Repeatedly filtering Plink files based on integer indices

[kose-y]

When using filter() with integer indices multiple times, the result is overwritten on the existing filtered SnpArray.

versioninfo()

Julia Version 1.0.1
Commit 0d713926f8 (2018-09-29 19:05 UTC)
Platform Info:
  OS: Linux (x86_64-pc-linux-gnu)
  CPU: Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-6.0.0 (ORCJIT, ivybridge)

const mouse = SnpArray(SnpArrays.datadir("mouse.bed"))

s0 = SnpArrays.filter(SnpArrays.datadir("mouse"), 1:2, 1:5)
s0

2×5 SnpArray:
 0x02  0x02  0x02  0x02  0x03
 0x02  0x02  0x03  0x02  0x02

s1 = SnpArrays.filter(SnpArrays.datadir("mouse"), 1:2, 1:3)
s2 = SnpArrays.filter(SnpArrays.datadir("mouse"), 1:2, 4:5)
#s3 = SnpArrays.filter(SnpArrays.datadir("mouse"), 3:4, 1:3);

s1

2×3 SnpArray:
 0x02  0x03  0x00
 0x02  0x02  0x00

s2

2×2 SnpArray:
 0x02  0x03
 0x02  0x02

s0

2×5 SnpArray:
 0x02  0x03  0x00  0x00  0x00
 0x02  0x02  0x00  0x00  0x00

[biona001]

One workaround is to make a copy in memory:

s0 = copy(SnpArrays.filter(SnpArrays.datadir("mouse"), 1:2, 1:5))
s1 = SnpArrays.filter(SnpArrays.datadir("mouse"), 1:2, 1:3)
s2 = SnpArrays.filter(SnpArrays.datadir("mouse"), 1:2, 4:5)

julia> s0
2×5 Array{UInt8,2}:
 0x02  0x02  0x02  0x02  0x03
 0x02  0x02  0x03  0x02  0x02

Though I'm not sure if this is expected behavior..

[kose-y]

Oh, I got it. The destination file (default argument is used) is unchanged for each filtering. Maybe we can change the default name each time the filter function is called?