fread - allow duplicate column indexes in the select
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Assessment
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Newbie friendliness
- 45/100
Research direction
Start at the fread entry point and reproduce the issue with the Plink BIM example using select = c(1, 4, 4). Trace where duplicate column indexes are rejected; done means the selection succeeds and returns the requested repeated column, with coverage for this behavior added to the relevant fread tests.
Written by the indexing model from the issue text.
Description
Example Plink BIM file:
fread("
21 rs11511647 0 26765 A T
X rs12218882 0 48172 T T
9 rs10904045 0 48426 A T
")
# V1 V2 V3 V4 V5 V6
# 1: 21 rs11511647 0 26765 A T
# 2: X rs12218882 0 48172 T T
# 3: 9 rs10904045 0 48426 A T
I need to convert it to BED format (chr, start, end), current solution:
fread("
21 rs11511647 0 26765 A T
X rs12218882 0 48172 T T
9 rs10904045 0 48426 A T
")[, c(1, 4, 4)]
# V1 V4 V4
# 1: 21 26765 26765
# 2: X 48172 48172
# 3: 9 48426 48426
Desired solution (feature?): allow duplicate column indexes in the select:
fread("
21 rs11511647 0 26765 A T
X rs12218882 0 48172 T T
9 rs10904045 0 48426 A T
", select = c(1, 4, 4))
# Error in fread("...", :
# Column number 4 ('V4') has been selected twice by select=
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