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[18.01] Rename datatype extension 'bam_native' to 'unsorted.bam'. #5674

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jmchilton commented Mar 12, 2018

We handle other bam types this way and other more specific variants of an extension (e.g. thermo.raw) so this feels like the more consistent thing to do.

Sorry for the last minute change to 18.01, I think it is important though.

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martenson commented Mar 12, 2018

Does this have consequences other than the namespace change?

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jmchilton commented Mar 12, 2018

@martenson Users may get a better extension when downloading the file - not sure.

The extensions are stored in the DB and referenced in tools though, so it is important to pick a good one and stick with it before releasing 18.01. We may need to update HDAs on usegalaxy.org in the DB to reflect this change.

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mvdbeek commented Mar 12, 2018

We don't have tools that write bam_native yet, I think, so this should be of limited impact.

@nsoranzo nsoranzo added this to the 18.01 milestone Mar 12, 2018

Rename datatype extension 'bam_native' to 'unsorted.bam'.
We handle other bam types this way and other more specific variants of an extension (e.g. thermo.raw) so this feels like the more consistent thing to do.
@@ -50,7 +50,7 @@ Highlights
- ``qname_sorted.bam``, that ensures that the file is queryname sorted (e.g. ``SO:queryname``);
- ``qname_input_sorted.bam``, that can be used to describe the output of aligners which generally keep mate pairs adjacent
- ``native_bam``, that makes no assumptions about the sort order of the file.
- ``unsorted.bam``, that makes no assumptions about the sort order of the file.
A huge thanks goes out to `@bgruening <https://github.com/bgruening>`__ and `@mvdbeek <https://github.com/mvdbeek>`__ who
implemented these datatypes.

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Maybe also reference this PR below.

@jennaj jennaj referenced this pull request Mar 12, 2018

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Testing and tool/doc updates #86

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@martenson martenson merged commit 4fea390 into galaxyproject:release_18.01 Mar 12, 2018

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@jennaj jennaj referenced this pull request Mar 15, 2018

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Tests for new bam datatypes #102

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