LICENSE.txt
MANIFEST.in
README.md
pyproject.toml
satmut_utils_env.yaml
setup.cfg
docs/satmut_utils_manual.md
src/analysis/__init__.py
src/analysis/aligners.py
src/analysis/coordinate_mapper.py
src/analysis/read_editor.py
src/analysis/read_preprocessor.py
src/analysis/references.py
src/analysis/seq_utils.py
src/analysis/variant_caller.py
src/core_utils/__init__.py
src/core_utils/feature_file_utils.py
src/core_utils/file_utils.py
src/core_utils/string_utils.py
src/core_utils/vcf_utils.py
src/satmut_utils/__init__.py
src/satmut_utils/definitions.py
src/satmut_utils/satmut_utils.py
src/satmut_utils.egg-info/PKG-INFO
src/satmut_utils.egg-info/SOURCES.txt
src/satmut_utils.egg-info/dependency_links.txt
src/satmut_utils.egg-info/entry_points.txt
src/satmut_utils.egg-info/not-zip-safe
src/satmut_utils.egg-info/top_level.txt
src/scripts/__init__.py
src/scripts/run_bowtie2_aligner.py
src/scripts/run_fastq_preprocessor.py
src/tests/__init__.py
src/tests/analysis/__init__.py
src/tests/analysis/test_aligners.py
src/tests/analysis/test_coordinate_mapper.py
src/tests/analysis/test_read_editor.py
src/tests/analysis/test_read_preprocessor.py
src/tests/analysis/test_references.py
src/tests/analysis/test_seq_utils.py
src/tests/analysis/test_variant_caller.py
src/tests/core_utils/__init__.py
src/tests/core_utils/test_feature_file_utils.py
src/tests/core_utils/test_file_utils.py
src/tests/core_utils/test_string_utils.py
src/tests/test_data/CBS.fa
src/tests/test_data/CBS.gff
src/tests/test_data/CBS_pEZY3.fa
src/tests/test_data/CBS_pEZY3.fa.1.bt2
src/tests/test_data/CBS_pEZY3.fa.2.bt2
src/tests/test_data/CBS_pEZY3.fa.3.bt2
src/tests/test_data/CBS_pEZY3.fa.4.bt2
src/tests/test_data/CBS_pEZY3.fa.fai
src/tests/test_data/CBS_pEZY3.fa.rev.1.bt2
src/tests/test_data/CBS_pEZY3.fa.rev.2.bt2
src/tests/test_data/CBS_pEZY3.gff
src/tests/test_data/CBS_pEZY3_primers.bed
src/tests/test_data/CBS_pEZY3_targets.bed
src/tests/test_data/CBS_sim.R1.fq.gz
src/tests/test_data/CBS_sim.R2.fq.gz
src/tests/test_data/CBS_sim.bam
src/tests/test_data/CBS_sim.bam.bai
src/tests/test_data/CBS_sim.vcf
src/tests/test_data/CBS_sim_primers.bed
src/tests/test_data/GRCh38.chr21.fa.gz
src/tests/test_data/PKNOX1.fa
src/tests/test_data/__init__.py
src/tests/test_data/appris_human_24_01_2019_selected.fa
src/tests/test_data/appris_human_24_01_2019_selected.fa.fai
src/tests/test_data/appris_human_v1_actual_regions_contigs.txt
src/tests/test_data/appris_human_v1_actual_regions_gene_ids.txt
src/tests/test_data/appris_human_v1_actual_regions_trx_ids.txt
src/tests/test_data/gencode.v29.annotation.gtf
src/tests/test_data/test_preprocess.bam
src/tests/test_data/test_preprocess.bam.bai
src/tests/test_data/test_preprocess.sam
src/tests/test_data/test_preprocess.sort.bam
src/tests/test_data/test_preprocess.sort.bam.bai