diff --git a/apis/spark/build.gradle b/apis/spark/build.gradle
index a30d198a0..f8d755c60 100644
--- a/apis/spark/build.gradle
+++ b/apis/spark/build.gradle
@@ -53,6 +53,7 @@ repositories {
 dependencies {
     compileOnly 'org.apache.spark:spark-sql_2.12:2.4.3'
     compileOnly 'org.apache.spark:spark-core_2.12:2.4.3'
+    implementation 'io.tiledb:tiledb-java:0.24.0'
     compile group: 'io.tiledb', name: 'tiledb-vcf-java', version: version
     compile 'com.amazonaws:aws-java-sdk:1.11.650'
 
diff --git a/apis/spark/src/main/java/io/tiledb/vcf/VCFDataSourceOptions.java b/apis/spark/src/main/java/io/tiledb/vcf/VCFDataSourceOptions.java
index afbefcae5..7624617bb 100644
--- a/apis/spark/src/main/java/io/tiledb/vcf/VCFDataSourceOptions.java
+++ b/apis/spark/src/main/java/io/tiledb/vcf/VCFDataSourceOptions.java
@@ -76,6 +76,14 @@ public Optional<URI> getBedURI() {
     return Optional.empty();
   }
 
+  /** @return Optional uri of BED array */
+  public Optional<URI> getBedArrayURI() {
+    if (options.containsKey("bed_array")) {
+      return Optional.of(URI.create(options.get("bed_array")));
+    }
+    return Optional.empty();
+  }
+
   /** @return Optional uri of SampleFile file */
   public Optional<URI> getSampleURI() {
     if (options.containsKey("samplefile")) {
diff --git a/apis/spark/src/main/java/io/tiledb/vcf/VCFDataSourceReader.java b/apis/spark/src/main/java/io/tiledb/vcf/VCFDataSourceReader.java
index 1580f5b44..322035236 100644
--- a/apis/spark/src/main/java/io/tiledb/vcf/VCFDataSourceReader.java
+++ b/apis/spark/src/main/java/io/tiledb/vcf/VCFDataSourceReader.java
@@ -1,9 +1,11 @@
 package io.tiledb.vcf;
 
+import io.tiledb.java.api.*;
 import io.tiledb.libvcfnative.VCFBedFile;
 import io.tiledb.libvcfnative.VCFReader;
 import io.tiledb.util.CredentialProviderUtils;
 import java.net.URI;
+import java.util.*;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -215,7 +217,19 @@ public List<InputPartition<ColumnarBatch>> planBatchInputPartitions() {
     // Create Spark input partitions
     List<List<String>> regions = null;
     if (options.getNewPartitionMethod().orElse(false)) {
-      regions = computeRegionPartitionsFromBedFile(numRangePartitions);
+
+      // Compute regions from bed array or bed file
+      Optional<URI> bedArrayURI = options.getBedArrayURI();
+      Optional<URI> bedURI = options.getBedURI();
+      if (bedArrayURI.isPresent()) {
+        regions = computeRegionPartitionsFromBedArray(numRangePartitions, bedArrayURI.get());
+      } else if (bedURI.isPresent()) {
+        regions = computeRegionPartitionsFromBedFile(numRangePartitions);
+      } else {
+        throw new RuntimeException(
+            "Can't use new_partition_method without setting bed_file or bed_array");
+      }
+
       numRangePartitions = regions.size();
       ranges_end = regions.size();
       log.info("New partition method has yielded " + numRangePartitions + " range partitions");
@@ -247,10 +261,99 @@ public List<InputPartition<ColumnarBatch>> planBatchInputPartitions() {
     return inputPartitions;
   }
 
