Add BGEN option to explicitly not include sample ids #59
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Signed-off-by: Henry D <[email protected]>
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## master #59 +/- ##
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+ Coverage 94.1% 94.11% +<.01%
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Files 73 74 +1
Lines 3560 3566 +6
Branches 331 326 -5
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+ Hits 3350 3356 +6
Misses 210 210
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kianfar77
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One suggestion. If you disagree let me know and I approve. The rest looks good.
| import io.projectglow.common.logging.{HlsMetricDefinitions, HlsTagDefinitions, HlsTagValues, HlsUsageLogging} | ||
| import io.projectglow.common.{GlowLogging, WithUtils} | ||
| import io.projectglow.sql.util.{ComDatabricksDataSource, SerializableConfiguration} | ||
| import io.projectglow.vcf.VCFOption |
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It may be a good idea to gather all bgen options (including this one) in a BGENOption object like what we did for VCFOption. It will be cleaner and creates separation of VCF and BGEN. Just a thought. Let me know if you disagree and I will approve.
Signed-off-by: Henry D <[email protected]>
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…ctglow#59) * name change Signed-off-by: Henry Davidge <[email protected]>
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* Add BGEN option to explicitly not include sampleIds Signed-off-by: Henry D <[email protected]> * organize datasource options Signed-off-by: Henry D <[email protected]> * add header Signed-off-by: Henry D <[email protected]> Signed-off-by: Henry Davidge <[email protected]>
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What changes are proposed in this pull request?
Previously, if a BGEN file contained sampleIds, they were always included in the emitted DataFrame. If a user didn't want them (common when dealing with large cohort sizes), they had to manually drop them.
Now, you can provide the same
includeSampleIdsoption used by the VCF and Plink datasources. If it isfalse, sample ids are not included in the output.cc @emaxwell
How is this patch tested?
(Details)