pytest_wdl.data_types package

Submodules

pytest_wdl.data_types.bam module

Convert BAM to SAM for diff.

class pytest_wdl.data_types.bam.BamDataFile(local_path: pathlib.Path, localizer: Optional[pytest_wdl.core.Localizer] = None, allowed_diff_lines: Optional[int] = 0)[source]

Bases: pytest_wdl.core.DataFile

Supports comparing output of BAM file. This uses pysam to convert BAM to SAM, so that DataFile can carry out a regular diff on the SAM files.

pytest_wdl.data_types.vcf module

Some tools that generate VCF (callers) will result in very slightly different qual scores and other floating-point-valued fields when run on different hardware. This handler ignores the QUAL and INFO columns and only compares the genotype (GT) field of sample columns. Only works for single-sample VCFs.

class pytest_wdl.data_types.vcf.VcfDataFile(local_path: pathlib.Path, localizer: Optional[pytest_wdl.core.Localizer] = None, allowed_diff_lines: Optional[int] = 0)[source]

Bases: pytest_wdl.core.DataFile

Module contents