Add induced_resistance to JSON called_genes and called variants output.

[Phelimb]

{

    "phylogenetics": {

            "species": {

            "M. Tuberculosis": "Major",

            },

            "lineage": {

            "European/American": "Major",

            },

    },

    "susceptibility" :{

            "rifampicin": "R",

            "isoniazid": "R",

            "pyrazinamide": "S",

            "ethambutol": "S",

            "kanamycin": "S",

            "capreomycin": "S",

            "amikacin": "S",

            "kanamycin": "S",

            "streptomycin": "R",

            "quinolones": "S",

    },

    "called_variants" :{

            "rpoB_D435X" :{

                    "R_cov": "100",

                    "S_cov": "9",

                    "induced_resistance":"rifampicin"

            },

            "katG_S315X" :{

                    "R_cov": "100",

                    "S_cov": "4",

                    "induced_resistance":"isoniazid"

            },

            "rpsL_K43R" :{

                    "R_cov": "100",

                    "S_cov": "4",

                    "induced_resistance":"streptomycin"

            },

    },

}

[iqbal-lab]

Causes segfault

./Mykrobe.predictor.staph --file ~/Desktop/demo/C00007086_R00000022.bam --install_dir ~/dev/git/myKrobe-predictor/ --progress --format JSON

{ "expected_depth": "89", "mean_read_length": "87", "species": { "S.aureus": "Major" }, "susceptibility" :{ "Gentamicin": "S", "Penicillin": "R", "Methicillin": "R", "Trimethoprim": "S", "Erythromycin": "R", "FusidicAcid": "S", "Ciprofloxacin": "R", "Rifampicin": "S", "Tetracycline": "S", "Vancomycin": "S", "Mupirocin": "S", "Clindamycin": "R(inducible)" }, "called_variants" :{ "gyrA_S84L" :{ "R_per_cov": "100", "S_per_cov": "0", "R_median_cov": "91", "S_median_cov": "0", "induced_resistance": "Ciprofloxacin" } }, "called_genes" :{ "blaZ" :{ "per_cov": "65", "median_cov": "88", Segmentation fault: 11

[Phelimb]

I just ran this without a problem... -bash-4.1$ ./Mykrobe.predictor.staph --file /data0/users/zam/C00007086_R00000022.bam --install_dir ~/myKrobe-predictor --format JSON { "expected_depth": "89", "mean_read_length": "87", "species": { "S.aureus": "Major" }, "susceptibility" :{ "Gentamicin": "S", "Penicillin": "R", "Methicillin": "R", "Trimethoprim": "S", "Erythromycin": "R", "FusidicAcid": "S", "Ciprofloxacin": "R", "Rifampicin": "S", "Tetracycline": "S", "Vancomycin": "S", "Mupirocin": "S", "Clindamycin": "R(inducible)" }, "called_variants" :{ "gyrA_S84L" :{ "R_per_cov": "100", "S_per_cov": "0", "R_median_cov": "91", "S_median_cov": "0", "induced_resistance": "Ciprofloxacin" } }, "called_genes" :{ "blaZ" :{ "per_cov": "65", "median_cov": "88", "induced_resistance": "Penicillin" }, "ermC" :{ "per_cov": "99", "median_cov": "539", "induced_resistance": "Erythromycin" }, "mecA" :{ "per_cov": "99", "median_cov": "122", "induced_resistance": "Methicillin" } }, "virulence_toxins" :{ "PVL": "negative" } }

[iqbal-lab]

Fixed.