.gitignore

modules/beast/test/2018_08_15_10_45_01_KPNIH1_ref_allele_unmapped_consensus_gubbins_masked.fa
modules/beast/test/2018_08_15_10_45_01_KPNIH1_ref_allele_unmapped_consensus_gubbins_masked_invar_site_counts.txt
modules/beast/test/2018_08_15_10_45_01_KPNIH1_ref_allele_unmapped_consensus_gubbins_masked_snp-sites.vcf
modules/beast/test/2018_08_15_10_45_01_KPNIH1_ref_allele_unmapped_consensus_gubbins_masked_var_sites.fa
modules/beast/test/2018_08_15_10_45_01_KPNIH1_ref_allele_unmapped_consensus_invar_site_counts.txt
modules/beast/test/2018_08_15_10_45_01_KPNIH1_ref_allele_unmapped_consensus_masked_recomb_positions.txt
modules/beast/test/2018_08_15_10_45_01_KPNIH1_ref_allele_unmapped_consensus_snp-sites.vcf
modules/beast/test/input_beast.txt
modules/beast/test/invar_base_counts.txt
modules/beast/test/model_finder_IQTREE_noDec_wDates_LA.tree
modules/beast/test/penn-st258_LA_bmt_ucln_bs_dta2_renamed.xml
modules/beast/test/penn-st258_LA_bmt_ucln_bs_dta2.xml
modules/beast/test/penn-st258_LA_bmt_ucln_bs_dta_renamed_st_invSites.xml
modules/beast/test/penn-st258_LA_bmt_ucln_bs_dta_renamed.xml
modules/beast/test/penn-st258_LA_bmt_ucln_bs_dta.xml
modules/beast/test/test_commands.sh
modules/beast/test/test_fasta_path.txt
modules/beast/test/test_gff_path.txt
*.pyc
._modules
modules/variant_diagnostics/*.pyc
modules/variant_diagnostics/config_settings.pyc
modules/variant_diagnostics/core_pipeline_core_prep_label.pyc
modules/variant_diagnostics/core_pipeline_core_prep_main.pyc
modules/variant_diagnostics/core_pipeline_core_prep.pyc
modules/variant_diagnostics/core_pipeline.pyc
modules/variant_diagnostics/core_prep.pyc
modules/variant_diagnostics/find_repeats.pyc
modules/variant_diagnostics/__init__.pyc
modules/variant_diagnostics/logging_subprocess.pyc
modules/variant_diagnostics/log_modules.pyc
modules/variant_diagnostics/mask_regions.pyc
modules/variant_diagnostics/parse_vcf_for_reason_individual_jobs.pyc
modules/variant_diagnostics/PBS_generate_jobs.pyc