+  List<List<String>> computeRegionPartitionsFromBedArray(
+      int desiredNumRangePartitions, URI arrayURI) {
+
+    // Read bed array
+
+    try {
+      Map<String, List<String>> mapOfRegions = new HashMap<>();
+      int counter = 0;
+
+      Context ctx = new Context();
+      Array bedArray = new Array(ctx, arrayURI.toString(), QueryType.TILEDB_READ);
+
+      String CONTIG = "alias contig";
+      String START = "alias start";
+      String END = "alias end";
+
+      String[] keys = new String[] {CONTIG, START, END};
+
+      NativeArray contigAliasNA = bedArray.getMetadata(CONTIG, Datatype.TILEDB_STRING_ASCII);
+      NativeArray startAliasNA = bedArray.getMetadata(START, Datatype.TILEDB_STRING_ASCII);
+      NativeArray endAliasNA = bedArray.getMetadata(END, Datatype.TILEDB_STRING_ASCII);
+
+      String contigAlias = new String((byte[]) contigAliasNA.toJavaArray());
+      String startAlias = new String((byte[]) startAliasNA.toJavaArray());
+      String endAlias = new String((byte[]) endAliasNA.toJavaArray());
+
+      Query query = new Query(bedArray);
+      query.setLayout(Layout.TILEDB_UNORDERED);
+
+      Pair<Long, Long> estSize = query.getEstResultSizeVar(ctx, contigAlias);
+
+      // todo unsafe casting needs to be addressed in the java api
+      // Prepare buffers
+      query.setDataBuffer(
+          contigAlias,
+          new NativeArray(ctx, estSize.getSecond().intValue(), Datatype.TILEDB_STRING_ASCII));
+      query.setOffsetsBuffer(
+          contigAlias, new NativeArray(ctx, estSize.getFirst().intValue(), Datatype.TILEDB_UINT64));
+      query.setDataBuffer(
+          startAlias, new NativeArray(ctx, estSize.getFirst().intValue(), Datatype.TILEDB_UINT64));
+      query.setDataBuffer(
+          endAlias, new NativeArray(ctx, estSize.getFirst().intValue(), Datatype.TILEDB_UINT64));
+
+      do {
+        query.submit();
+        // get buffers
+        long[] contigOffsets = (long[]) query.getVarBuffer(contigAlias);
+        byte[] contigData = (byte[]) query.getBuffer(contigAlias);
+
+        String[] contigs = io.tiledb.java.api.Util.bytesToStrings(contigOffsets, contigData);
+        long[] start = (long[]) query.getBuffer(startAlias);
+        long[] end = (long[]) query.getBuffer(endAlias);
+
+        if (!(contigs.length == start.length && start.length == end.length)) {
+          throw new RuntimeException("There was an error reading the bed array");
+        }
+
+        // Put regions in map
+        for (int i = 0; i < contigs.length; i++) {
+          String shortContig = contigs[i].replace("chr", "");
+          String region = shortContig + ":" + start[i] + "-" + end[i] + ":" + counter;
+          counter++;
+
+          // Check if the key exists in the map
+          if (mapOfRegions.containsKey(shortContig)) {
+            // If the key exists, append the region string to the existing list
+            mapOfRegions.get(shortContig).add(region);
+          } else {
+            // If the key doesn't exist, create a new list with the region string
+            List<String> newList = new ArrayList<>();
+            newList.add(region);
+            mapOfRegions.put(shortContig, newList);
+          }
+        }
+      } while (query.getQueryStatus() == QueryStatus.TILEDB_INCOMPLETE);
+
+      List<List<String>> res = new LinkedList<>(mapOfRegions.values());
+
+      sortRegions(res, desiredNumRangePartitions);
+
+      return res;
+
+    } catch (TileDBError err) {
+      throw new RuntimeException(err);
+    }
+  }
+
   List<List<String>> computeRegionPartitionsFromBedFile(int desiredNumRangePartitions) {
     Optional<URI> bedURI = options.getBedURI();
-    if (!bedURI.isPresent()) {
-      throw new RuntimeException("Can't use new_partition_method without setting bed_file");
+    Optional<URI> bedArrayURI = options.getBedArrayURI();
+    if (!bedURI.isPresent() && !bedArrayURI.isPresent()) {
+      throw new RuntimeException(
+          "Can't use new_partition_method without setting bed_file or bed_array");
     }
 
     log.info("Init VCFReader for partition calculation");
@@ -273,15 +376,22 @@ List<List<String>> computeRegionPartitionsFromBedFile(int desiredNumRangePartiti
     Map<String, List<String>> mapOfRegions = bedFile.getContigRegionStrings();
     List<List<String>> res = new LinkedList<>(mapOfRegions.values());
 
+    sortRegions(res, desiredNumRangePartitions);
+
+    bedFile.close();
+    vcfReader.close();
+
+    return res;
+  }
+
+  private void sortRegions(List<List<String>> res, int desiredNumRangePartitions) {
     // Sort the region list by size of regions in contig, largest first
     res.sort(Comparator.comparingInt(List<String>::size).reversed());
 
-    // Keep splitting the larges region lists until we have the desired minimum number of range
+    // Keep splitting the largest region lists until we have the desired minimum number of range
     // Partitions, we stop if the large region has a size of 10 or less
     while (res.size() < desiredNumRangePartitions && res.get(0).size() >= 10) {
-
       List<String> top = res.remove(0);
-
       List<String> first = new LinkedList<>(top.subList(0, top.size() / 2));
       List<String> second = new LinkedList<>(top.subList(top.size() / 2, top.size()));
       res.add(first);
@@ -291,10 +401,5 @@ List<List<String>> computeRegionPartitionsFromBedFile(int desiredNumRangePartiti
       res.sort(Comparator.comparingInt(List::size));
       Collections.reverse(res);
     }
-
-    bedFile.close();
-    vcfReader.close();
-
-    return res;
   }
 }
diff --git a/apis/spark/src/main/java/io/tiledb/vcf/VCFInputPartitionReader.java b/apis/spark/src/main/java/io/tiledb/vcf/VCFInputPartitionReader.java
index a423e02e4..2a120098e 100644
--- a/apis/spark/src/main/java/io/tiledb/vcf/VCFInputPartitionReader.java
+++ b/apis/spark/src/main/java/io/tiledb/vcf/VCFInputPartitionReader.java
@@ -304,6 +304,12 @@ private void initVCFReader() {
       if (bedURI.isPresent()) {
         vcfReader.setBedFile(bedURI.get().toString());
       }
+
+      // Set BED array
+      Optional<URI> bedArrayURI = options.getBedArrayURI();
+      if (bedArrayURI.isPresent()) {
+        vcfReader.setBedFile(bedArrayURI.get().toString());
+      }
     } else {
       if (rangePartitionInfo.getRegions().isEmpty()) {
         throw new RuntimeException(
diff --git a/apis/spark/src/test/java/io/tiledb/vcf/VCFDataSourceOptionsTest.java b/apis/spark/src/test/java/io/tiledb/vcf/VCFDataSourceOptionsTest.java
index 37a6d43f9..da41467ad 100644
--- a/apis/spark/src/test/java/io/tiledb/vcf/VCFDataSourceOptionsTest.java
+++ b/apis/spark/src/test/java/io/tiledb/vcf/VCFDataSourceOptionsTest.java
@@ -90,6 +90,12 @@ public void testBedURIOptionMissing() {
     Assert.assertFalse(options.getBedURI().isPresent());
   }
 
