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Scala copy method not supported in abstract classes such as AlignmentRecordRDD #1599

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heuermh opened this Issue Jul 11, 2017 · 4 comments

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heuermh commented Jul 11, 2017

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devin-petersohn Jul 11, 2017

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Are you wanting to add def copy(...) to RDDBoundAlignmentRecordRDD and DatasetBoundAlignmentRecordRDD?

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devin-petersohn commented Jul 11, 2017

Are you wanting to add def copy(...) to RDDBoundAlignmentRecordRDD and DatasetBoundAlignmentRecordRDD?

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heuermh Jul 11, 2017

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No, it isn't present on AlignmentRecordRDD, which is abstract

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heuermh commented Jul 11, 2017

No, it isn't present on AlignmentRecordRDD, which is abstract

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Are you wanting an abstract definition in AlignmentRecordRDD, and then implementations in the above mentioned classes?

If you don't want changes in ADAM, you could just use the Companion object:
AlignmentRecordRDD(rdd, sequences, recordGroups)

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devin-petersohn commented Jul 12, 2017

Are you wanting an abstract definition in AlignmentRecordRDD, and then implementations in the above mentioned classes?

If you don't want changes in ADAM, you could just use the Companion object:
AlignmentRecordRDD(rdd, sequences, recordGroups)

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That was my fix in bigdatagenomics/cannoli#56. The copy method is some Scala magick, I'm not sure if we want to add explict ones everywhere.

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heuermh commented Jul 12, 2017

That was my fix in bigdatagenomics/cannoli#56. The copy method is some Scala magick, I'm not sure if we want to add explict ones everywhere.

fnothaft added a commit to fnothaft/adam that referenced this issue Jul 12, 2017

[ADAM-1599] Add explicit functions for updating GenomicRDD metadata.
Resolves bigdatagenomics#1599. Adds functions that replaces or appends to the
sequence dictionary/record groups/header lines/sample metadata that is attached
to a GenomicRDD. This is necessary as a59b8ed
eliminated the `copy` methods that were attached to all implementations of
`GenomicRDD` by making the exposed implementations abstract classes instead of
case classes.

@fnothaft fnothaft added this to the 0.23.0 milestone Jul 12, 2017

fnothaft added a commit to fnothaft/adam that referenced this issue Jul 12, 2017

[ADAM-1599] Add explicit functions for updating GenomicRDD metadata.
Resolves bigdatagenomics#1599. Adds functions that replaces or appends to the
sequence dictionary/record groups/header lines/sample metadata that is attached
to a GenomicRDD. This is necessary as a59b8ed
eliminated the `copy` methods that were attached to all implementations of
`GenomicRDD` by making the exposed implementations abstract classes instead of
case classes.

devin-petersohn added a commit that referenced this issue Jul 12, 2017

[ADAM-1599] Add explicit functions for updating GenomicRDD metadata.
Resolves #1599. Adds functions that replaces or appends to the
sequence dictionary/record groups/header lines/sample metadata that is attached
to a GenomicRDD. This is necessary as a59b8ed
eliminated the `copy` methods that were attached to all implementations of
`GenomicRDD` by making the exposed implementations abstract classes instead of
case classes.

@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018

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