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@brentp is humble.
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arq5x committed Apr 8, 2015
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0.13.0
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1. Major `query` speed improvements thanks to Brent Pedersen. For example, the following query goes from 43 seconds in version 0.12.2 to 11 seconds in 0.13.0. All queries involving `gt_*` fields should be substantially faster.
1. Major `query` speed improvements. For example, the following query goes from 43 seconds in version 0.12.2 to 11 seconds in 0.13.0. All queries involving `gt_*` fields should be substantially faster.
::

$ gemini query \
-q "select chrom, start, (gts).(*) from variants" data/tmaster.db \
--gt-filter "(gt_depths).(*).(>=20).(all)" > /dev/null

2. Speed improvements to `load` thanks to Brent Pedersen. The following went from 7 minutes 9 seconds to 6 minutes 21 seconds.
2. Speed improvements to `load`. The following went from 7 minutes 9 seconds to 6 minutes 21 seconds.
::

$ gemini load -t VEP -v data/v100K.vcf.gz data/tmaster.db --cores 4

3. We added the `gt_phred_ll_homref`, `gt_phred_ll_het`, `gt_phred_ll_homalt` columns to database. These are the genotype likelihoods pulled from the GL or PL columns of the VCF if available. They can all be queried and filtered in the same way as existing gt_* columns. In future releases, we are planning tp use genotype likelihood to assign likelihoods to de novo mutations, mendelian violations, and variants meeting other inheritance patterns. This is being led by Brent Pedersen.
3. We added the `gt_phred_ll_homref`, `gt_phred_ll_het`, `gt_phred_ll_homalt` columns to database. These are the genotype likelihoods pulled from the GL or PL columns of the VCF if available. They can all be queried and filtered in the same way as existing gt_* columns. In future releases, we are planning tp use genotype likelihood to assign likelihoods to de novo mutations, mendelian violations, and variants meeting other inheritance patterns.

4. Fixed bugs related to splitting multiple alts (thanks to @jdh237)

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