+  @Test
+  public void testBedArrayURIOptionMissing() {
+    VCFDataSourceOptions options = new VCFDataSourceOptions(new DataSourceOptions(new HashMap<>()));
+    Assert.assertFalse(options.getBedArrayURI().isPresent());
+  }
+
   @Test
   public void testBedURIOption() {
     URI expectedURI = URI.create("s3://foo/bar");
@@ -100,12 +106,28 @@ public void testBedURIOption() {
     Assert.assertEquals(expectedURI, options.getBedURI().get());
   }
 
+  @Test
+  public void testBedArrayURIOption() {
+    URI expectedURI = URI.create("s3://foo/bar");
+    HashMap<String, String> optionMap = new HashMap<>();
+    optionMap.put("bed_array", expectedURI.toString());
+    VCFDataSourceOptions options = new VCFDataSourceOptions(new DataSourceOptions(optionMap));
+    Assert.assertTrue(options.getBedArrayURI().isPresent());
+    Assert.assertEquals(expectedURI, options.getBedArrayURI().get());
+  }
+
   @Test
   public void testSampleURIOptionMissing() {
     VCFDataSourceOptions options = new VCFDataSourceOptions(new DataSourceOptions(new HashMap<>()));
     Assert.assertFalse(options.getBedURI().isPresent());
   }
 
+  @Test
+  public void testArraySampleURIOptionMissing() {
+    VCFDataSourceOptions options = new VCFDataSourceOptions(new DataSourceOptions(new HashMap<>()));
+    Assert.assertFalse(options.getBedArrayURI().isPresent());
+  }
+
   @Test
   public void testSampleURIOption() {
     URI expectedURI = URI.create("s3://foo/bar");
diff --git a/apis/spark/src/test/java/io/tiledb/vcf/VCFDatasourceTest.java b/apis/spark/src/test/java/io/tiledb/vcf/VCFDatasourceTest.java
index 406c28865..d348bbdb2 100644
--- a/apis/spark/src/test/java/io/tiledb/vcf/VCFDatasourceTest.java
+++ b/apis/spark/src/test/java/io/tiledb/vcf/VCFDatasourceTest.java
@@ -25,7 +25,7 @@
 public class VCFDatasourceTest extends SharedJavaSparkSession {
 
   private String testSampleGroupURI(String sampleGroupName) {
-    Path arraysPath = Paths.get("src", "test", "resources", "arrays", "v3", sampleGroupName);
+    Path arraysPath = Paths.get("src", "test", "resources", "arrays", "v4", sampleGroupName);
     return "file://".concat(arraysPath.toAbsolutePath().toString());
   }
 
@@ -39,6 +39,16 @@ private String testSimpleBEDFile() {
     return "file://".concat(path.toAbsolutePath().toString());
   }
 
+  private String testSimpleBEDArray() {
+    Path arrayPath = Paths.get("src", "test", "resources", "arrays", "bed_array");
+    return "file://".concat(arrayPath.toAbsolutePath().toString());
+  }
+
+  private String testLargeBEDArray() {
+    Path arrayPath = Paths.get("src", "test", "resources", "arrays", "largebedarray");
+    return "file://".concat(arrayPath.toAbsolutePath().toString());
+  }
+
   private String testLargeBEDFile() {
     Path path = Paths.get("src", "test", "resources", "E001_15_coreMarks_dense.bed.gz");
     return "file://".concat(path.toAbsolutePath().toString());
@@ -450,6 +460,93 @@ public void testSamplePartition() {
     }
   }
 
+  @Test
+  public void testNewPartitionWithBedArray() {
+    int rangePartitions = 32;
+    int samplePartitions = 2;
+    Dataset<Row> dfRead =
+        session()
+            .read()
+            .format("io.tiledb.vcf")
+            .option("uri", testSampleGroupURI("ingested_2samples", "v4"))
+            .option("bed_array", testLargeBEDArray())
+            .option("new_partition_method", true)
+            .option("range_partitions", rangePartitions)
+            .option("sample_partitions", samplePartitions)
+            .option("tiledb.vcf.log_level", "TRACE")
+            .load();
+
+    List<Row> rows =
+        dfRead
+            .select("sampleName", "contig", "posStart", "posEnd", "queryBedStart", "queryBedEnd")
+            .collectAsList();
+
+    // query from bed file line 184134 (0-indexed line numbers)
+    // 1	10600	540400	15_Quies	0	.	10600	540400	255,255,255
+
+    // NOTE: queryBedEnd returns the half-open value from the bed file,
+    //       not the inclusive value used by tiledb-vcf
+    int expectedBedStart = 10600; // 0-indexed
+    int expectedBedEnd = 540400; // half-open
+
+    for (int i = 0; i < rows.size(); i++) {
+      System.out.println(
+          String.format(
+              "*** %s, %s, pos=%d-%d, query=%d-%d",
+              rows.get(i).getString(0),
+              rows.get(i).getString(1),
+              rows.get(i).getInt(2),
+              rows.get(i).getInt(3),
+              rows.get(i).getInt(4),
+              rows.get(i).getInt(5)));
+      Assert.assertEquals(expectedBedStart, rows.get(i).getInt(4));
+      Assert.assertEquals(expectedBedEnd, rows.get(i).getInt(5));
+    }
+  }
+
+  @Test
+  public void testNewPartitionWithBedArrayVsBedFile() {
+    int rangePartitions = 32;
+    int samplePartitions = 2;
+    Dataset<Row> dfRead =
+        session()
+            .read()
+            .format("io.tiledb.vcf")
+            .option("uri", testSampleGroupURI("ingested_2samples", "v4"))
+            .option("bedfile", testLargeBEDFile())
+            .option("new_partition_method", true)
+            .option("range_partitions", rangePartitions)
+            .option("sample_partitions", samplePartitions)
+            .option("tiledb.vcf.log_level", "TRACE")
+            .load();
+
+    List<Row> rows =
+        dfRead
+            .select("sampleName", "contig", "posStart", "posEnd", "queryBedStart", "queryBedEnd")
+            .orderBy("contig")
+            .collectAsList();
+
+    Dataset<Row> dfRead2 =
+        session()
+            .read()
+            .format("io.tiledb.vcf")
+            .option("uri", testSampleGroupURI("ingested_2samples", "v4"))
+            .option("bed_array", testLargeBEDArray())
+            .option("new_partition_method", true)
+            .option("range_partitions", rangePartitions)
+            .option("sample_partitions", samplePartitions)
+            .option("tiledb.vcf.log_level", "TRACE")
+            .load();
+
+    List<Row> rows2 =
+        dfRead2
+            .select("sampleName", "contig", "posStart", "posEnd", "queryBedStart", "queryBedEnd")
+            .orderBy("contig")
+            .collectAsList();
+
+    Assert.assertEquals(rows, rows2);
+  }
+
   @Test
   public void testNewPartition() {
     int rangePartitions = 32;
@@ -521,6 +618,20 @@ public void testBedFile() {
     Assert.assertEquals(10, rows.size());
   }
 
