feat: Added ability to read tandem repeats with GenotypesTR #204
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aryarm
reviewed
Apr 7, 2023
aryarm
reviewed
Apr 7, 2023
| @@ -11,6 +11,7 @@ | |||
| import numpy.typing as npt | |||
| from cyvcf2 import VCF, Variant | |||
| from pysam import VariantFile, TabixFile | |||
| from . import tr_harmonizer as trh | |||
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Suggested change
| from . import tr_harmonizer as trh | |
| try: | |
| import trtools.utils.tr_harmonizer as trh | |
| except ModuleNotFoundError: | |
| from . import tr_harmonizer as trh |
might wanna try to import from trtools first just in case there's any new code from there that we should be using
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Updated data/genotypes.py to include GenotypesTR which has the ability to read in tandem repeat variant caller vcf data: expansion hunter, gangstr, hipstr, advntr, and popstr.