Allow for naming differences in unbarcoded bam files from SMRT Link deplexing #482
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kjsanger
reviewed
Dec 9, 2024
| @@ -400,7 +400,7 @@ sub _get_tag_name_from_fname { | |||
| sub _is_allowed_fname { | |||
| my ($self, $file, $fnames) = @_; | |||
| my @exists = grep { $file =~ m{[.] $_ [.]}smx } @{ $fnames }; | |||
| return @exists == 1 ? 1 : 0; | |||
| return @exists >= 1 ? 1 : 0; | |||
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As we're already using List::AllUtils qw[any] I think it may read better when expressed as:
return any @exists;
rather than a ternary?
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Occasional re-deplexing is run via SMRT Link after lab errors are resolved e.g. data from instrument is not deplexed correctly.
In the output for SMRT Link deplexing files containing reads where the barcode is not determined (like tag zero in Illumina) were called movie_name.unbarcoded.bam but are now called movie_name.hifi_reads.unbarcoded.bam