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Correct nullable string validity map treatment (#517)
* Correct nullable string validity map treatment * Add NEWS entry about breaking change [ci skip] * Reads can now account for legacy validity mode on string buffer * Add a test for legacy validity using an legacy array * Adjust .Rbuildignore to allow sample data in * Also set for shmen case * Support legacy_validity writes * Add converter function, script wrapper and test * Updated news, moved script [ci skip] * Conversion from (or to) legacy_validity copies with metadata * Small metadata documentation edit * Tweak bspm option for r-ci * Identify dimension names and use as new dimensions * Set bspm to version 0.3.10 for now
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Original file line number | Diff line number | Diff line change |
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#!/usr/bin/env Rscript | ||
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## load docopt and tiledb | ||
suppressMessages({ | ||
library(docopt) # for command-line argument parsing and help generation | ||
library(tiledb) | ||
}) | ||
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## configuration for docopt | ||
doc <- "Usage: convert.t [-h] [-v] [-d] [-t] [-o OUTDIR | -u] INDIR | ||
-o --out OUTDIR write converted array into OUTDIR, if not given conversion in place [default: ] | ||
-u --usetmp do not require output directory and use a temporary directory [default: FALSE] | ||
-t --tolegacy convert to (instead of from) legacy validity mode | ||
-v --verbose show extra output while processing | ||
-d --debug show extra debug information | ||
-h --help show this help tex | ||
" | ||
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opt <- docopt(doc) # docopt parsing | ||
#if (opt$debug) print(opt) | ||
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tiledb:::.legacy_validity(inuri=opt$INDIR, | ||
outdir=opt$out, | ||
fromlegacy=!opt$tolegacy, | ||
tolegacy=opt$tolegacy, | ||
usetmp=opt$usetmp, | ||
verbose=opt$verbose, | ||
debug=opt$debug) |
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