I would like to use a GDS file to an external software called SNPhylo. However, I am getting an error when trying to use this external software:
Error in index.gdsn(gdsobj, "sample.id") :
No class name 'dStr8' in the GDS system.
Reading the news about the GDS files in GitHub, this 'dStr8' format seems to be something new (https://github.com/zhengxwen/gdsfmt/blob/master/NEWS). Then I tried to create a GDS without this 'dStr8' by modifying the options in snpgdsCreateGeno
function of SNPRelate without success. i.e. compress.annotation="LZMA_RA" & compress.geno="LZMA_RA":
+ [ ] *
|--+ sample.id { Str8 128 LZMA_ra(22.4%), 362B }
|--+ snp.id { Str8 135131 LZMA_ra(14.0%), 223.2K }
|--+ snp.position { Int32 135131 LZMA_ra(40.9%), 216.1K }
|--+ snp.chromosome { Int32 135131 LZMA_ra(0.06%), 346B }
\--+ genotype { Bit2 135131x128 LZMA_ra(43.3%), 1.8M } *
&
+ [ ] *
|--+ sample.id { Str8 128 LZMA(20.8%), 336B }
|--+ snp.id { Str8 135131 LZMA(14.0%), 223.2K }
|--+ snp.position { Int32 135131 LZMA(40.9%), 216.1K }
|--+ snp.chromosome { Int32 135131 LZMA(0.06%), 320B }
\--+ genotype { Bit2 135131x128 LZMA(41.3%), 1.7M } *
I would be grateful if someone help me to use the right options in snpgdsCreateGeno
to create a GDS file compatible SNPhylo.
Please downgrade the gdsfmt package. snpgdsCreateGeno() has no option to control the type of characters.