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Merge discvr-23.11 to discvr-24.3 #159

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merged 5 commits into from
Jun 5, 2024
+22 −4
Merged

Merge discvr-23.11 to discvr-24.3 #159

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2cf9cc8
Update logic used to filter variant coding potential
bbimber May 14, 2024
6316d31
Add more filtering of SnpEff coding potential
bbimber May 16, 2024
4e9bd3b
Add filter to ETL
bbimber May 30, 2024
e551197
Add MCC field for litter
bbimber Jun 4, 2024
e4f15bf
Merge discvr-23.11 to discvr-24.3
bbimber Jun 5, 2024
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1 change: 1 addition & 0 deletions MccColony/resources/queries/study/demographics/.qview.xml
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Expand Up @@ -26,6 +26,7 @@
<column name="Id/MostRecentWeight/MostRecentWeightGrams"/>
<column name="Id/MostRecentWeight/MostRecentWeightDate"/>
<column name="alternateIds"/>
<column name="litterId"/>
<column name="excludeFromCensus"/>
<column name="Id/mostRecentObservations/availability::observation">
<properties>
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5 changes: 2 additions & 3 deletions mGAP/src/org/labkey/mgap/pipeline/mGapSummarizer.java
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Expand Up @@ -174,7 +174,7 @@ private static class FieldData
public static void filterCodingPotential(Set<String> codingPotential)
{
//due to overlapping transcripts, this is often added. remove these less-specific terms in order
for (String type : Arrays.asList("intragenic_variant", "non_coding_transcript_variant", "intron_variant"))
for (String type : Arrays.asList("custom", "intergenic_variant", "intragenic_variant"))
{
if (codingPotential.size() > 1)
{
Expand All @@ -184,9 +184,8 @@ public static void filterCodingPotential(Set<String> codingPotential)

if (codingPotential.contains("synonymous_variant") || codingPotential.contains("missense_variant"))
{
codingPotential.remove("intergenic_variant");
codingPotential.remove("intragenic_variant");
codingPotential.remove("non_coding_transcript_variant");
codingPotential.remove("intron_variant");
}
}

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4 changes: 4 additions & 0 deletions mcc/resources/queries/mcc/aggregatedDemographics.sql
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Expand Up @@ -19,6 +19,7 @@ SELECT
WHEN d.calculated_status = 'Alive' AND (SELECT COUNT(f.flag.value) as total FROM "/data/Colonies/SNPRC/".study.flags f WHERE f.Id = d.Id AND f.isActive = true) > 0 THEN true
ELSE false
END as u24_status,
d.litterId,
d.Id.mostRecentDeparture.mostRecentDeparture,
o.availability,
o.current_housing_status,
Expand Down Expand Up @@ -67,6 +68,7 @@ SELECT
WHEN d.calculated_status = 'Alive' AND (SELECT COUNT(f.flag.value) as total FROM "/data/Colonies/WNPRC/".study.flags f WHERE f.Id = d.Id AND f.isActive = true) > 0 THEN true
ELSE false
END as u24_status,
d.litterId,
d.Id.mostRecentDeparture.mostRecentDeparture,
o.availability,
o.current_housing_status,
Expand Down Expand Up @@ -112,6 +114,7 @@ SELECT
d.objectid,
d.calculated_status,
d.u24_status,
d.litterId,
d.Id.mostRecentDeparture.mostRecentDeparture,
o.availability,
o.current_housing_status,
Expand Down Expand Up @@ -160,6 +163,7 @@ SELECT
d.objectid,
d.calculated_status,
d.u24_status,
d.litterId,
d.Id.mostRecentDeparture.mostRecentDeparture,
o.availability,
o.current_housing_status,
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9 changes: 8 additions & 1 deletion mcc/resources/queries/study/demographics.query.xml
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Expand Up @@ -9,7 +9,7 @@
<deleteUrl />
<columns>
<column columnName="Id">
<url></url>
<url />
</column>
<column columnName="date">
<isHidden>true</isHidden>
Expand Down Expand Up @@ -121,6 +121,13 @@
<column columnName="alternateIds">
<columnTitle>Alternate IDs</columnTitle>
</column>
<column columnName="litterId">
<columnTitle>Litter ID</columnTitle>
<url>/query/executeQuery.view?schemaName=study&amp;
query.queryName=Demographics&amp;
query.litterId~eq=${litterId}
</url>
</column>
<column columnName="remark">

</column>
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1 change: 1 addition & 0 deletions mcc/resources/queries/study/demographics/.qview.xml
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Expand Up @@ -36,6 +36,7 @@
<column name="usage_current"/>
<column name="usage_future"/>
<column name="date_of_observations"/>
<column name="litterId"/>
</columns>
<sorts>
<sort column="Id" descending="false"/>
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3 changes: 3 additions & 0 deletions mcc/resources/referenceStudy/study/datasets/datasets_metadata.xml
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Expand Up @@ -685,6 +685,9 @@
<column columnName="excludeFromCensus">
<datatype>boolean</datatype>
</column>
<column columnName="litterId">
<datatype>varchar</datatype>
</column>
</columns>
<tableTitle>Demographics</tableTitle>
</table>
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3 changes: 3 additions & 0 deletions primeseq/resources/etls/mcc.xml
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Expand Up @@ -12,6 +12,9 @@
<column>sire</column>
<column>gender</column>
</sourceColumns>
<sourceFilters>
<sourceFilter column="Id" value="" operator="isnonblank"/>
</sourceFilters>
</source>
<destination schemaName="laboratory" queryName="subjects" targetOption="truncate" bulkLoad="true">
<constants>
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