When consensus reads are calculated with the --verbose-read-names parameter record ids of a consensus group are written into the record name.
As this might result in long record names leading tools to fail during postprocessing this PR changes the parameters behavior by writing the record ids into the fastqs description fields as following ID:Z:<id1,id2,...>.
This allows bwa mem to annotate move the record ids to bam records by the ID-tag.
To represent the parameters new behavior it has also been renamed as --annotate_record_ids.
When consensus reads are calculated with the
--verbose-read-names
parameter record ids of a consensus group are written into the record name. As this might result in long record names leading tools to fail during postprocessing this PR changes the parameters behavior by writing the record ids into the fastqs description fields as followingID:Z:<id1,id2,...>
. This allowsbwa mem
to annotate move the record ids to bam records by theID
-tag. To represent the parameters new behavior it has also been renamed as--annotate_record_ids
.