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rust-bio / rust-bio-tools

A set of command line utilities based on Rust-Bio.
MIT License
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feat: consensus reads - move record ids to description field #250

Closed FelixMoelder closed 1 year ago

FelixMoelder commented 1 year ago

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.

FelixMoelder commented 1 year ago

Fixed some tests which failed due to changes in htslib. vcf files require at least one sample after FORMAT field.