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Users should be able to save files as -single without merging them #1161

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fnothaft opened this issue Sep 10, 2016 · 0 comments
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Users should be able to save files as -single without merging them #1161

fnothaft opened this issue Sep 10, 2016 · 0 comments
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0.20.0

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@fnothaft
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For example, in AlignmentRecordRDD we allow for saving to a single SAM/BAM file, where we write a header and headerless shards, and we then merge them all. The disadvantage of merging the files while running in the same Spark context is that we hold all of the cluster resources (all of the executors) while running a long single node task. We should:

  • Add a -headerless option, that saves as if we are going to save -single, but doesn't merge the files.
  • Add a CLI module to merge all of the files separate from a given Spark job.
@fnothaft fnothaft mentioned this issue Sep 11, 2016
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fnothaft added a commit to fnothaft/adam that referenced this issue Sep 12, 2016
@fnothaft
[ADAM-1161] Add -deferMerging and MergeShards.
ccc4372 
Resolves bigdatagenomics#1161. When used with `-single`, `-deferMerging` allows a user to
postpone merging files that were written as if they were to be merged. Then,
the user can run the `MergeShards` CLI module later to merge the shards.
@fnothaft fnothaft mentioned this issue Sep 12, 2016
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@heuermh heuermh modified the milestone: 0.20.0 Sep 13, 2016
@heuermh heuermh mentioned this issue Sep 13, 2016
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fnothaft added a commit to fnothaft/adam that referenced this issue Sep 14, 2016
@fnothaft
[ADAM-1161] Add -deferMerging and MergeShards.
635e837 
Resolves bigdatagenomics#1161. When used with `-single`, `-deferMerging` allows a user to
postpone merging files that were written as if they were to be merged. Then,
the user can run the `MergeShards` CLI module later to merge the shards.
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@heuermh @fnothaft