Enhancement: sample ID handling

[ptrebert]

Hi,
I am using sniffles v2.2 and I have a few suggestions regarding the handling of the sample ID:

1. my BAM files have the sample ID in the SM tag. Based on the closed issue Better format of the VCF output #211 , I was assuming that this would be used in the VCF output, but the VCFs generated by sniffles simply state SAMPLE as sample ID
2. the parameter --sample-id solves this issue, yes, but the help/description does not make that obvious:

Custom ID for this sample, used for later multi-sample calling (stored in .snf)

3. Of course, having to set the sample ID explicitly as a parameter is something that users may often forget or overlook. Hence, if the BAM contains the sample info, would be great to use it and overwrite that if --sample-id is set.
4. just for completeness, there is also an open issue related to this for the force calling mode --sample-id does not work in force calling mode #427

Thanks for developing this great tool!
Best,
Peter

[fritzsedlazeck]

Thanks @ptrebert
@hermannromanek this should be an easy fix I think. Maybe we can include that in the next release in a few months.
Thanks
Fritz

[ahcm]

And the last resort should be filename and not "SAMPLE", which would make bcftools merge work. imho