.git_archival.txt
.gitattributes
.gitignore
LICENSE
README.rst
pyproject.toml
.github/dependabot.yml
.github/workflows/main.yaml
.github/workflows/publish-to-pypi.yml
scripts/aln2basecnt
scripts/compute_mds
scripts/convert_qr
scripts/convert_reference
scripts/coverage
scripts/coverage_depth_qc
scripts/coverage_stats
scripts/extract_consensus
scripts/extract_coverage_intervals
scripts/extract_sam
scripts/extract_seq
scripts/frameshift_deletions_checks
scripts/gather_coverage
scripts/mapper
scripts/min_coverage
scripts/minority_freq
scripts/pair_sequences
scripts/paired_end_read_merger
scripts/predict_num_reads
scripts/prepare_primers
scripts/remove_gaps_msa
smallgenomeutilities/__checkPath__.py
smallgenomeutilities/__init__.py
smallgenomeutilities/__mapper_impl__.py
smallgenomeutilities/__pileup__.py
smallgenomeutilities/_version.py
smallgenomeutilities.egg-info/PKG-INFO
smallgenomeutilities.egg-info/SOURCES.txt
smallgenomeutilities.egg-info/dependency_links.txt
smallgenomeutilities.egg-info/requires.txt
smallgenomeutilities.egg-info/top_level.txt
tests/conda_lint_env.yaml
tests/conda_testsgmu_env.yaml
tests/test_aln2basecnt.py
tests/test_coverage_depth_qc.py
tests/test_frameshift_deletions_checks.py
tests/test_paired_end_read_merger.py
tests/test_prepare_primers.py
tests/mini_sam/mini.sam
tests/mini_sam/mini_merged.sam
tests/test_aln2basecnt/mini.basecnt.tsv
tests/test_aln2basecnt/mini.coverage.tsv
tests/test_aln2basecnt/mini.stats.yaml
tests/test_aln2basecnt/mini_merged.basecnt.tsv
tests/test_aln2basecnt/mini_merged.coverage.tsv
tests/test_aln2basecnt/mini_merged.stats.ini
tests/test_aln2basecnt/stopgain_with_deletions.basecnt.tsv
tests/test_aln2basecnt/stopgain_with_deletions.coverage.tsv
tests/test_aln2basecnt/stopgain_with_deletions.stats.yaml
tests/test_aln2basecnt/stoploss.basecnt.tsv
tests/test_aln2basecnt/stoploss.coverage.tsv
tests/test_aln2basecnt/stoploss.stats.yaml
tests/test_aln2basecnt/stoploss_with_deletions.basecnt.tsv
tests/test_aln2basecnt/stoploss_with_deletions.coverage.tsv
tests/test_aln2basecnt/stoploss_with_deletions.stats.yaml
tests/test_aln2basecnt/stoploss_with_insertions.basecnt.tsv
tests/test_aln2basecnt/stoploss_with_insertions.coverage.tsv
tests/test_aln2basecnt/stoploss_with_insertions.stats.yaml
tests/test_coverage_depth_qc/chrom.size
tests/test_coverage_depth_qc/coverage.tsv
tests/test_coverage_depth_qc/qc_abs.json
tests/test_coverage_depth_qc/qc_irma.json
tests/test_coverage_depth_qc/qc_rel.json
tests/test_coverage_depth_qc/qc_samtools.json
tests/test_coverage_depth_qc/results/tables/A_NA_N1-coverage.txt
tests/test_frameshift_deletions_checks/Genes_NC_045512.2.GFF3
tests/test_frameshift_deletions_checks/NC_045512.2.fasta
tests/test_frameshift_deletions_checks/README.md
tests/test_frameshift_deletions_checks/stopgain.chain
tests/test_frameshift_deletions_checks/stopgain.cram
tests/test_frameshift_deletions_checks/stopgain.cram.crai
tests/test_frameshift_deletions_checks/stopgain.fasta
tests/test_frameshift_deletions_checks/stopgain.tsv
tests/test_frameshift_deletions_checks/stopgain_nogap.chain
tests/test_frameshift_deletions_checks/stopgain_nogap.fasta
tests/test_frameshift_deletions_checks/stopgain_with_deletions.chain
tests/test_frameshift_deletions_checks/stopgain_with_deletions.cram
tests/test_frameshift_deletions_checks/stopgain_with_deletions.cram.crai
tests/test_frameshift_deletions_checks/stopgain_with_deletions.fasta
tests/test_frameshift_deletions_checks/stopgain_with_deletions.tsv
tests/test_frameshift_deletions_checks/stopgain_with_deletions_nogap.chain
tests/test_frameshift_deletions_checks/stopgain_with_deletions_nogap.fasta
tests/test_frameshift_deletions_checks/stopgain_with_insertions.chain
tests/test_frameshift_deletions_checks/stopgain_with_insertions.cram
tests/test_frameshift_deletions_checks/stopgain_with_insertions.cram.crai
tests/test_frameshift_deletions_checks/stopgain_with_insertions.fasta
tests/test_frameshift_deletions_checks/stopgain_with_insertions.tsv
tests/test_frameshift_deletions_checks/stopgain_with_insertions_nogap.chain
tests/test_frameshift_deletions_checks/stopgain_with_insertions_nogap.fasta
tests/test_frameshift_deletions_checks/stoploss.chain
tests/test_frameshift_deletions_checks/stoploss.cram
tests/test_frameshift_deletions_checks/stoploss.cram.crai
tests/test_frameshift_deletions_checks/stoploss.fasta
tests/test_frameshift_deletions_checks/stoploss.tsv
tests/test_frameshift_deletions_checks/stoploss_nogap.chain
tests/test_frameshift_deletions_checks/stoploss_nogap.fasta
tests/test_frameshift_deletions_checks/stoploss_with_deletions.chain
tests/test_frameshift_deletions_checks/stoploss_with_deletions.cram
tests/test_frameshift_deletions_checks/stoploss_with_deletions.cram.crai
tests/test_frameshift_deletions_checks/stoploss_with_deletions.fasta
tests/test_frameshift_deletions_checks/stoploss_with_deletions.tsv
tests/test_frameshift_deletions_checks/stoploss_with_deletions_nogap.chain
tests/test_frameshift_deletions_checks/stoploss_with_deletions_nogap.fasta
tests/test_frameshift_deletions_checks/stoploss_with_insertions.chain
tests/test_frameshift_deletions_checks/stoploss_with_insertions.cram
tests/test_frameshift_deletions_checks/stoploss_with_insertions.cram.crai
tests/test_frameshift_deletions_checks/stoploss_with_insertions.fasta
tests/test_frameshift_deletions_checks/stoploss_with_insertions.tsv
tests/test_frameshift_deletions_checks/stoploss_with_insertions_nogap.chain
tests/test_frameshift_deletions_checks/stoploss_with_insertions_nogap.fasta
tests/test_paired_end_read_merger/mini.sam
tests/test_paired_end_read_merger/mini_merged.sam
tests/test_paired_end_read_merger/mini_merged_with_unpaired.sam
tests/test_paired_end_read_merger/mini_unaligned.sam
tests/test_paired_end_read_merger/mini_unpaired.sam
tests/test_prepare_primers/README.md
tests/test_prepare_primers/SARS-CoV-2.bed
tests/test_prepare_primers/SARS-CoV-2.insert.bed
tests/test_prepare_primers/SARS-CoV-2.primer.fasta
tests/test_prepare_primers/SARS-CoV-2.tsv
tests/test_prepare_primers/SARs-CoV-2_v5.3.2_400.primer.bed