[Bioc-devel] gds nodes dimensions are inconsistent

[Liu, Qian]

Hi Xiuwen,

Thank you very much for the prompt response. I'll look at the new functions and make necessary changes in my packages.

Best,
Qian
________________________________
From: Xiuwen Zheng <zhengx using u.washington.edu>
Sent: Tuesday, February 11, 2020 3:58 PM
To: Liu, Qian <Qian.Liu using RoswellPark.org>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: gds nodes dimensions are inconsistent

Hi Qian,

I have modified the GDS file in the SeqArray package.
"annotation/info/AA" should have fewer values than "annotation/info/AC", since it is a variable-length vector in the new GDS file.
VCF format allows storing variable-length data, so SeqArray also allows variable-length data.

seqGetData() has been updated in SeqArray_1.27.8, with a new option '.padNA' for padding array with NA if possible.
Please revise your package according to the new function in SeqArray.

Best wishes,

Xiuwen



On Tue, Feb 11, 2020 at 12:45 PM Liu, Qian <Qian.Liu using roswellpark.org<mailto:Qian.Liu using roswellpark.org>> wrote:
Dear Dr. Zheng & SeqArray maintainer,

I have a Bioconductor package called "GDSArray" that interfaces GDS file nodes as DelayedArray instances. In this new Bioc devel version of 3.11, this package failed all platforms. The debugging shows inconsistent dimensions calculated from different SeqArray / gdsfmt functions. Following is some reproducible code showing that the "annotation/info/AA" node has different dimension from "AC" and the overall "num.variant" calculated from "SeqSummary". It works fine in the Bioc 3.10 (dimension of AA is 1348).Thanks!

Best,
Qian


```{r}
library(SeqArray)
file <- seqExampleFileName("gds")
f <- seqOpen(file)
objdesp.gdsn(index.gdsn(f, "annotation/info/AA"))$dim
## [1] 1328
objdesp.gdsn(index.gdsn(f, "annotation/info/AC"))$dim
## [1] 1348
seqSummary(f, verbose=FALSE)$num.variant
## [1] 1348
seqClose(f)

!> sessionInfo()
 R Under development (unstable) (2020-01-07 r77631)
 Platform: x86_64-pc-linux-gnu (64-bit)
 Running under: Ubuntu 18.04.3 LTS

 Matrix products: default
 BLAS:   /home/qian/miniconda3/envs/r-devel/lib/R/lib/libRblas.so
 LAPACK: /home/qian/miniconda3/envs/r-devel/lib/R/lib/libRlapack.so

 locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
 [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

 attached base packages:
 [1] stats     graphics  grDevices utils     datasets  methods   base

 other attached packages:
 [1] SeqArray_1.27.8 gdsfmt_1.23.5

 loaded via a namespace (and not attached):
  [1] IRanges_2.21.2         Biostrings_2.55.4      crayon_1.3.4
  [4] bitops_1.0-6           GenomeInfoDb_1.23.1    stats4_4.0.0
  [7] zlibbioc_1.33.1        XVector_0.27.0         S4Vectors_0.25.11
 [10] tools_4.0.0            RCurl_1.95-4.12        parallel_4.0.0
 [13] compiler_4.0.0         BiocGenerics_0.33.0    GenomicRanges_1.39.1
 [16] GenomeInfoDbData_1.2.2
```




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