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