+  @Test
+  public void testBedArray() {
+    Dataset<Row> dfRead =
+        session()
+            .read()
+            .format("io.tiledb.vcf")
+            .option("uri", testSampleGroupURI("ingested_2samples"))
+            .option("samplefile", testSampleFile())
+            .option("bed_array", testSimpleBEDArray())
+            .load();
+    List<Row> rows = dfRead.select("sampleName").collectAsList();
+    Assert.assertEquals(10, rows.size());
+  }
+
   @Test
   public void testSchemaShowTopN() {
     Dataset<Row> dfRead = testSampleDataset();
diff --git a/apis/spark3/build.gradle b/apis/spark3/build.gradle
index 2a535d2a7..dc5800dc4 100644
--- a/apis/spark3/build.gradle
+++ b/apis/spark3/build.gradle
@@ -53,6 +53,7 @@ repositories {
 dependencies {
     compileOnly 'org.apache.spark:spark-sql_2.12:3.2.0'
     compileOnly 'org.apache.spark:spark-core_2.12:3.2.0'
+    implementation 'io.tiledb:tiledb-java:0.24.0'
     compile group: 'io.tiledb', name: 'tiledb-vcf-java', version: version
     compile 'com.amazonaws:aws-java-sdk:1.11.650'
 
diff --git a/apis/spark3/src/main/java/io/tiledb/vcf/VCFBatch.java b/apis/spark3/src/main/java/io/tiledb/vcf/VCFBatch.java
index 94a3aa7fa..136c2f307 100644
--- a/apis/spark3/src/main/java/io/tiledb/vcf/VCFBatch.java
+++ b/apis/spark3/src/main/java/io/tiledb/vcf/VCFBatch.java
@@ -2,10 +2,12 @@
 
 import static io.tiledb.vcf.VCFScanBuilder.pushedSampleNames;
 
+import io.tiledb.java.api.*;
 import io.tiledb.libvcfnative.VCFBedFile;
 import io.tiledb.libvcfnative.VCFReader;
 import io.tiledb.util.CredentialProviderUtils;
 import java.net.URI;
+import java.util.*;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -158,7 +160,19 @@ public InputPartition[] planInputPartitions() {
     // Create Spark input partitions
     List<List<String>> regions = null;
     if (options.getNewPartitionMethod().orElse(false)) {
-      regions = computeRegionPartitionsFromBedFile(numRangePartitions);
+
+      // Compute regions from bed array or bed file
+      Optional<URI> bedArrayURI = options.getBedArrayURI();
+      Optional<URI> bedURI = options.getBedURI();
+      if (bedArrayURI.isPresent()) {
+        regions = computeRegionPartitionsFromBedArray(numRangePartitions, bedArrayURI.get());
+      } else if (bedURI.isPresent()) {
+        regions = computeRegionPartitionsFromBedFile(numRangePartitions);
+      } else {
+        throw new RuntimeException(
+            "Can't use new_partition_method without setting bed_file or bed_array");
+      }
+
       numRangePartitions = regions.size();
       ranges_end = regions.size();
       log.info("New partition method has yielded " + numRangePartitions + " range partitions");
@@ -192,11 +206,95 @@ public InputPartition[] planInputPartitions() {
     return partitionsArray;
   }
 
