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[ADAM-1530] Support loading GO:query (S/CR/B)AMs as fragments. #1531

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merged 1 commit into from May 17, 2017

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fnothaft commented May 17, 2017

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.

[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.

@fnothaft fnothaft added this to the 0.23.0 milestone May 17, 2017

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coveralls May 17, 2017

Coverage Status

Coverage increased (+0.2%) to 82.136% when pulling f2b7c3e on fnothaft:issues/1530-query-grouped into 7fc5b4f on bigdatagenomics:master.

coveralls commented May 17, 2017

Coverage Status

Coverage increased (+0.2%) to 82.136% when pulling f2b7c3e on fnothaft:issues/1530-query-grouped into 7fc5b4f on bigdatagenomics:master.

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AmplabJenkins May 17, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2018/
Test PASSed.

AmplabJenkins commented May 17, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2018/
Test PASSed.

@heuermh heuermh merged commit e02fcce into bigdatagenomics:master May 17, 2017

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codacy/pr Not so good... This pull request quality could be better.
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coverage/coveralls Coverage increased (+0.2%) to 82.136%
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heuermh May 17, 2017

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Thank you, @fnothaft

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heuermh commented May 17, 2017

Thank you, @fnothaft

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

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