VCF support for RLE and fix to same-as-reference allele normalization to RLE #589
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jsstevenson
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jsstevenson
…s <= MAX_LITERAL_STATE_LENGTH, defaulted to 15
larrybabb
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I will defer to others for the final review on this PR. It looks comprehensive and well covered from a testing standpoint.
Great job Kyle!
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Additional changes may be needed. See: #592 |
jsstevenson
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👍 Generally looks good, some small things/maybe stuff to talk through tomorrow
| info_field_num, | ||
| "Integer", | ||
| ( | ||
| "The repeat subunit length values from ReferenceLengthExpression states for the GA4GH VRS " |
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can this be repeat_subunit_length or repeatSubunitLength or something just to make it clear that it's a specific property
| vrs_field_data, | ||
| assembly, | ||
| vrs_data_key=data, | ||
| vrs_data_key=data, # TODO unused? |
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Might be okay to remove. It appears that this was used historically to add individual alleles as a key into an accumulated dictionary of everything in the VCF. Doesn't seem to get used anymore, and it feels clumsy to be using a tab-separated string rather than a tuple or something anyway.
| # Short State.sequence will be included in output VCF if <= this value, | ||
| # otherwise output will be emitted as the "." character. | ||
| MAX_LITERAL_STATE_LENGTH = 15 |
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placeholder for thinking through implications of this, briefly mentioned on slack
| # Pysam outputs "." for missing values. | ||
| record.info[k.value] = [ | ||
| value or k.default_value() for value in vrs_field_data[k.value] | ||
| None if v in ("", None) else v for v in vrs_field_data[k.value] |
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double checking -- does this convert sequences that are an empty string into None/"."?
Close #577
Close #587