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Update handling of INFO/END when writing records in VCF #1201

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Update handling of INFO/END when writing records in VCF #1201

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feb1125
Updated handling of INFO/END when writing records in VCF
rickymagner Jun 29, 2023
c034a39
Revert computing END value to previous for consistency with setters
rickymagner Jun 29, 2023
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8 changes: 2 additions & 6 deletions pysam/libcbcf.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -1188,20 +1188,16 @@ cdef inline bcf_sync_end(VariantRecord record):
else:
ref_len = 0

# Delete INFO/END if no alleles are present or if rlen is equal to len(ref)
# Delete INFO/END if no alleles are present or if not present in header
# Always keep END for symbolic alleles
if not has_symbolic_allele(record) and (not record.ptr.n_allele or record.ptr.rlen == ref_len):
if not has_symbolic_allele(record) and (not record.ptr.n_allele) or end_id < 0:
# If INFO/END is not defined in the header, it doesn't exist in the record
if end_id >= 0:
info = bcf_get_info(hdr, record.ptr, b'END')
if info and info.vptr:
if bcf_update_info(hdr, record.ptr, b'END', NULL, 0, info.type) < 0:
raise ValueError('Unable to delete END')
else:
# Create END header, if not present
if end_id < 0:
record.header.info.add('END', number=1, type='Integer', description='Stop position of the interval')

# Update to reflect stop position
bcf_info_set_value(record, b'END', record.ptr.pos + record.ptr.rlen)

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