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