+  List<List<String>> computeRegionPartitionsFromBedArray(
+      int desiredNumRangePartitions, URI arrayURI) {
+
+    // Read bed array
+
+    try {
+      Map<String, List<String>> mapOfRegions = new HashMap<>();
+      int counter = 0;
+
+      Context ctx = new Context();
+      Array bedArray = new Array(ctx, arrayURI.toString(), QueryType.TILEDB_READ);
+
+      String CONTIG = "alias contig";
+      String START = "alias start";
+      String END = "alias end";
+
+      String[] keys = new String[] {CONTIG, START, END};
+
+      NativeArray contigAliasNA = bedArray.getMetadata(CONTIG, Datatype.TILEDB_STRING_ASCII);
+      NativeArray startAliasNA = bedArray.getMetadata(START, Datatype.TILEDB_STRING_ASCII);
+      NativeArray endAliasNA = bedArray.getMetadata(END, Datatype.TILEDB_STRING_ASCII);
+
+      String contigAlias = new String((byte[]) contigAliasNA.toJavaArray());
+      String startAlias = new String((byte[]) startAliasNA.toJavaArray());
+      String endAlias = new String((byte[]) endAliasNA.toJavaArray());
+
+      Query query = new Query(bedArray);
+      query.setLayout(Layout.TILEDB_UNORDERED);
+
+      Pair<Long, Long> estSize = query.getEstResultSizeVar(ctx, contigAlias);
+
+      // todo unsafe casting needs to be addressed in the java api
+      // Prepare buffers
+      query.setDataBuffer(
+          contigAlias,
+          new NativeArray(ctx, estSize.getSecond().intValue(), Datatype.TILEDB_STRING_ASCII));
+      query.setOffsetsBuffer(
+          contigAlias, new NativeArray(ctx, estSize.getFirst().intValue(), Datatype.TILEDB_UINT64));
+      query.setDataBuffer(
+          startAlias, new NativeArray(ctx, estSize.getFirst().intValue(), Datatype.TILEDB_UINT64));
+      query.setDataBuffer(
+          endAlias, new NativeArray(ctx, estSize.getFirst().intValue(), Datatype.TILEDB_UINT64));
+
+      do {
+        query.submit();
+        // get buffers
+        long[] contigOffsets = (long[]) query.getVarBuffer(contigAlias);
+        byte[] contigData = (byte[]) query.getBuffer(contigAlias);
+
+        String[] contigs = io.tiledb.java.api.Util.bytesToStrings(contigOffsets, contigData);
+        long[] start = (long[]) query.getBuffer(startAlias);
+        long[] end = (long[]) query.getBuffer(endAlias);
+
+        if (!(contigs.length == start.length && start.length == end.length)) {
+          throw new RuntimeException("There was an error reading the bed array");
+        }
+
+        // Put regions in map
+        for (int i = 0; i < contigs.length; i++) {
+          String shortContig = contigs[i].replace("chr", "");
+          String region = shortContig + ":" + start[i] + "-" + end[i] + ":" + counter;
+          counter++;
+
+          // Check if the key exists in the map
+          if (mapOfRegions.containsKey(shortContig)) {
+            // If the key exists, append the region string to the existing list
+            mapOfRegions.get(shortContig).add(region);
+          } else {
+            // If the key doesn't exist, create a new list with the region string
+            List<String> newList = new ArrayList<>();
+            newList.add(region);
+            mapOfRegions.put(shortContig, newList);
+          }
+        }
+      } while (query.getQueryStatus() == QueryStatus.TILEDB_INCOMPLETE);
+
+      List<List<String>> res = new LinkedList<>(mapOfRegions.values());
+
+      sortRegions(res, desiredNumRangePartitions);
+
+      return res;
+
+    } catch (TileDBError err) {
+      throw new RuntimeException(err);
+    }
+  }
+
   List<List<String>> computeRegionPartitionsFromBedFile(int desiredNumRangePartitions) {
     Optional<URI> bedURI = options.getBedURI();
-    if (!bedURI.isPresent()) {
-      throw new RuntimeException("Can't use new_partition_method without setting bed_file");
-    }
 
     log.info("Init VCFReader for partition calculation");
     String uriString = options.getDatasetURI().get().toString();
@@ -217,16 +315,22 @@ List<List<String>> computeRegionPartitionsFromBedFile(int desiredNumRangePartiti
 
     Map<String, List<String>> mapOfRegions = bedFile.getContigRegionStrings();
     List<List<String>> res = new LinkedList<>(mapOfRegions.values());
+    sortRegions(res, desiredNumRangePartitions);
+
+    bedFile.close();
+    vcfReader.close();
 
+    return res;
+  }
+
+  private void sortRegions(List<List<String>> res, int desiredNumRangePartitions) {
     // Sort the region list by size of regions in contig, largest first
     res.sort(Comparator.comparingInt(List<String>::size).reversed());
 
-    // Keep splitting the larges region lists until we have the desired minimum number of range
+    // Keep splitting the largest region lists until we have the desired minimum number of range
     // Partitions, we stop if the large region has a size of 10 or less
     while (res.size() < desiredNumRangePartitions && res.get(0).size() >= 10) {
-
       List<String> top = res.remove(0);
-
       List<String> first = new LinkedList<>(top.subList(0, top.size() / 2));
       List<String> second = new LinkedList<>(top.subList(top.size() / 2, top.size()));
       res.add(first);
@@ -236,11 +340,6 @@ List<List<String>> computeRegionPartitionsFromBedFile(int desiredNumRangePartiti
       res.sort(Comparator.comparingInt(List::size));
       Collections.reverse(res);
     }
-
-    bedFile.close();
-    vcfReader.close();
-
-    return res;
   }
 
   @Override
diff --git a/apis/spark3/src/main/java/io/tiledb/vcf/VCFDataSourceOptions.java b/apis/spark3/src/main/java/io/tiledb/vcf/VCFDataSourceOptions.java
index 55774f5bb..5e4d77456 100644
--- a/apis/spark3/src/main/java/io/tiledb/vcf/VCFDataSourceOptions.java
+++ b/apis/spark3/src/main/java/io/tiledb/vcf/VCFDataSourceOptions.java
@@ -75,6 +75,14 @@ public Optional<URI> getBedURI() {
     return Optional.empty();
   }
 
