diff --git a/tests/example_collate.txt b/tests/example_collate.txt index 0840729..f65153f 100644 --- a/tests/example_collate.txt +++ b/tests/example_collate.txt @@ -1,7 +1,7 @@ sample main_lineage sub_lineage spoligotype drtype target_median_depth pct_reads_mapped num_reads_mapped num_dr_variants num_other_variants rifampicin isoniazid ethambutol pyrazinamide moxifloxacin levofloxacin bedaquiline delamanid pretomanid linezolid streptomycin amikacin kanamycin capreomycin clofazimine ethionamide por5A_bcftools lineage4 lineage4.3.4.2 - MDR-TB 59.0 99.9 54238 4 24 rpoB p.Ser450Leu (1.00) inhA c.-777C>T (1.00) embB p.Met306Val (1.00) pncA p.Val125Gly (1.00) - - - - - - - - - - - inhA c.-777C>T (1.00) por5A_freebayes lineage4 lineage4.3.4.2 - MDR-TB 59.0 99.9 54238 4 24 rpoB p.Ser450Leu (1.00) inhA c.-777C>T (1.00) embB p.Met306Val (1.00) pncA p.Val125Gly (1.00) - - - - - - - - - - - inhA c.-777C>T (1.00) -por5A_gatk lineage4 lineage4.3.4.2 - MDR-TB 59.0 99.9 54238 4 28 rpoB p.Ser450Leu (1.00) inhA c.-777C>T (1.00) embB p.Met306Val (1.00) pncA p.Val125Gly (1.00) - - - - - - - - - - - inhA c.-777C>T (1.00) +por5A_gatk lineage4 lineage4.3.4.2 - MDR-TB 59.0 99.9 54238 4 24 rpoB p.Ser450Leu (1.00) inhA c.-777C>T (1.00) embB p.Met306Val (1.00) pncA p.Val125Gly (1.00) - - - - - - - - - - - inhA c.-777C>T (1.00) por5A_lofreq lineage4 lineage4.3.4.2 - MDR-TB 59.0 99.9 54238 4 23 rpoB p.Ser450Leu (1.00) inhA c.-777C>T (1.00) embB p.Met306Val (1.00) pncA p.Val125Gly (1.00) - - - - - - - - - - - inhA c.-777C>T (1.00) -por5A_pilon lineage4 lineage4.3.4.2 - MDR-TB 59.0 99.9 54238 4 25 rpoB p.Ser450Leu (1.00) inhA c.-777C>T (1.00) embB p.Met306Val (1.00) pncA p.Val125Gly (1.00) - - - - - - - - - - - inhA c.-777C>T (1.00) +por5A_pilon lineage4 lineage4.3.4.2 - MDR-TB 59.0 99.9 54238 4 24 rpoB p.Ser450Leu (1.00) inhA c.-777C>T (1.00) embB p.Met306Val (1.00) pncA p.Val125Gly (1.00) - - - - - - - - - - - inhA c.-777C>T (1.00) por5_vcf lineage4 lineage4.3.4.2 - MDR-TB 4 24 rpoB p.Ser450Leu (1.00) inhA c.-777C>T (1.00) embB p.Met306Val (1.00) pncA p.Val125Gly (1.00) - - - - - - - - - - - inhA c.-777C>T (1.00)