
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Showing 7 changed files with 16 additions and 16 deletions.
4 changes: 2 additions & 2 deletions lib/VertRes/Utils/Mappers/bowtie2.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -108,7 +108,7 @@ sub name {
Usage : $obj->split_fastq(read1 => 'reads_1.fastq',
read2 => 'reads_2.fastq',
split_dir => '/path/to/desired/split_dir',
chunk_size => 1000000000);
chunk_size => 1000000000000);
Function: Split the fastq(s) into multiple smaller files. This is just a
convienience alias to VertRes::Utils::FastQ::split, with syntax
more similar to do_mapping().
Expand All @@ -125,7 +125,7 @@ sub name {
sub split_fastq {
my ($self, %args) = @_;
unless ($args{chunk_size}) {
$args{chunk_size} = 1000000000;
$args{chunk_size} = 1000000000000;
}

return $self->SUPER::split_fastq(%args);
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4 changes: 2 additions & 2 deletions lib/VertRes/Utils/Mappers/bwa.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -105,7 +105,7 @@ sub name {
Usage : $obj->split_fastq(read1 => 'reads_1.fastq',
read2 => 'reads_2.fastq',
split_dir => '/path/to/desired/split_dir',
chunk_size => 1000000000);
chunk_size => 1000000000000);
Function: Split the fastq(s) into multiple smaller files. This is just a
convienience alias to VertRes::Utils::FastQ::split, with syntax
more similar to do_mapping().
Expand All @@ -122,7 +122,7 @@ sub name {
sub split_fastq {
my ($self, %args) = @_;
unless ($args{chunk_size}) {
$args{chunk_size} = 1000000000;
$args{chunk_size} = 1000000000000;
}

return $self->SUPER::split_fastq(%args);
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6 changes: 3 additions & 3 deletions lib/VertRes/Utils/Mappers/maq.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -106,7 +106,7 @@ sub name {
Usage : $obj->split_fastq(read1 => 'reads_1.fastq',
read2 => 'reads_2.fastq',
split_dir => '/path/to/desired/split_dir',
chunk_size => 57600000);
chunk_size => 1000000000000);
Function: Split the fastq(s) into multiple smaller files. This is just a
convienience alias to VertRes::Utils::FastQ::split, with syntax
more similar to do_mapping().
Expand All @@ -116,14 +116,14 @@ sub name {
read0 => 'reads.fastq'
split_dir => '/path/to/desired/split_dir'
chunk_size => int (max number of bases per chunk, default 57600000)
chunk_size => int (max number of bases per chunk, default 1000000000000)
=cut

sub split_fastq {
my ($self, %args) = @_;
unless ($args{chunk_size}) {
$args{chunk_size} = 57600000;
$args{chunk_size} = 1000000000000;
}

return $self->SUPER::split_fastq(%args);
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4 changes: 2 additions & 2 deletions lib/VertRes/Utils/Mappers/smalt.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -108,7 +108,7 @@ sub name {
Usage : $obj->split_fastq(read1 => 'reads_1.fastq',
read2 => 'reads_2.fastq',
split_dir => '/path/to/desired/split_dir',
chunk_size => 1000000000);
chunk_size => 1000000000000);
Function: Split the fastq(s) into multiple smaller files. This is just a
convienience alias to VertRes::Utils::FastQ::split, with syntax
more similar to do_mapping().
Expand All @@ -125,7 +125,7 @@ sub name {
sub split_fastq {
my ($self, %args) = @_;
unless ($args{chunk_size}) {
$args{chunk_size} = 1000000000;
$args{chunk_size} = 1000000000000;
}

return $self->SUPER::split_fastq(%args);
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6 changes: 3 additions & 3 deletions lib/VertRes/Utils/Mappers/ssaha.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -110,7 +110,7 @@ sub name {
Usage : $obj->split_fastq(read1 => 'reads_1.fastq',
read2 => 'reads_2.fastq',
split_dir => '/path/to/desired/split_dir',
chunk_size => 10000000);
chunk_size => 1000000000000);
Function: Split the fastq(s) into multiple smaller files. This is just a
convienience alias to VertRes::Utils::FastQ::split, with syntax
more similar to do_mapping().
Expand All @@ -120,14 +120,14 @@ sub name {
read0 => 'reads.fastq'
split_dir => '/path/to/desired/split_dir'
chunk_size => int (max number of bases per chunk, default 10000000)
chunk_size => int (max number of bases per chunk, default 1000000000000)
=cut

sub split_fastq {
my ($self, %args) = @_;
unless ($args{chunk_size}) {
$args{chunk_size} = 10000000;
$args{chunk_size} = 1000000000000;
}

return $self->SUPER::split_fastq(%args);
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4 changes: 2 additions & 2 deletions lib/VertRes/Utils/Mappers/stampy.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -106,7 +106,7 @@ sub name {
Usage : $obj->split_fastq(read1 => 'reads_1.fastq',
read2 => 'reads_2.fastq',
split_dir => '/path/to/desired/split_dir',
chunk_size => 1000000000);
chunk_size => 1000000000000);
Function: Split the fastq(s) into multiple smaller files. This is just a
convienience alias to VertRes::Utils::FastQ::split, with syntax
more similar to do_mapping().
Expand All @@ -123,7 +123,7 @@ sub name {
sub split_fastq {
my ($self, %args) = @_;
unless ($args{chunk_size}) {
$args{chunk_size} = 1000000000;
$args{chunk_size} = 1000000000000;
}

return $self->SUPER::split_fastq(%args);
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4 changes: 2 additions & 2 deletions lib/VertRes/Utils/Mappers/tophat.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -108,7 +108,7 @@ sub name {
Usage : $obj->split_fastq(read1 => 'reads_1.fastq',
read2 => 'reads_2.fastq',
split_dir => '/path/to/desired/split_dir',
chunk_size => 1000000000);
chunk_size => 1000000000000);
Function: Split the fastq(s) into multiple smaller files. This is just a
convienience alias to VertRes::Utils::FastQ::split, with syntax
more similar to do_mapping().
Expand All @@ -125,7 +125,7 @@ sub name {
sub split_fastq {
my ($self, %args) = @_;
unless ($args{chunk_size}) {
$args{chunk_size} = 1000000000;
$args{chunk_size} = 1000000000000;
}

return $self->SUPER::split_fastq(%args);
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