Hadoop-BAM and htsjdk upgrades, Spark tool changes. #1469
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Ping me once this is ready |
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@droazen Hadoop-BAM has been released now so this is ready for review now whenever you can get to it. There are two other changes included that are unrelated to the tickets listed above:
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| initializeReference(); | ||
| initializeReads(sparkContext); // reference must be intialized before reads |
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intialized -> initialized
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Review complete -- back to @cmnbroad |
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I think I addressed everything. Back to @droazen. |
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👍 merge when ready |
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Feb 19, 2016
Hadoop-BAM and htsjdk upgrades, Spark tool changes.
This was referenced Feb 19, 2016
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Requires upgrades to Hadoop-BAM (not yet released) and htsjdk.
Fixes #1346, #1261, #1175, #1326, #1259, and much of the underlying code for #1270, which will be enabled in a separate PR.