Mark gaps instead of discarding #185
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standage
commented
Sep 13, 2024
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| if record.is_del or record.is_refskip or skip_read(record.alignment): | ||
| if skip_read(record.alignment): | ||
| continue | ||
| aligned_base = record.alignment.query_sequence[record.query_position] | ||
| if record.is_del or record.is_refskip: | ||
| aligned_base = "-" | ||
| else: | ||
| aligned_base = record.alignment.query_sequence[record.query_position] |
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This change is the main event.
Comment on lines
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| def test_type_marker_has_indel_spanning_snp(): | ||
| bam = data_file("bam/indel_snp.bam") | ||
| tsv = data_file("def/indel_snp.tsv") | ||
| result = mhapi.type(bam, tsv) | ||
| assert "mh09WL-026" in result.data["markers"] | ||
| for allele in result.data["markers"]["mh09WL-026"]["typing_result"]: | ||
| snp_alleles = allele.split(",") | ||
| assert len(snp_alleles) == 6 | ||
| assert snp_alleles[-2] == "-" |
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In this PR, the empirical haplotype calling algorithm was updated so that indel gaps are marked as
-instead of being left empty. Closes #183.