Write CRAM on Spark. #1488
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Write CRAM on Spark. #1488
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cmnbroad
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| @@ -83,24 +88,58 @@ public SparkHeaderlessBAMOutputFormat() { | |||
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| } | |||
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| // Output format class for writing CRAM files through saveAsNewAPIHadoopFile. Must be public. | |||
| public static class SparkCRAMOutputFormat extends KeyIgnoringCRAMOutputFormat<NullWritable> { | |||
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This class is identical to SparkBAMOutputFormat -- is it only a separate class because setHeader() is static and we might want a different header for the two output formats, or is there some deeper reason?
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Its only because the two classes have different base classes that live in Hadoop-BAM. I don't see any useful way to consolidate them here, though going forward we may want to change AnySAMOutputFormat in Hadoop-BAM to delegate based on file extension similar to the way AnySAMInputFormat does.
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Created HadoopGenomics/Hadoop-BAM#72.
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Review complete -- back to @cmnbroad. Merge after addressing comments. |
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#1270. Depends on #1469, which should be reviewed first and then I can remove the first commit from this branch.