+  /** @return Optional uri of BED array */
+  public Optional<URI> getBedArrayURI() {
+    if (options.containsKey("bed_array")) {
+      return Optional.of(URI.create(options.get("bed_array")));
+    }
+    return Optional.empty();
+  }
+
   /** @return Optional uri of SampleFile file */
   public Optional<URI> getSampleURI() {
     if (options.containsKey("samplefile")) {
diff --git a/apis/spark3/src/main/java/io/tiledb/vcf/VCFPartitionReader.java b/apis/spark3/src/main/java/io/tiledb/vcf/VCFPartitionReader.java
index b63b5a66e..a465c3f69 100644
--- a/apis/spark3/src/main/java/io/tiledb/vcf/VCFPartitionReader.java
+++ b/apis/spark3/src/main/java/io/tiledb/vcf/VCFPartitionReader.java
@@ -305,6 +305,12 @@ private void initVCFReader() {
       if (bedURI.isPresent()) {
         vcfReader.setBedFile(bedURI.get().toString());
       }
+
+      // Set BED array
+      Optional<URI> bedArrayURI = options.getBedArrayURI();
+      if (bedArrayURI.isPresent()) {
+        vcfReader.setBedFile(bedArrayURI.get().toString());
+      }
     } else {
       if (rangePartitionInfo.getRegions().isEmpty()) {
         throw new RuntimeException(
diff --git a/apis/spark3/src/test/java/io/tiledb/vcf/VCFDataSourceOptionsTest.java b/apis/spark3/src/test/java/io/tiledb/vcf/VCFDataSourceOptionsTest.java
index 474bc71df..7e4878fd0 100644
--- a/apis/spark3/src/test/java/io/tiledb/vcf/VCFDataSourceOptionsTest.java
+++ b/apis/spark3/src/test/java/io/tiledb/vcf/VCFDataSourceOptionsTest.java
@@ -99,12 +99,28 @@ public void testBedURIOption() {
     Assert.assertEquals(expectedURI, options.getBedURI().get());
   }
 
+  @Test
+  public void testBedArrayURIOption() {
+    URI expectedURI = URI.create("s3://foo/bar");
+    HashMap<String, String> optionMap = new HashMap<>();
+    optionMap.put("bed_array", expectedURI.toString());
+    VCFDataSourceOptions options = new VCFDataSourceOptions(new DataSourceOptions(optionMap));
+    Assert.assertTrue(options.getBedArrayURI().isPresent());
+    Assert.assertEquals(expectedURI, options.getBedArrayURI().get());
+  }
+
   @Test
   public void testSampleURIOptionMissing() {
     VCFDataSourceOptions options = new VCFDataSourceOptions(new DataSourceOptions(new HashMap<>()));
     Assert.assertFalse(options.getBedURI().isPresent());
   }
 
+  @Test
+  public void testBedArrayURIOptionMissing() {
+    VCFDataSourceOptions options = new VCFDataSourceOptions(new DataSourceOptions(new HashMap<>()));
+    Assert.assertFalse(options.getBedArrayURI().isPresent());
+  }
+
   @Test
   public void testSampleURIOption() {
     URI expectedURI = URI.create("s3://foo/bar");
diff --git a/apis/spark3/src/test/java/io/tiledb/vcf/VCFDatasourceTest.java b/apis/spark3/src/test/java/io/tiledb/vcf/VCFDatasourceTest.java
index 406c28865..542909a1a 100644
--- a/apis/spark3/src/test/java/io/tiledb/vcf/VCFDatasourceTest.java
+++ b/apis/spark3/src/test/java/io/tiledb/vcf/VCFDatasourceTest.java
@@ -25,7 +25,7 @@
 public class VCFDatasourceTest extends SharedJavaSparkSession {
 
   private String testSampleGroupURI(String sampleGroupName) {
-    Path arraysPath = Paths.get("src", "test", "resources", "arrays", "v3", sampleGroupName);
+    Path arraysPath = Paths.get("src", "test", "resources", "arrays", "v4", sampleGroupName);
     return "file://".concat(arraysPath.toAbsolutePath().toString());
   }
 
@@ -34,6 +34,16 @@ private String testSampleGroupURI(String sampleGroupName, String version) {
     return "file://".concat(arraysPath.toAbsolutePath().toString());
   }
 
+  private String testSimpleBEDArray() {
+    Path arrayPath = Paths.get("src", "test", "resources", "arrays", "bed_array");
+    return "file://".concat(arrayPath.toAbsolutePath().toString());
+  }
+
+  private String testLargeBEDArray() {
+    Path arrayPath = Paths.get("src", "test", "resources", "arrays", "largebedarray");
+    return "file://".concat(arrayPath.toAbsolutePath().toString());
+  }
+
   private String testSimpleBEDFile() {
     Path path = Paths.get("src", "test", "resources", "simple.bed");
     return "file://".concat(path.toAbsolutePath().toString());
@@ -507,6 +517,93 @@ public void testNewPartition() {
     }
   }
 
