gsutil cp -r gs://pepper-deepvariant/pichuan/xm_experiments/156193069/wu_1/best/* /private/groups/patenlab/anovak/projects/hprc/lr-giraffe/models/hifi/2025-03-26/
rm -f /private/groups/patenlab/anovak/projects/hprc/lr-giraffe/models/hifi/2025-03-26/model.example-info.json
# Add a model.example-info.json so the model can be used with the same DeepVariant container as the r10y2025 model
# This one is modified from that and
# <https://ucsc-gi.slack.com/archives/C01D0M09G5D/p1752857468224469?thread_ts=1752070255.893099&cid=C01D0M09G5D>
# and also
# docker run --rm google/deepvariant:CL782981885 cat /opt/models/pacbio/model.example_info.json
# and
# <https://ucsc-gi.slack.com/archives/C01D0M09G5D/p1753216962639059?thread_ts=1753215519.655039&cid=C01D0M09G5D>
# with legacy AC turned off and reverse_haplotypes dropped
cat > /private/groups/patenlab/anovak/projects/hprc/lr-giraffe/models/hifi/2025-03-26/model.example_info.json <<'EOF2'
{
  "version": "1.9.0",
  "shape": [100, 147, 9],
  "channels": [1, 2, 3, 4, 5, 6, 7, 9, 10],
  "flags_for_calling": {
    "parse_sam_aux_fields": true,
    "sort_by_haplotypes": true,
    "phase_reads": true,
    "realign_reads": false,
    "vsc_min_fraction_indels": 0.12,
    "alt_aligned_pileup": "diff_channels",
    "trim_reads_for_pileup": true,
    "pileup_image_height": 100,
    "pileup_image_width": 147,
    "min_mapping_quality": 0,
    "track_ref_reads": true,
    "partition_size": 25000,
    "normalize_reads": true,
    "keep_legacy_allele_counter_behavior": false
  }
}
EOF2