test_class.declarator: vd
test_class.modifier: static
test_class.original_string: static VariantDataset vd;
test_class.type: VariantDataset
test_class.var_name: vd
test_class.declarator: sparkConf
test_class.modifier: static
test_class.original_string: static SparkConf sparkConf;
test_class.type: SparkConf
test_class.var_name: sparkConf
test_class.declarator: sparkSession
test_class.modifier: static
test_class.original_string: static SparkSession sparkSession;
test_class.type: SparkSession
test_class.var_name: sparkSession
test_class.declarator: temporaryFolder = new TemporaryFolder()
test_class.modifier: @Rule
      public
test_class.original_string: @Rule
      public TemporaryFolder temporaryFolder = new TemporaryFolder();
test_class.type: TemporaryFolder
test_class.var_name: temporaryFolder
test_class.file: hpg-bigdata-core/src/test/java/org/opencb/hpg/bigdata/core/lib/VariantDatasetTest.java
test_class.identifier: VariantDatasetTest
test_case.body: @Test
      public void filters() {
  
          long count = 0;
          try {
              initDataset();
              System.out.println("--------------------------------------");
  
              //vd.studyFilter("stats.maf", "1000g::all<=0.4").show();
              //vd.studyFilter("stats.maf", "hgva@hsapiens_grch37:1000GENOMES_phase_3::ASW==0.008196721").show();
  //            vd.studyFilter("stats.refAlleleCount", "hgva@hsapiens_grch37:1000GENOMES_phase_3::ASW==121").show();
  
  //            long count = vd.annotationfilter("consequenceTypes.sequenceOntologyTerms.accession", "SO:0001566").count();
  
  //            count = vd.annotationFilter("populationFrequencies.altAlleleFreq", "1000G:CEU < 1.2,1000G:ASW < 1.25")
  //                    .count();
  //            vd.annotationfilter("populationFrequencies", "1000G:ASW < 0.2").count();
  
  //            long count = vd.annotationfilter("consequenceTypes.sequenceOntologyTerms.accession", "SO:0001566")
  //            long count = vd//.annotationfilter("consequenceTypes.sequenceOntologyTerms.name", "missense_variant")
  //                    .annotationFilter("conservation.phylop", "< 0.2")
  //                    .annotationFilter("conservation.phastCons", "< 0.4")
  //                    .idFilter("rs587604674")
  //                    .count();
  
  
  //            String ids = "rs587604674,rs587603352";
  //            count = vd.idFilter(Arrays.asList(StringUtils.split(ids, ","))).count();
  
  //            count = vd.annotationFilter("conservation", "phylop<0.3,phastCons<0.1").count();
              String types = "SNP,SNV";
              count = vd.typeFilter(new ArrayList<>(Arrays.asList(StringUtils.split(types, ",")))).count();
  
  //            System.out.println(vd.annotationfilter("consequenceTypes.sequenceOntologyTerms.name", "missense_variant")
  //                    .select("annotation.consequenceTypes.sequenceOntologyTerms").count());
  
  //            System.out.println(vd.idfilter("rs587604674").count());
  //            System.out.println(vd.annotationfilter("id", "ENSG00000233866").count());
              //scala> spark.sql("select * from v10k lateral view explode(annotation.consequenceTypes) act as ct lateral view explode(ct.sequenceOntologyTerms) ctso as so where so.accession = 'SO:0001566'").count()
              //res6: Long = 4437
  
  //            vd.select(vd.col("studies")).show(2);
              System.out.println("--------------------------------------");
              System.out.println("count = " + count);
              System.out.println("--------------------------------------");
  //            System.out.println(vd.count());
  //            System.out.println(vd.filter("start >= 564477").filter("end <= 729948").count());
  //            System.out.println(vd.groupBy("chromosome").avg("start").sort("chromosome").take(3)[0]);
  //            System.out.println(vd.describe("studies"));
  //            System.out.println("---->>> " + vd.select("studies.files").head());
  //            System.out.println("---->>> " + vd.select("studies.files").select("attributes").head());
  //            System.out.println(vd.filter("studies.files[0].attributes.AF = '0.009'"));
  //            System.out.println(vd.filter("studies.files.attributes.AF = '0.009'"));
              vd.sparkSession.sparkContext().stop();
  
