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Queryname sorted check should check for queryname grouped as well #1530

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fnothaft opened this Issue May 16, 2017 · 0 comments

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fnothaft commented May 16, 2017

See https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala#L506-L534. Our goal is to check whether files have paired reads are grouped together, which is satisfied by sort order = queryname or group order = queryname.

@fnothaft fnothaft added the bug label May 16, 2017

@fnothaft fnothaft added this to the 0.23.0 milestone May 16, 2017

@fnothaft fnothaft self-assigned this May 16, 2017

@fnothaft fnothaft changed the title from Queryname sorted check should check for queryname grouped instead to Queryname sorted check should check for queryname grouped as well May 16, 2017

fnothaft added a commit to fnothaft/adam that referenced this issue May 17, 2017

[ADAM-1530] Support loading GO:query (S/CR/B)AMs as fragments.
Resolves bigdatagenomics#1530. Adds support for loading (S/CR/B)AM files that are globally
unsorted yet have group order set to query (read name) as Fragments.
Additionally, adds two unit tests. In the process of running the unit tests,
I found an issue in `SingleReadBucket` that was dropping a read from each
pair after the first pair in a partition due to an odd behavior in the
`Iterator.takeWhile` function, which drops the first item that does not
get taken.

heuermh added a commit that referenced this issue May 17, 2017

[ADAM-1530] Support loading GO:query (S/CR/B)AMs as fragments.
Resolves #1530. Adds support for loading (S/CR/B)AM files that are globally
unsorted yet have group order set to query (read name) as Fragments.
Additionally, adds two unit tests. In the process of running the unit tests,
I found an issue in `SingleReadBucket` that was dropping a read from each
pair after the first pair in a partition due to an odd behavior in the
`Iterator.takeWhile` function, which drops the first item that does not
get taken.

@heuermh heuermh added this to Completed in Release 0.23.0 May 30, 2017

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