+  @Test
+  public void testNewPartitionWithBedArray() {
+    int rangePartitions = 32;
+    int samplePartitions = 2;
+    Dataset<Row> dfRead =
+        session()
+            .read()
+            .format("io.tiledb.vcf")
+            .option("uri", testSampleGroupURI("ingested_2samples", "v4"))
+            .option("bed_array", testLargeBEDArray())
+            .option("new_partition_method", true)
+            .option("range_partitions", rangePartitions)
+            .option("sample_partitions", samplePartitions)
+            .option("tiledb.vcf.log_level", "TRACE")
+            .load();
+
+    List<Row> rows =
+        dfRead
+            .select("sampleName", "contig", "posStart", "posEnd", "queryBedStart", "queryBedEnd")
+            .collectAsList();
+
+    // query from bed file line 184134 (0-indexed line numbers)
+    // 1	10600	540400	15_Quies	0	.	10600	540400	255,255,255
+
+    // NOTE: queryBedEnd returns the half-open value from the bed file,
+    //       not the inclusive value used by tiledb-vcf
+    int expectedBedStart = 10600; // 0-indexed
+    int expectedBedEnd = 540400; // half-open
+
+    for (int i = 0; i < rows.size(); i++) {
+      System.out.println(
+          String.format(
+              "*** %s, %s, pos=%d-%d, query=%d-%d",
+              rows.get(i).getString(0),
+              rows.get(i).getString(1),
+              rows.get(i).getInt(2),
+              rows.get(i).getInt(3),
+              rows.get(i).getInt(4),
+              rows.get(i).getInt(5)));
+      Assert.assertEquals(expectedBedStart, rows.get(i).getInt(4));
+      Assert.assertEquals(expectedBedEnd, rows.get(i).getInt(5));
+    }
+  }
+
+  @Test
+  public void testNewPartitionWithBedArrayVsBedFile() {
+    int rangePartitions = 32;
+    int samplePartitions = 2;
+    Dataset<Row> dfRead =
+        session()
+            .read()
+            .format("io.tiledb.vcf")
+            .option("uri", testSampleGroupURI("ingested_2samples", "v4"))
+            .option("bedfile", testLargeBEDFile())
+            .option("new_partition_method", true)
+            .option("range_partitions", rangePartitions)
+            .option("sample_partitions", samplePartitions)
+            .option("tiledb.vcf.log_level", "TRACE")
+            .load();
+
+    List<Row> rows =
+        dfRead
+            .select("sampleName", "contig", "posStart", "posEnd", "queryBedStart", "queryBedEnd")
+            .orderBy("contig")
+            .collectAsList();
+
+    Dataset<Row> dfRead2 =
+        session()
+            .read()
+            .format("io.tiledb.vcf")
+            .option("uri", testSampleGroupURI("ingested_2samples", "v4"))
+            .option("bed_array", testLargeBEDArray())
+            .option("new_partition_method", true)
+            .option("range_partitions", rangePartitions)
+            .option("sample_partitions", samplePartitions)
+            .option("tiledb.vcf.log_level", "TRACE")
+            .load();
+
+    List<Row> rows2 =
+        dfRead2
+            .select("sampleName", "contig", "posStart", "posEnd", "queryBedStart", "queryBedEnd")
+            .orderBy("contig")
+            .collectAsList();
+
+    Assert.assertEquals(rows, rows2);
+  }
+
   @Test
   public void testBedFile() {
     Dataset<Row> dfRead =
@@ -521,6 +618,20 @@ public void testBedFile() {
     Assert.assertEquals(10, rows.size());
   }
 
