source_audit: data/external/k562_molecular_sources_audit.yaml
target_assembly: hg19
candidate_contact_sources: 2
candidate_contact_matrices: 1
ready_contact_matrices: 0
plan_records:
- family: reference_hic
  accession: ENCFF621AIY
  assembly: GRCh38
  file_format: hic
  output_type: mapping quality thresholded contact matrix
  status: released
  file_size: 33783625697
  md5sum: 71e5dc072beddbdcda11c9016696e142
  download_url: https://www.encodeproject.org/files/ENCFF621AIY/@@download/ENCFF621AIY.hic
  s3_uri: s3://encode-public/2022/05/15/0571c671-3645-4f92-beae-51dfd3f42c36/ENCFF621AIY.hic
  local_path: data/raw/k562_molecular/reference_hic/ENCFF621AIY.hic
  local_exists: false
  action: requires_assembly_strategy_before_use
- family: reference_hic
  accession: ENCFF134PUN
  assembly: GRCh38
  file_format: bed
  output_type: contact domains
  status: archived
  file_size: 58070147883
  md5sum: cd12d922bb71692d98f924c04e72d038
  download_url: https://www.encodeproject.org/files/ENCFF134PUN/@@download/ENCFF134PUN.bed.gz
  s3_uri: s3://encode-public/2023/04/12/9c79af08-d830-4e4d-ae35-bae09c98b328/ENCFF134PUN.bed.gz
  local_path: data/raw/k562_molecular/reference_hic/ENCFF134PUN.bed.gz
  local_exists: false
  action: not_a_contact_matrix
recommended_next_action: 'No assembly-matched local contact matrix is ready. Current
  ENCODE K562 .hic candidate is GRCh38 while the Gasperini benchmark is treated as
  hg19. Choose one controlled path: create a GRCh38/liftOver candidate table with
  QC, or use an hg19-compatible contact source. Then dump sparse pixels and run scripts/build_k562_contact_features.py.'
example_sparse_build_command: PYTHONPATH=src .venv/bin/python scripts/build_k562_contact_features.py
  --contacts data/interim/k562_contacts/k562_10kb_pixels.tsv.gz --contact-assembly
  hg19 --resolution-bp 10000