Explictly warn/fail when an indel is encountered

[nh13]

Currently, on the first base in the ref/alt alleles are stored and compared, which can lead to misleading results if the input VCF has indels. See this line:

demuxlet/cmd_cram_demuxlet.cpp

Line 322 in 537ba94

allele = ( base == scl.snps[i].ref ) ? 0 : ( ( base == scl.snps[i].alt ) ? 1 : 2 );

[nh13]

The current behavior is that any read will be counted towards the reference allele.

[yimmieg]

Hi Nils, Thank you for bringing this up. Hyun may have some bandwidth to push a commit to fix this. J Sent from a phone. Excuse the typos.

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On Jan 20, 2021, at 12:38 PM, Nils Homer ***@***.***> wrote:  The current behavior is that any read will be counted towards the reference allele. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[nh13]

Excellent! I think the main issue is that it is comparing the first base in the allele, versus the full allele from the VCF and the bases starting at the mapped position the the read.