Adding scripts to liftover gnomAD. Also bugfixes for Funcotator NIO. #5514
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* Added WDLs and some arguments to lift over gnomAD * Added chain file for b37->hg38 and arguments for liftover. * Limited to 1000 records in memory. * Added stack trace option to all wdls and sub tasks. * Fixed output to be consistent with local files for indexing. * Added timing information on wdls. * Added a wdl/json to create a TSV from gnomAD allele freq data. * Updated indexFeatureFile wdl, added params for run to index gnomAD. * Added json file for indexing a large gnomad file. * Fixed critical issues with NIO data sources. * Updates to the test script to save output and point to full cloud data. * Added some logging hooks to SeekableByteChannelPrefetcher
jonn-smith
changed the title
Codecov Report
@@ Coverage Diff @@
## master #5514 +/- ##
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- Coverage 87.076% 87.069% -0.006%
- Complexity 31320 31323 +3
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Files 1921 1921
Lines 144564 144577 +13
Branches 15951 15949 -2
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+ Hits 125880 125882 +2
- Misses 12895 12902 +7
- Partials 5789 5793 +4
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LeeTL1220
approved these changes
Dec 12, 2018
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@jonn-smith If you answer my questions and make changes, feel free to merge.
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How was this verified to work? Did you give the results to the comms team to post somewhere?
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For now the resulting liftover file hasn't been validated. The liftover of gnomAD resulting from using this file is going to be QC'd, then it will have been verified.
I haven't yet given them the liftover file.
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I'm working with them now.
scripts/funcotator/data_sources/gnomAD/mergeVcfs_gnomadPartialOutput.json
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src/main/java/org/broadinstitute/hellbender/utils/nio/SeekableByteChannelPrefetcher.java
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src/main/java/org/broadinstitute/hellbender/utils/nio/SeekableByteChannelPrefetcher.java
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src/main/java/org/broadinstitute/hellbender/utils/nio/SeekableByteChannelPrefetcher.java
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src/main/java/org/broadinstitute/hellbender/utils/nio/SeekableByteChannelPrefetcher.java
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I haven't reviewed this since I made the changes to it to see what should stay, so it may need a fair bit of work.