Deprecated files in GATK-SV #870
Description
Below is a compilation of files that I believe can be deprecated by moving them to the internal repository.
src/svtk/svtk/standardize/std_delly.py.src/svtk/svtk/standardize/std_lumpy.py.src/svtk/svtk/standardize/std_melt.py.src/svtk/svtk/standardize/std_smoove.py.src/sv-pipeline/04_variant_resolution/scripts/aggregate_dn.py.src/sv-pipeline/04_variant_resolution/scripts/eliminate_redundancies.py.src/sv-pipeline/04_variant_resolution/scripts/final_filter.py.src/sv-pipeline/04_variant_resolution/scripts/make_concordant_multiallelic_alts.py.src/sv-pipeline/04_variant_resolution/scripts/merge_linked_depth_calls.py.src/sv-pipeline/04_variant_resolution/scripts/merge_pesr_depth.py.src/sv-pipeline/04_variant_resolution/scripts/overlap_pass.py.src/sv-pipeline/04_variant_resolution/scripts/remove_added_pilot_variants.py.src/sv-pipeline/04_variant_resolution/scripts/scrape_stats.py: .src/sv_utils/src/sv_utils/fix_vcf.py.src/sv_utils/src/sv_utils/genomics_io.py.src/sv_utils/src/sv_utils/interval_overlaps.py.src/svtest/svtest/cli/vcf.py.src/svtest/svtest/utils/VCFUtils.py.src/svtk/svtk/utils/rdtest.py.