Avoid 'dStr8' format in the GDS files
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@vinicius-henrique-da-silva-6713
Last seen 13 months ago
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 • 1.0k views
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Please downgrade the gdsfmt package. snpgdsCreateGeno() has no option to control the type of characters.

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