Modifying interleaved fastq format to be hadoop version independent. #289
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massie
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Jul 5, 2014
Modifying interleaved fastq format to be hadoop version independent.
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Thanks, Frank! |
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Final modifications. Removed the isSplittable function, as the method signature depends on the Hadoop version (specifically, the InputFileFormat API changes from Hadoop 2.2->2.3). Now, we inherit directly from the base InputFileFormat implementation, which always returns true (i.e., the file can be split). As a condition of this, we must disallow compressed interleaved FASTQ files. This condition is OK because compressed files cannot be split, and the interleaved FASTQ format (which is our own ad hoc definition of a file format) is only used to make splitting simpler.
Also, I noticed that the adam-core module still incorrectly depended on the old adam-format submodule. This was not causing tests to fail because Sonatype still contains a snapshot of adam-format. We should probably delete that snapshot...