Cleanup GenomicsDB vid combine protobuf mapping overrides #6190
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@ldgauthier, would you like to change constant STRAND_BIAS_TABLE_COMBINE to ELEMENT_WISE_INT_SUM? |
ldgauthier
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Oct 1, 2019
| @@ -36,6 +37,50 @@ | |||
| private static final String STRAND_BIAS_TABLE_COMBINE = "strand_bias_table"; | |||
| private static final String GDB_TYPE_FLOAT = "float"; | |||
| private static final String GDB_TYPE_INT = "int"; | |||
| // private static final String MOVE_TO_FORMAT = "move_to_FORMAT"; | |||
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I'd rather leave this because I have some work in development that does use it.
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Actually, I added this based on the email thread and left it commented out to stop the compiler complaining about unused variables. Please feel free to uncomment as necessary.
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I have uncommented MOVE_TO_FORMAT too.
| @@ -36,6 +37,50 @@ | |||
| private static final String STRAND_BIAS_TABLE_COMBINE = "strand_bias_table"; | |||
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@nalinigans -- yes, changing this to ELEMENT_WISE_INT_SUM is a great idea!
droazen
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Oct 8, 2019
)" This reverts commit 609dafe.
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nalinigans
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* Move vid combine protobuf mapping overrides from GenomicsDB ExportConfiguration to Import * Comment out MOVE_TO_FORMAT as it is not used as yet * Change AS_QUALapprox combine operation to element wise int sum
droazen
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Oct 24, 2019
…ckaged (#6206) * Use GenomicsDB 1.1.2.2. Also add junit to check if native Linux and Mac OSX shared libraries are included in genomicsdb.jar * Revert back 712bfc4 with move to GenomicsDB 1.1.2.2 * Cleanup GenomicsDB vid combine protobuf mapping overrides (#6190) * Move vid combine protobuf mapping overrides from GenomicsDB ExportConfiguration to Import * Comment out MOVE_TO_FORMAT as it is not used as yet * Change AS_QUALapprox combine operation to element wise int sum
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Move vid combine protobuf mapping overrides from GenomicsDB ExportConfiguration to Import. Overrides can still be performed via ExportConfiguration, but recommended to modify the mappings during the import phase as not all mappings can be effectively modified during export/queries.
There is a whole bunch of hardcoded allele-specific fields whose vid mappings are hardcoded in GenomicsDB - see https://github.com/GenomicsDB/GenomicsDB/blob/master/src/main/java/org/genomicsdb/importer/Constants.java. There is no harm in specifying the mappings in gatk as well. But, at some point we should move the mappings from GenomicsDB to gatk, as these are gatk-specific annotations.