              assert(count == 98);
          } catch (Exception e) {
              e.printStackTrace();
          }
          vd.sparkSession.sparkContext().stop();
      }
test_case.class_method_signature: VariantDatasetTest.filters()
test_case.full_signature: @Test public void filters()
test_case.identifier: filters
test_case.invocations: initDataset println count typeFilter asList split println println println stop sparkContext printStackTrace stop sparkContext
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void filters()
focal_class.declarator: variantParseQuery
focal_class.modifier: private
focal_class.original_string: private VariantParseQuery variantParseQuery;
focal_class.type: VariantParseQuery
focal_class.var_name: variantParseQuery
focal_class.declarator: sql
focal_class.modifier: private
focal_class.original_string: private String sql;
focal_class.type: String
focal_class.var_name: sql
focal_class.file: hpg-bigdata-core/src/main/java/org/opencb/hpg/bigdata/core/lib/VariantDataset.java
focal_class.identifier: VariantDataset
focal_class.interfaces: implements Serializable
focal_class.class_method_signature: VariantDataset.VariantDataset(SparkSession sparkSession)
focal_class.full_signature: public  VariantDataset(SparkSession sparkSession)
focal_class.identifier: VariantDataset
focal_class.modifiers: public
focal_class.parameters: (SparkSession sparkSession)
focal_class.signature:  VariantDataset(SparkSession sparkSession)
focal_class.class_method_signature: VariantDataset.updateDataset(Query query)
focal_class.full_signature: @Override protected void updateDataset(Query query)
focal_class.identifier: updateDataset
focal_class.modifiers: @Override protected
focal_class.parameters: (Query query)
focal_class.return: void
focal_class.signature: void updateDataset(Query query)
focal_class.class_method_signature: VariantDataset.updateQuery(String key, List<String> values, boolean and)
focal_class.full_signature: private void updateQuery(String key, List<String> values, boolean and)
focal_class.identifier: updateQuery
focal_class.modifiers: private
focal_class.parameters: (String key, List<String> values, boolean and)
focal_class.return: void
focal_class.signature: void updateQuery(String key, List<String> values, boolean and)
focal_class.class_method_signature: VariantDataset.reset()
focal_class.full_signature: public void reset()
focal_class.identifier: reset
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void reset()
focal_class.class_method_signature: VariantDataset.executeSql(String sql)
focal_class.full_signature: public Dataset executeSql(String sql)
focal_class.identifier: executeSql
focal_class.modifiers: public
focal_class.parameters: (String sql)
focal_class.return: Dataset
focal_class.signature: Dataset executeSql(String sql)
focal_class.class_method_signature: VariantDataset.getSql()
focal_class.full_signature: @Override public String getSql()
focal_class.identifier: getSql
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getSql()
focal_class.class_method_signature: VariantDataset.idFilter(String value)
focal_class.full_signature: public VariantDataset idFilter(String value)
focal_class.identifier: idFilter
focal_class.modifiers: public
focal_class.parameters: (String value)
focal_class.return: VariantDataset
focal_class.signature: VariantDataset idFilter(String value)
focal_class.class_method_signature: VariantDataset.idFilter(List<String> values)
focal_class.full_signature: public VariantDataset idFilter(List<String> values)
focal_class.identifier: idFilter
focal_class.modifiers: public
focal_class.parameters: (List<String> values)
focal_class.return: VariantDataset
focal_class.signature: VariantDataset idFilter(List<String> values)
focal_class.class_method_signature: VariantDataset.idFilter(List<String> values, boolean and)
focal_class.full_signature: public VariantDataset idFilter(List<String> values, boolean and)
focal_class.identifier: idFilter
focal_class.modifiers: public
focal_class.parameters: (List<String> values, boolean and)
focal_class.return: VariantDataset
focal_class.signature: VariantDataset idFilter(List<String> values, boolean and)
focal_class.class_method_signature: VariantDataset.typeFilter(String value)
focal_class.full_signature: public VariantDataset typeFilter(String value)
focal_class.identifier: typeFilter
focal_class.modifiers: public
focal_class.parameters: (String value)
focal_class.return: VariantDataset
focal_class.signature: VariantDataset typeFilter(String value)
focal_class.class_method_signature: VariantDataset.typeFilter(List<String> values)
focal_class.full_signature: public VariantDataset typeFilter(List<String> values)
