Update JSON with summary block/new info while preserving tags used by GPAS

[iqbal-lab]

JSON should be identical to that from 0.3.7 but a) with line breaks, eg indent =2, b) with an additional summary block, containing:

“Summary”: { “command”: “viridian run_one_sample fq1 fq2”, "options": { "debug": true, "tech": "ont", … etc … "max_percent_amps_fail": 50.0, "max_cons_n_percent": 50.0 }, “Version”: “v0.1.0”, “Finished_running”: true, “Success”: true, “Progress”: [ {“Task”: “Minimap2”, “Success”: True, “start”: “12:01:00”, “end”: “13:02”, “error”: null}, {“Task”: “Samtools sort”, “Success”: True, “start”: “13:02:00”, “end”: “13:02”, “error”: null}, {“Task”: “Samtools sort”, “Success”: False, “start”: “13:02:00”, “end”: “13:02”, “error”: “insert coin”},

], "cwd": "blah", "start_time": "2022-03-25T08:37:53", "end_time": "2022-03-25T08:38:00", "hostname": "thehoff", "run_time": "0:00:07.262877", } # end of summary

“Results”: { “Consensus”: “AAAAAAAAAAAA”, “reference_start”: 52, “reference_end”: 29006, “Amplicons”: {“scheme”: “artic-v3”, “total_amplicons”: 100, “Successful_amplicons”: 99, “fragment_matches”: 20000000, “fragment_mismatches”: 2121, }, “Coverage”: { “total_reads”: 200002121, “Total_fragments”: 100001070, “Reference_coverage”: 25000, “Reference_length”: 29000, “Average_amplicon_depth”: 300 } “Self_qc”: “Masked_by_assembler”: 20, “Total_masked_incl_self_qc”: 40, “Low_frs_only”: 2, “Amplicon_bias”: 10, “Low_depth_only”: 0, "Low_frs_and_low_depth":1, (combinations of filters) }

“Details”: { … all the key values that are in 0.3.7 …except get rid of old run_summary “Self_qc”: { “Masked_positions”: [{“position”: 2, “filters”: [“low_frs”, “in_primer”], {“position”: 10, “filters”: [“amplicon_bias”]}

}

I attach here a CSV of the keys/tags used by GPAS

gpas_viridian_keys_used.csv

Of the things in that CSV, we want to remove the following:

$.viridian.amplicons[].polish_data.Reads matching $.viridian.amplicons[].polish_data.Reads matching forward strand $.viridian.amplicons[*].polish_data.Reads matching reverse strand $.run_summary.options.log_liftover $.run_summary.options.trim_5prime

I think is fine to rename so long as we can provide a mapping.

[jeff-k]

what does the $ mean in the field names?

[iqbal-lab]

i think he just dumped it from somewhere/APEX