Refactor some file writing and reading logic #450
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Test PASSed. |
| @@ -64,6 +64,36 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord]) | |||
| rdd.filter(overlapsQuery) | |||
| } | |||
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| def maybeSaveBam(args: ADAMSaveArgs): Boolean = { | |||
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I like how clean this code is. Looks good!
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+1 LGTM. |
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Squash and rebase on master please and I'll merge this. |
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+1, LGTM as well. |
- read “OQ” attr from structured SAMRecord field converting into and out of BAM using ADAM was dropping the “OQ” attr; HTSJDK puts it in its own field but ADAM was looking for it in the catch-all attributes field. - style nits / long lines - ADAMMain formatting - apply predicate shorthand - move adamBamLoad into ADAMContext I'm a little torn about this one, since I see the motivation for having AlignmentRecordContext own logic for things we know will be AlignmentRecords, but adamBamLoad also is called from and calls into (via implicit conversion from SparkContext back into ADAMContext) other things in ADAMContext that made it feel like a more natural fit inside of ADAMContext. - factor out parquet-saving config - factor multi-format saving out of Transform - add helper for saving only aligned records a.k.a. BAM or ADAM records; no FASTQs
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squashed and rebased! |
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Test PASSed. |
massie
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Nov 3, 2014
Refactor some file writing and reading logic
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Thanks, Ryan! |
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adamParquetSavemethod that encapsulates the most common file-writing step at the end of ADAM commands, using the existingParquetArgsoptions as well as anoutputPathoption.outputPathfile extensionsPer usual, commits are in fairly logical chunks, but I'll squash if it looks good.