1. Modified vcf_parse to update rlen only when an END INFO tag is seen -

Issue: https://github.com/broadinstitute/gamgee/issues/191
1. Modified vcf_parse to update rlen only when an END INFO tag is seen -the END tag is NOT encoded into v->shared.s
2. Modified vcf_write to add END INFO tag if required

Can we get @eitanbanks and @rpopoin in this tread as well?  I am concerned
that there could also be plain "blocks" that are not necessarily reference
blocks and our assumptions would fail then.

Is it possible for a structural variant to use the <NON-REF> allele but
also other alleles to represent a block in the VCF spec?

God this would all be so much easier if Ellen was actually a field in the
VCF file and we didn't have this END info field.

On Tuesday, September 9, 2014, jmthibault79 <notifications@github.com>
wrote:

> In vcf.c:
>
> > @@ -1993,6 +2002,12 @@ int vcf_format(const bcf_hdr_t *h, const bcf1_t *v, kstring_t *s)
> >  {
> >      int i;
> >      bcf_unpack((bcf1_t*)v, BCF_UN_ALL);
> > +    //2 alleles, first is REF and 2nd is NON_REF and rlen > 1, update END tag in INFO
> > +    if(v->n_allele == 2 &&  v->rlen > 1 && (strcmp(v->d.allele[1], "<NON_REF>") == 0))
>
> That would be pretty cool, yeah.
>
> Actually I see that is already handled as VCF_OTHER in
> vcf.c:bcf_set_variant_type(), interesting. Not sure if that suits us or if
> VCF_NON_REF is needed. Probably better to split this off into a separate
> issue anyway.
>
> —
> Reply to this email directly or view it on GitHub
> <https://github.com/broadinstitute/htslib/pull/5/files#r17319289>.
>


-- 

Mauricio Carneiro, Ph.D.
http://www.broadinstitute.org/~carneiro/