Remove CHR2 and END2 for CPX at the end of CleanVcf

[epiercehoffman]

Updates

Remove CHR2 and END2 fields (if they exist) for all CPX records at the end of CleanVcf. These fields are redundant with the information in CPX_INTERVALS and are currently inconsistent and confusing (#377).

Testing

• Validated all WDLs and JSONs with womtool & terra validation script
• Rebuilt sv_pipeline_docker (us.gcr.io/broad-dsde-methods/eph/sv-pipeline:eph-cpx-remove-chr2-end2-6feed34) and tested CleanVcf with reference panel data. The workflow ran successfully and the resulting VCF did not have CHR2 or END2 fields for CPX records.

Note

Downstream workflows should be tested and updated if needed to comply with this change.

[mwalker174]

Thanks! LGTM, just a small GATK update will be needed for SVConcordance downstream.