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[ADAM-1803] Refactor GenomicRDD.writeTextRdd to util.TextRddWriter. #1809

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merged 2 commits into from Nov 22, 2017

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@heuermh heuermh commented Nov 21, 2017

Fixes #1803

More things needed to move than I would've preferred; I tried to keep visibility as narrow as possible.

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@AmplabJenkins AmplabJenkins commented Nov 21, 2017

Test PASSed.
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@fnothaft fnothaft left a comment

Few small nits, otherwise LGTM! Thanks @heuermh!

import org.apache.hadoop.conf.Configuration
import org.apache.hadoop.fs.{ FileSystem, Path }
import org.apache.spark.SparkContext
import org.bdgenomics.utils.misc.Logging

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Got an extra space here.

package org.bdgenomics.adam.rdd
package org.bdgenomics.adam.util

import java.io.{ InputStream, OutputStream }

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Extra space after this line too.

import org.apache.hadoop.conf.Configuration
import org.apache.hadoop.fs.{ FileSystem, Path }
import org.apache.spark.SparkContext
import org.apache.spark.broadcast.Broadcast
import org.bdgenomics.utils.misc.Logging

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Extra space here too.

*/
package org.bdgenomics.adam.util

import org.apache.hadoop.fs.{ Path, FileSystem }

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fnothaft Nov 22, 2017
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The order of Path and FileSystem should be swapped.

@@ -55,7 +54,7 @@ import org.bdgenomics.adam.sql.{
NucleotideContigFragment => NucleotideContigFragmentProduct,
Variant => VariantProduct
}
import org.bdgenomics.adam.util.ADAMFunSuite
import org.bdgenomics.adam.util.{ ManualRegionPartitioner, ADAMFunSuite }

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fnothaft Nov 22, 2017
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The order of ManualRegionPartitioner and ADAMFunSuite should be swapped.

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@AmplabJenkins AmplabJenkins commented Nov 22, 2017

Test PASSed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2488/
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@fnothaft fnothaft merged commit 895fd64 into bigdatagenomics:master Nov 22, 2017
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codacy/pr Good work! A positive pull request.
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@fnothaft fnothaft commented Nov 22, 2017

Merged! Thanks @heuermh!

@heuermh heuermh deleted the heuermh:text-rdd-writer branch Nov 22, 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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