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Making example code compatible with current ADAM build #1641

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devin-petersohn commented Jul 26, 2017

Resolves #1633.

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coveralls Jul 26, 2017

Coverage Status

Coverage remained the same at 83.961% when pulling 01a649f on devin-petersohn:issue#1633 into c8a2202 on bigdatagenomics:master.

coveralls commented Jul 26, 2017

Coverage Status

Coverage remained the same at 83.961% when pulling 01a649f on devin-petersohn:issue#1633 into c8a2202 on bigdatagenomics:master.

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AmplabJenkins Jul 26, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2286/
Test PASSed.

AmplabJenkins commented Jul 26, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2286/
Test PASSed.

@fnothaft

These changes are OK, but we're probably going to gut the intro as written, so I'd suggest we don't merge these changes.

For example, the following code snippet will print the top 10 21-mers in `NA2114` from 1000 Genomes.
For example, the following code snippet will print the top 10 21-mers in
`NA2114` from 1000 Genomes.

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fnothaft Jul 26, 2017

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2114 -> 21144

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fnothaft Jul 26, 2017

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2114 -> 21144

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fnothaft Aug 2, 2017

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Ping!

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fnothaft Aug 2, 2017

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Ping!

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devin-petersohn Aug 2, 2017

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Are we not just closing this PR? Or are we merging this with #1653? I only ask because your review comment suggested we don't merge.

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devin-petersohn Aug 2, 2017

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Are we not just closing this PR? Or are we merging this with #1653? I only ask because your review comment suggested we don't merge.

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fnothaft Aug 2, 2017

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Oh sorry, that's right. Yes, let's close this and revisit later.

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fnothaft Aug 2, 2017

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Oh sorry, that's right. Yes, let's close this and revisit later.

// Generate, count and sort 21-mers
val kmers = reads.flatMap { read =>
read.getSequence.sliding(21).map(k => (k, 1L))
}.reduceByKey((k1: Long, k2: Long) => k1 + k2)
}.reduceByKey(_ + _)

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fnothaft Jul 26, 2017

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Use countKmers(21) instead?

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fnothaft Jul 26, 2017

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Use countKmers(21) instead?

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devin-petersohn Jul 26, 2017

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Why are we gutting the intro? I thought it was just the README that we were significantly overhauling.

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devin-petersohn commented Jul 26, 2017

Why are we gutting the intro? I thought it was just the README that we were significantly overhauling.

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fnothaft Jul 26, 2017

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Just like the README, the intro in the docs isn't really an intro, inasmuch as it is a jumble of links and miscellaneous examples.

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fnothaft commented Jul 26, 2017

Just like the README, the intro in the docs isn't really an intro, inasmuch as it is a jumble of links and miscellaneous examples.

@fnothaft fnothaft closed this Aug 2, 2017

@heuermh heuermh added this to the 0.23.0 milestone Dec 7, 2017

@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018

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