focal_class.identifier: typeFilter
focal_class.modifiers: public
focal_class.parameters: (List<String> values)
focal_class.return: VariantDataset
focal_class.signature: VariantDataset typeFilter(List<String> values)
focal_class.class_method_signature: VariantDataset.studyFilter(String key, String value)
focal_class.full_signature: public VariantDataset studyFilter(String key, String value)
focal_class.identifier: studyFilter
focal_class.modifiers: public
focal_class.parameters: (String key, String value)
focal_class.return: VariantDataset
focal_class.signature: VariantDataset studyFilter(String key, String value)
focal_class.class_method_signature: VariantDataset.studyFilter(String key, List<String> values)
focal_class.full_signature: public VariantDataset studyFilter(String key, List<String> values)
focal_class.identifier: studyFilter
focal_class.modifiers: public
focal_class.parameters: (String key, List<String> values)
focal_class.return: VariantDataset
focal_class.signature: VariantDataset studyFilter(String key, List<String> values)
focal_class.class_method_signature: VariantDataset.studyFilter(String key, List<String> values, boolean and)
focal_class.full_signature: public VariantDataset studyFilter(String key, List<String> values, boolean and)
focal_class.identifier: studyFilter
focal_class.modifiers: public
focal_class.parameters: (String key, List<String> values, boolean and)
focal_class.return: VariantDataset
focal_class.signature: VariantDataset studyFilter(String key, List<String> values, boolean and)
focal_class.class_method_signature: VariantDataset.sampleFilter(String key, String value)
focal_class.full_signature: public VariantDataset sampleFilter(String key, String value)
focal_class.identifier: sampleFilter
focal_class.modifiers: public
focal_class.parameters: (String key, String value)
focal_class.return: VariantDataset
focal_class.signature: VariantDataset sampleFilter(String key, String value)
focal_class.class_method_signature: VariantDataset.sampleFilter(String key, List<String> values)
focal_class.full_signature: public VariantDataset sampleFilter(String key, List<String> values)
focal_class.identifier: sampleFilter
focal_class.modifiers: public
focal_class.parameters: (String key, List<String> values)
focal_class.return: VariantDataset
focal_class.signature: VariantDataset sampleFilter(String key, List<String> values)
focal_class.class_method_signature: VariantDataset.annotationFilter(String key, String value)
focal_class.full_signature: public VariantDataset annotationFilter(String key, String value)
focal_class.identifier: annotationFilter
focal_class.modifiers: public
focal_class.parameters: (String key, String value)
focal_class.return: VariantDataset
focal_class.signature: VariantDataset annotationFilter(String key, String value)
focal_class.class_method_signature: VariantDataset.annotationFilter(String key, List<String> values)
focal_class.full_signature: public VariantDataset annotationFilter(String key, List<String> values)
focal_class.identifier: annotationFilter
focal_class.modifiers: public
focal_class.parameters: (String key, List<String> values)
focal_class.return: VariantDataset
focal_class.signature: VariantDataset annotationFilter(String key, List<String> values)
focal_class.class_method_signature: VariantDataset.annotationFilter(String key, List<String> values, boolean and)
focal_class.full_signature: public VariantDataset annotationFilter(String key, List<String> values, boolean and)
focal_class.identifier: annotationFilter
focal_class.modifiers: public
focal_class.parameters: (String key, List<String> values, boolean and)
focal_class.return: VariantDataset
focal_class.signature: VariantDataset annotationFilter(String key, List<String> values, boolean and)
focal_class.class_method_signature: VariantDataset.iterator()
focal_class.full_signature: public Iterator<Variant> iterator()
focal_class.identifier: iterator
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: Iterator<Variant>
focal_class.signature: Iterator<Variant> iterator()
focal_class.superclass: extends ParentDataset<VariantDataset>
focal_method.body: public VariantDataset typeFilter(String value) {
          query.put("type", value);
          return this;
      }
focal_method.class_method_signature: VariantDataset.typeFilter(String value)
focal_method.full_signature: public VariantDataset typeFilter(String value)
focal_method.identifier: typeFilter
focal_method.invocations: put
focal_method.modifiers: public
focal_method.parameters: (String value)
focal_method.return: VariantDataset
focal_method.signature: VariantDataset typeFilter(String value)