Question: Avoid 'dStr8' format in the GDS files
0
gravatar for Vinicius Henrique da Silva
2.7 years ago by
Brazil

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.

 

snprelatesnp • 498 views
ADD COMMENTlink written 2.7 years ago by Vinicius Henrique da Silva40

Please downgrade the gdsfmt package. snpgdsCreateGeno() has no option to control the type of characters.

ADD REPLYlink written 17 months ago by zhengx30
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