Capture uploaded allele correctly for VCF input #1744
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likhitha-surapaneni
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| my $alt_allele_count; | ||
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| foreach my $alt(@alleles) { | ||
| if (length($ref_allele_string) != length($alt) or $original_allele_string =~ /^-/){ |
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@likhitha-surapaneni , it seems we are checking only if ref allele is - with $original_allele_string =~ /^-/ unlike for any allele like before. Was it intended?
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$original_allele_string contains both ref_allele and alt_alleles in the same string separated by "/"
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true, but with ^ you are only checking - allele for ref and missing deletions?
| # print("Before rejoin\n"); | ||
| # use Data::Dumper; | ||
| # print(Dumper($ib->buffer)); |
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should we remove the comments?
| # Updating a flag to minimise multi-allelic variants in split_variants/rejoin_variants | ||
| $vf->{minimised} = 1; |
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Multi-allelic is not getting minimised for default format. For example - 1 961320 961324 GCAGG/GCA/GCAG +
But in the output still getting MINIMISED=1, (without the PR they are also not minimised but there is no MINIMISED=1).
Ticket: ENSVAR-5858