Testing bap

This directory holds the automated test suite (pytest) and the small data fixtures it runs against.

Quick start

Install the package with its test dependencies, then run the fast suite:

pip install -e .[test]

# Fast: unit + CLI smoke tests only (no external tools needed)
pytest -m "not integration"

The fast suite requires no bioinformatics tools and runs in under a second. It is what CI runs on every push (see .github/workflows/ci.yml).

What each test file covers

File	Scope	External tools
test_helpers.py	Unit tests for the pure functions in bap/bapHelp.py (sequence math, file helpers, tool discovery, the run_cmd subprocess wrapper) and mitoChr.	none
test_cli_smoke.py	In-process click.testing.CliRunner checks that every active CLI imports, renders --help, and reports --version; verifies bap2 support lists built-in genomes.	none
test_integration.py	End-to-end bap2 bam run against a bundled hg19 .bam, asserting the final .bap.bam, .barcodeTranslate.tsv, and .fragments.tsv.gz are produced.	samtools, bedtools, R, snakemake

Shared fixtures (paths to the bundled data, small_bam) live in conftest.py.

Running the integration tests

Integration tests are marked with @pytest.mark.integration and skip automatically when samtools, bedtools, R, or snakemake are not on PATH, so the default pytest run stays green on a bare machine.

To run them, install the external tools (plus the R packages the pipeline uses: Rsamtools, GenomicAlignments, GenomicRanges, dplyr, data.table) and then:

# Run everything, including integration tests
pytest

# Run only the integration tests
pytest -m integration

A convenient way to get the external tools is conda/mamba:

mamba install -c bioconda -c conda-forge samtools bedtools snakemake bioconductor-genomicalignments bioconductor-rsamtools r-dplyr r-data.table

Test data

• data/ — small indexed .bam files (jaccardPairsForIGV.bam, small_mix.bam, test.small.bam), a peaks bed, a whitelist, and a barcode prior table used by the pipeline tests.
• fastq_br/ — small BioRad and Scale-ATAC FASTQs for barcode-parsing tests.
• for_frag/ — pre-computed annotated fragment files used to exercise the fragment / adjacent-Tn5 code paths.

Manual smoke tests

The commands below are handy for exercising the full pipeline by hand against the bundled data (run from this tests/ directory). They require the external tools listed above.

Basic run

bap2 bam -i data/jaccardPairsForIGV.bam -bt XB -r hg19 -z -o bap2

Note: the legacy bap (v1) command is deprecated — use bap2.

Species-mix / peaks-file output

bap2 bam -i data/small_mix.bam -bt XB -ji 0.0001 -r hg19-mm10 -z --mapq 0 -bf 10 -o SM

Skip merging when a prior is known

bap2 bam -i data/jaccardPairsForIGV.bam -bt XB -r hg19 -z -o bap2 \
  -pf data/test.small.peaks.bed -bp data/jaccardPairsTest_sep.tsv

BioRad barcode parsing

bap-barcode v2.1 -a fastq_br/biorad_v2_R1.fastq.gz -b fastq_br/biorad_v2_R2.fastq.gz -o test

Scale-ATAC barcode parsing

bap-scale -f fastq_br/scale -s ScaleTest -o ScalePro