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SortBamSpark is missing SORT_ORDER parameter #1260

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akiezun opened this issue Dec 5, 2015 · 0 comments · Fixed by #4545
Closed

SortBamSpark is missing SORT_ORDER parameter #1260

akiezun opened this issue Dec 5, 2015 · 0 comments · Fixed by #4545
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enhancement Spark

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@akiezun
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akiezun commented Dec 5, 2015

SortBamSpark does not have a SORT_ORDER parameter

once this is fixed - renable tests in SortBamSparkIntegrationTest
@droazen droazen added this to the beta milestone Jan 5, 2016
@droazen droazen removed this from the beta milestone Mar 28, 2016
@davidbenjamin davidbenjamin self-assigned this May 5, 2017
@davidbenjamin davidbenjamin removed their assignment Jun 12, 2017
@tomwhite tomwhite mentioned this issue Jul 19, 2017
Closed
lbergelson added a commit that referenced this issue Mar 20, 2018
@lbergelson
adding --sort-order option to SortSamSpark
4d05b6e 
adding a --sort-order option to SortSamSpark to let users specify the what order to sort in
enabling disabled tests
fixing the tests which weren't actually asserting anything

closes #1260
lbergelson added a commit that referenced this issue Mar 20, 2018
@lbergelson
adding --sort-order option to SortSamSpark
74bcb52 
adding a --sort-order option to SortSamSpark to let users specify the what order to sort in
enabling disabled tests
fixing the tests which weren't actually asserting anything

closes #1260
@lbergelson lbergelson mentioned this issue Mar 20, 2018
Merged
lbergelson added a commit that referenced this issue May 25, 2018
@lbergelson
adding --sort-order option to SortSamSpark
d37cede 
adding a --sort-order option to SortSamSpark to let users specify the what order to sort in
enabling disabled tests
fixing the tests which weren't actually asserting anything

closes #1260

work in progress

in progress

refactoring

using new SparkUtils method
jamesemery pushed a commit that referenced this issue Jun 5, 2018
@lbergelson @jamesemery
adding --sort-order option to SortSamSpark
a29ab53 
adding a --sort-order option to SortSamSpark to let users specify the what order to sort in
enabling disabled tests
fixing the tests which weren't actually asserting anything

closes #1260

work in progress

in progress

refactoring

using new SparkUtils method
lbergelson added a commit that referenced this issue Jun 11, 2018
@lbergelson
adding --sort-order option to SortSamSpark (#4545)
1751c85 
* adding --sort-order option to SortSamSpark

adding a --sort-order option to SortSamSpark to let users specify the what order to sort in
enabling disabled tests
fixing the tests which weren't actually asserting anything

* closes #1260

* adding hack to get around HadoopGenomics/Hadoop-BAM#199
  created SplitSortingSamInputFormat which empirically fixes the issue although we don't necessarily completely understand the problem
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adding --sort-order option to SortSamSpark broadinstitute/gatk
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@droazen @akiezun @davidbenjamin