├── .ci └── install_dependencies.sh ├── .gitignore ├── .travis.yml ├── LICENSE ├── MANIFEST.in ├── README.md ├── requirements.txt ├── setup.py ├── simutator ├── __init__.py ├── __main__.py ├── batch_genome_mutator.py ├── genome_mutator.py ├── simulate_reads.py ├── tasks │ ├── __init__.py │ ├── mutate_fasta.py │ └── simulate_reads.py └── utils.py ├── tests ├── __init__.py ├── batch_genome_mutator_test.py ├── data │ ├── batch_genome_mutator │ │ └── run_all_mutations.fa │ └── genome_mutator │ │ ├── ComplexMutator_mutate_fasta.in.fa │ │ ├── ComplexMutator_mutate_fasta.out.fa │ │ ├── ComplexMutator_mutate_fasta.out.mutated.vcf │ │ ├── ComplexMutator_mutate_fasta.out.ref.vcf │ │ ├── DeletionMutator_mutate_fasta.in.fa │ │ ├── DeletionMutator_mutate_fasta.out.fa │ │ ├── DeletionMutator_mutate_fasta.out.mutated.vcf │ │ ├── DeletionMutator_mutate_fasta.out.ref.vcf │ │ ├── InsertionMutator_mutate_fasta.in.fa │ │ ├── InsertionMutator_mutate_fasta.out.fa │ │ ├── InsertionMutator_mutate_fasta.out.mutated.vcf │ │ ├── InsertionMutator_mutate_fasta.out.ref.vcf │ │ ├── SnpMutator_mutate_fasta.in.fa │ │ ├── SnpMutator_mutate_fasta.out.fa │ │ ├── SnpMutator_mutate_fasta.out.mutated.vcf │ │ └── SnpMutator_mutate_fasta.out.ref.vcf ├── genome_mutator_test.py ├── simulate_reads_test.py └── utils_test.py └── tox.ini /.ci/install_dependencies.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/simutator/HEAD/.ci/install_dependencies.sh -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/simutator/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 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