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adam files with outdated formats throw FileNotFoundException #1804

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akmorrow13 opened this Issue Nov 15, 2017 · 2 comments

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akmorrow13 commented Nov 15, 2017

scala> val x = sc.loadGenotypes("/data/platinum/analysis/NA12878_pedigree.gt.adam")
java.io.FileNotFoundException: Couldn't find any files matching /data/platinum/analysis/NA12878_pedigree.gt.adam
  at org.bdgenomics.adam.rdd.ADAMContext.getFsAndFilesWithFilter(ADAMContext.scala:1354)
  at org.bdgenomics.adam.rdd.ADAMContext.loadAvroSamples(ADAMContext.scala:1187)
  at org.bdgenomics.adam.rdd.ADAMContext.loadParquetGenotypes(ADAMContext.scala:2161)
  at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadGenotypes$1.apply(ADAMContext.scala:2814)
  at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadGenotypes$1.apply(ADAMContext.scala:2809)
  at scala.Option.fold(Option.scala:158)
  at org.apache.spark.rdd.Timer.time(Timer.scala:48)
  at org.bdgenomics.adam.rdd.ADAMContext.loadGenotypes(ADAMContext.scala:2807)
  ... 50 elided

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fnothaft Nov 15, 2017

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We've generally treated this as a won't fix until we hit 1.0.0.

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fnothaft commented Nov 15, 2017

We've generally treated this as a won't fix until we hit 1.0.0.

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akmorrow13 Nov 19, 2017

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Closing with #1805

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akmorrow13 commented Nov 19, 2017

Closing with #1805

@akmorrow13 akmorrow13 closed this Nov 19, 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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