Adding json mode

[johandahlberg]

This adds a new mode json mode to CheckQC. When this flag is used it will print the reports as json to stdout. This is useful to pass the results to other programs, and will make it easier to add webservice capabilities to CheckQC in the future.

Here is an example of that this will look like:

$ checkqc --json tests/resources/170726_D00118_0303_BCB1TVANXX/ 2> /dev/null | python -m json.tool
{
    "ClusterPFHandler": [
        {
            "type": "warning",
            "message": "Cluster PF was to low on lane 1, it was: 117.93 M",
            "data": {
                "lane": 1,
                "lane_pf": 117929896,
                "threshold": "unknown"
            }
        },
        {
            "type": "warning",
            "message": "Cluster PF was to low on lane 7, it was: 122.26 M",
            "data": {
                "lane": 7,
                "lane_pf": 122263375,
                "threshold": "unknown"
            }
        },
        {
            "type": "warning",
            "message": "Cluster PF was to low on lane 8, it was: 177.02 M",
            "data": {
                "lane": 8,
                "lane_pf": 177018999,
                "threshold": "unknown"
            }
        }
    ],
    "ReadsPerSampleHandler": [
        {
            "type": "warning",
            "message": "Number of reads for sample Sample_pq-27 was too low on lane 7, it was: 6.893 M",
            "data": {
                "lane": 7,
                "number_of_samples": 12,
                "sample_id": "Sample_pq-27",
                "sample_reads": 6.893002,
                "threshold": 90
            }
        },
        {
            "type": "warning",
            "message": "Number of reads for sample Sample_pq-28 was too low on lane 7, it was: 7.104 M",
            "data": {
                "lane": 7,
                "number_of_samples": 12,
                "sample_id": "Sample_pq-28",
                "sample_reads": 7.10447,
                "threshold": 90
            }
        }
    ]
}

[codecov[bot]]

Codecov Report

Merging #28 into master will increase coverage by 0.03%. The diff coverage is 93.54%.

@@            Coverage Diff             @@
##           master      #28      +/-   ##
==========================================
+ Coverage   93.34%   93.38%   +0.03%     
==========================================
  Files          16       16              
  Lines         526      544      +18     
==========================================
+ Hits          491      508      +17     
- Misses         35       36       +1

Impacted Files	Coverage Δ
checkQC/handlers/yield_handler.py	90.9% <100%> (ø)	:arrow_up:
checkQC/qc_engine.py	100% <100%> (ø)	:arrow_up:
checkQC/handlers/reads_per_sample_handler.py	96.15% <100%> (ø)	:arrow_up:
checkQC/handlers/error_rate_handler.py	87.87% <100%> (ø)	:arrow_up:
checkQC/handlers/cluster_pf_handler.py	95.45% <100%> (ø)	:arrow_up:
checkQC/handlers/q30_handler.py	95.45% <100%> (ø)	:arrow_up:
...heckQC/handlers/undetermined_percentage_handler.py	95.83% <100%> (ø)	:arrow_up:
checkQC/app.py	88.37% <87.5%> (+1.52%)	:arrow_up:
checkQC/handlers/qc_handler.py	90.78% <90%> (-0.39%)	:arrow_down:

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