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Don't convert .{different-type}.adam in loadAlignments and loadFragments #1456

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heuermh opened this Issue Mar 23, 2017 · 0 comments

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heuermh commented Mar 23, 2017

I don't like the .{type}.adam file extension conversions in the type-guessing methods, since we don't use or document that convention elsewhere.

In ADAMContext.loadFragments

} else if (filePath.endsWith(".reads.adam")) {
  log.info(s"Loading $filePath as ADAM AlignmentRecords and converting to Fragments.")
  loadAlignments(filePath).toFragments

And ADAMContext.loadAlignments

} else if (filePath.endsWith("contig.adam")) {
  log.info(s"Loading $filePath as Parquet of NucleotideContigFragment and converting to AlignmentRecords. Projection is ignored.")
  AlignmentRecordRDD.unaligned(loadParquetContigFragments(filePath).toReads)
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