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What should our API at the command line look like? #1178

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heuermh opened this Issue Sep 20, 2016 · 1 comment

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heuermh commented Sep 20, 2016

With transformFormats in 8cec2c0, we introduced a single CLI command that helps both ways, in that it transforms from native formats to ADAM Parquet and vice versa.

Looking at our current list of commands, perhaps we should extend this pattern

adam2fasta
adam2fastq
adam2vcf
allelecount
anno2adam
count_contig_kmers
count_kmers
depth
fasta2adam
flagstat
flatten
fragments2reads
listdict
mergeShards
print
reads2coverage
reads2fragments
transform
transformFeatures
vcf2adam
view
wigfix2bed

Taking it to the extreme (where all the conversion operations fit under a single transform command) is going too far; I'm looking for a nice balance.

We could also take this opportunity to make sure all the commands and command line arguments are named consistently (e.g. camelCase vs. snake_case vs. whatever-you-call-it-with-dashes).

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fnothaft Mar 3, 2017

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I think this has substantial overlap with #1327; I'm going to close in favor of the other ticket, as it is more actionable. @heuermh please reopen if you disagree.

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fnothaft commented Mar 3, 2017

I think this has substantial overlap with #1327; I'm going to close in favor of the other ticket, as it is more actionable. @heuermh please reopen if you disagree.

@fnothaft fnothaft closed this Mar 3, 2017

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