Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with
or
.
Download ZIP
Browse files

add all MYMETA files to ignore; temporarily reverted Mapstats and Tra…

…ckQC_Bam to their schema13-compatible forms
  • Loading branch information...
commit 080f73816d54808565b311ba24f4fe2a28cc1575 1 parent d3ff124
@sb10 sb10 authored
View
2  .gitignore
@@ -1,5 +1,5 @@
previously.txt
-MYMETA.yml
+MYMETA.*
modules/VRTrack/Testconfig.pm
.*~
*~
View
18 modules/VRTrack/Mapstats.pm
@@ -88,8 +88,7 @@ sub fields_dispatch {
target_bases_20X => sub { $self->target_bases_20X(@_)},
target_bases_50X => sub { $self->target_bases_50X(@_)},
target_bases_100X => sub { $self->target_bases_100X(@_)},
- exome_design_id => sub { $self->exome_design_id(@_)},
- percentage_reads_with_transposon => sub { $self->percentage_reads_with_transposon(@_)});
+ exome_design_id => sub { $self->exome_design_id(@_)});
return \%fields;
}
@@ -979,19 +978,4 @@ sub _get_child_methods {
return qw(images);
}
-=head2 percentage_reads_with_transposon
-
- Arg [1] : percentage_reads_with_transposon
- Example : my $exome_design_id = $mapstats->percentage_reads_with_transposon(73.23);
- $mapstats->percentage_reads_with_transposon();
- Description: Get/Set the percetage of reads with a transposon for a lane
- ReturnType : Float
-
-=cut
-
-sub percentage_reads_with_transposon {
- my $self = shift;
- return $self->_get_set('percentage_reads_with_transposon', 'number', @_);
-}
-
1;
View
5 modules/VertRes/Pipelines/TrackQC_Bam.pm
@@ -954,10 +954,6 @@ sub update_db
# Length of reference sequence mapped (for TrackQC_Fasta pipeline.)
my $sequence_mapped = undef;
if ( -e "$sample_dir/${name}.cover" ) { $sequence_mapped = do "$sample_dir/${name}.cover"; }
-
-
- my $percentage_reads_with_transposon = undef;
- if ( -e "$sample_dir/${name}.transposon" ) { $percentage_reads_with_transposon = do "$sample_dir/${name}.transposon"; }
$vrtrack->transaction_start();
@@ -988,7 +984,6 @@ sub update_db
$mapping->rmdup_bases_mapped($rmdup_bases_mapped_c);
$mapping->adapter_reads($nadapters);
$mapping->clip_bases($bases_total-$bases_trimmed);
- $mapping->percentage_reads_with_transposon($percentage_reads_with_transposon);
$mapping->mean_insert($avg_isize);
$mapping->sd_insert($sd_isize);
Please sign in to comment.
Something went wrong with that request. Please try again.