add imputed tsv creator and refactor

broadinstitute · Feb 1, 2021 · ef2c5b7 · ef2c5b7
1 parent f26547b
commit ef2c5b7
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Showing 4 changed files with 7 additions and 144 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/variantdb/IngestUtils.java b/src/main/java/org/broadinstitute/hellbender/tools/variantdb/IngestUtils.java
@@ -1,6 +1,5 @@
 package org.broadinstitute.hellbender.tools.variantdb;
 
-<<<<<<< HEAD
 import com.google.cloud.bigquery.TableResult;
 import htsjdk.variant.vcf.VCFHeader;
 import org.apache.commons.lang3.StringUtils;
@@ -10,12 +9,6 @@
 import org.broadinstitute.hellbender.utils.bigquery.BigQueryUtils;
 import org.broadinstitute.hellbender.utils.bigquery.QueryAPIRowReader;
 import org.broadinstitute.hellbender.utils.bigquery.TableReference;
-=======
-import htsjdk.variant.vcf.VCFHeader;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.broadinstitute.hellbender.exceptions.UserException;
->>>>>>> 298a745a1... change structure, add compressed option to ingest
 import org.broadinstitute.hellbender.utils.genotyper.IndexedSampleList;
 import org.broadinstitute.hellbender.utils.genotyper.SampleList;
 

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/variantdb/arrays/ArrayExtractCohort.java b/src/main/java/org/broadinstitute/hellbender/tools/variantdb/arrays/ArrayExtractCohort.java
@@ -12,7 +12,10 @@
 import org.broadinstitute.hellbender.engine.GATKTool;
 import org.broadinstitute.hellbender.tools.variantdb.CommonCode;
 import org.broadinstitute.hellbender.tools.variantdb.arrays.tables.ProbeInfo;
+<<<<<<< HEAD
 import org.broadinstitute.hellbender.tools.variantdb.arrays.tables.ProbeQcMetrics;
+=======
+>>>>>>> a47100a8d... add imputed tsv creator and refactor
 import org.broadinstitute.hellbender.tools.variantdb.arrays.tables.SampleList;
 import org.broadinstitute.hellbender.tools.variantdb.nextgen.ExtractCohort;
 import org.broadinstitute.hellbender.tools.walkers.annotator.Annotation;
@@ -198,7 +201,11 @@ protected void onStartup() {
 
         Map<Long, ProbeInfo> probeIdMap;
         if (probeCsvExportFile == null) {
+<<<<<<< HEAD
             probeIdMap = ProbeInfo.getProbeIdMapWithStorageAPI(probeTableName, printDebugInformation);
+=======
+            probeIdMap = ProbeInfo.getProbeIdMapFromBQ(probeTableName, printDebugInformation);
+>>>>>>> a47100a8d... add imputed tsv creator and refactor
         } else {
             probeIdMap = ProbeInfo.getProbeIdMapFromExport(probeCsvExportFile);
         }

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/variantdb/arrays/ProbeInfo.java b/src/main/java/org/broadinstitute/hellbender/tools/variantdb/arrays/ProbeInfo.java
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/variantdb/arrays/ProbeInfoSchema.java b/src/main/java/org/broadinstitute/hellbender/tools/variantdb/arrays/ProbeInfoSchema.java