switched CigarBuilder's order for adjacent indels to be deletion first

[davidbenjamin]

Closes #6473 and resolves a few forum issues about GenomicsDB not supporting MNPs.

@ldgauthier

[ldgauthier]

I did see the updated CigarBuilder unit tests, but I thought you said you'd add a regression test with the user's data? Not a deal breaker for me, though. Otherwise looks good.

[davidbenjamin]

but I thought you said you'd add a regression test with the user's data

I must have. There is a regression test now.

[mlaylwar]

I am experiencing this issue, which I thought was solved. I have used version 4.1.7.0 haplotype caller, then when I use combineGVCFs I receive the error: A USER ERROR has occurred: Bad input: Combining gVCFs containing MNPs is not supported. Unknown contained a MNP at A1:684599

I didn't set any value for -max-mnp-dist as the docs say that default is already set to 0. Any idea how to get around this error?

Thanks

[davidbenjamin]

@mlaylwar What are the reference and MNP alleles at this position?

[mlaylwar]

I don't have these files anymore I'm afraid. I can probably recreate if necessary

…

On Thu, 20 Aug 2020 at 10:02, David Benjamin ***@***.***> wrote: @mlaylwar <https://github.com/mlaylwar> What are the reference and MNP alleles at this position? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#6510 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AECOYSTK6TQTMGIQJV2SJXDSBSRORANCNFSM4LOG4HKA> .