VCF2GDS error with phased VCF files

zhengxwen / SeqArray

Data management of large-scale whole-genome sequence variant calls (Development version only)

http://www.bioconductor.org/packages/SeqArray

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VCF2GDS error with phased VCF files #34

Closed dtaliun closed 6 years ago

dtaliun commented 6 years ago

Message:

Error in seqVCF2GDS(vcffile, gdsfile.tmp, fmt.import = fmt.import, storage.option = "LZMA_RA", : Invalid integer conversion '1|1'

SessionInfo: R version 3.5.1 (2018-07-02) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.5 LTS SeqArray_1.21.4 gdsfmt_1.17.4

zhengxwen commented 6 years ago

It is the issue as #32. I am tracking the changes from R_3.4.3 to R_3.5.1, and I am afraid it is not easy to fix this issue. Please use R_3.4.3 for an immediate solution.

dtaliun commented 6 years ago

Thanks, R_3.4.4 works also

zhengxwen commented 6 years ago

Could you please test this commit https://github.com/zhengxwen/SeqArray/commit/67b4c314deb05b6888416b9a7ae718f870df5cba to see whether it is fixed or not?

library("devtools")
install_github("zhengxwen/SeqArray")

dtaliun commented 6 years ago

This commit works for R_3.5.1