+  @Test
+  public void testBedArray() {
+    Dataset<Row> dfRead =
+        session()
+            .read()
+            .format("io.tiledb.vcf")
+            .option("uri", testSampleGroupURI("ingested_2samples"))
+            .option("samplefile", testSampleFile())
+            .option("bed_array", testSimpleBEDArray())
+            .load();
+    List<Row> rows = dfRead.select("sampleName").collectAsList();
+    Assert.assertEquals(10, rows.size());
+  }
+
   @Test
   public void testSchemaShowTopN() {
     Dataset<Row> dfRead = testSampleDataset();
diff --git a/libtiledbvcf/test/inputs/arrays/bed_array/__commits/__1704394421914_1704394421914_0c4b280ae02a4fcb84d4eaca629cba3e_20.wrt b/libtiledbvcf/test/inputs/arrays/bed_array/__commits/__1704394421914_1704394421914_0c4b280ae02a4fcb84d4eaca629cba3e_20.wrt
new file mode 100644
index 000000000..e69de29bb
diff --git a/libtiledbvcf/test/inputs/arrays/bed_array/__fragments/__1704394421914_1704394421914_0c4b280ae02a4fcb84d4eaca629cba3e_20/__fragment_metadata.tdb b/libtiledbvcf/test/inputs/arrays/bed_array/__fragments/__1704394421914_1704394421914_0c4b280ae02a4fcb84d4eaca629cba3e_20/__fragment_metadata.tdb
new file mode 100644
index 000000000..0dd0bff86
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/bed_array/__fragments/__1704394421914_1704394421914_0c4b280ae02a4fcb84d4eaca629cba3e_20/__fragment_metadata.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/bed_array/__fragments/__1704394421914_1704394421914_0c4b280ae02a4fcb84d4eaca629cba3e_20/a0.tdb b/libtiledbvcf/test/inputs/arrays/bed_array/__fragments/__1704394421914_1704394421914_0c4b280ae02a4fcb84d4eaca629cba3e_20/a0.tdb
new file mode 100644
index 000000000..37289c23f
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/bed_array/__fragments/__1704394421914_1704394421914_0c4b280ae02a4fcb84d4eaca629cba3e_20/a0.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/bed_array/__fragments/__1704394421914_1704394421914_0c4b280ae02a4fcb84d4eaca629cba3e_20/a0_var.tdb b/libtiledbvcf/test/inputs/arrays/bed_array/__fragments/__1704394421914_1704394421914_0c4b280ae02a4fcb84d4eaca629cba3e_20/a0_var.tdb
new file mode 100644
index 000000000..1961f325c
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/bed_array/__fragments/__1704394421914_1704394421914_0c4b280ae02a4fcb84d4eaca629cba3e_20/a0_var.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/bed_array/__fragments/__1704394421914_1704394421914_0c4b280ae02a4fcb84d4eaca629cba3e_20/a1.tdb b/libtiledbvcf/test/inputs/arrays/bed_array/__fragments/__1704394421914_1704394421914_0c4b280ae02a4fcb84d4eaca629cba3e_20/a1.tdb
new file mode 100644
index 000000000..cde4803ec
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/bed_array/__fragments/__1704394421914_1704394421914_0c4b280ae02a4fcb84d4eaca629cba3e_20/a1.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/bed_array/__fragments/__1704394421914_1704394421914_0c4b280ae02a4fcb84d4eaca629cba3e_20/a2.tdb b/libtiledbvcf/test/inputs/arrays/bed_array/__fragments/__1704394421914_1704394421914_0c4b280ae02a4fcb84d4eaca629cba3e_20/a2.tdb
new file mode 100644
index 000000000..7ecbf615d
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/bed_array/__fragments/__1704394421914_1704394421914_0c4b280ae02a4fcb84d4eaca629cba3e_20/a2.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/bed_array/__fragments/__1704394421914_1704394421914_0c4b280ae02a4fcb84d4eaca629cba3e_20/d0.tdb b/libtiledbvcf/test/inputs/arrays/bed_array/__fragments/__1704394421914_1704394421914_0c4b280ae02a4fcb84d4eaca629cba3e_20/d0.tdb
new file mode 100644
index 000000000..37289c23f
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/bed_array/__fragments/__1704394421914_1704394421914_0c4b280ae02a4fcb84d4eaca629cba3e_20/d0.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/bed_array/__meta/__1704394421898_1704394421898_3232bb05077445b097ec812ee8dcb3c4 b/libtiledbvcf/test/inputs/arrays/bed_array/__meta/__1704394421898_1704394421898_3232bb05077445b097ec812ee8dcb3c4
new file mode 100644
index 000000000..15562847a
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/bed_array/__meta/__1704394421898_1704394421898_3232bb05077445b097ec812ee8dcb3c4 differ
diff --git a/libtiledbvcf/test/inputs/arrays/bed_array/__meta/__1704394441555_1704394441555_14afe6300cc14af0ab7e728ccc7b1353 b/libtiledbvcf/test/inputs/arrays/bed_array/__meta/__1704394441555_1704394441555_14afe6300cc14af0ab7e728ccc7b1353
new file mode 100644
index 000000000..76f3345be
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/bed_array/__meta/__1704394441555_1704394441555_14afe6300cc14af0ab7e728ccc7b1353 differ
diff --git a/libtiledbvcf/test/inputs/arrays/bed_array/__schema/__1704394421897_1704394421897_52be1c228f394206a626570e261005e8 b/libtiledbvcf/test/inputs/arrays/bed_array/__schema/__1704394421897_1704394421897_52be1c228f394206a626570e261005e8
new file mode 100644
index 000000000..454e16663
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/bed_array/__schema/__1704394421897_1704394421897_52be1c228f394206a626570e261005e8 differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__commits/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21.wrt b/libtiledbvcf/test/inputs/arrays/largebedarray/__commits/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21.wrt
new file mode 100644
index 000000000..e69de29bb
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__commits/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21.wrt b/libtiledbvcf/test/inputs/arrays/largebedarray/__commits/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21.wrt
new file mode 100644
index 000000000..e69de29bb
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/__fragment_metadata.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/__fragment_metadata.tdb
new file mode 100644
index 000000000..f6a257510
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/__fragment_metadata.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a0.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a0.tdb
new file mode 100644
index 000000000..22870405f
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a0.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a1.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a1.tdb
new file mode 100644
index 000000000..6933981a4
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a1.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a1_var.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a1_var.tdb
new file mode 100644
index 000000000..a26558a7e
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a1_var.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a2.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a2.tdb
new file mode 100644
index 000000000..72cda8c4a
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a2.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a3.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a3.tdb
new file mode 100644
index 000000000..e028bd403
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a3.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a3_var.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a3_var.tdb
new file mode 100644
index 000000000..3d90219ed
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a3_var.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a4.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a4.tdb
new file mode 100644
index 000000000..818070921
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a4.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a5.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a5.tdb
new file mode 100644
index 000000000..4e1f1c1e7
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a5.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a6.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a6.tdb
new file mode 100644
index 000000000..c3fc7cfb4
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a6.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a6_var.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a6_var.tdb
new file mode 100644
index 000000000..d0d5cc7ab
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/a6_var.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/d0.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/d0.tdb
new file mode 100644
index 000000000..33082fa5b
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/d0.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/d0_var.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/d0_var.tdb
new file mode 100644
index 000000000..edb788598
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/d0_var.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/d1.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/d1.tdb
new file mode 100644
index 000000000..7dac6000b
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/d1.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/d1_var.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/d1_var.tdb
new file mode 100644
index 000000000..fac8b22e9
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/d1_var.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/d2.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/d2.tdb
new file mode 100644
index 000000000..818070921
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813523990_1706813523990_40565d50e72b402105d07b7d1e8de386_21/d2.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/__fragment_metadata.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/__fragment_metadata.tdb
new file mode 100644
index 000000000..c4225e438
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/__fragment_metadata.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a0.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a0.tdb
new file mode 100644
index 000000000..577fde5ca
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a0.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a1.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a1.tdb
new file mode 100644
index 000000000..4d42bb586
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a1.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a1_var.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a1_var.tdb
new file mode 100644
index 000000000..9e1b31908
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a1_var.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a2.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a2.tdb
new file mode 100644
index 000000000..41ef1ca09
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a2.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a3.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a3.tdb
new file mode 100644
index 000000000..bcc4faa56
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a3.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a3_var.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a3_var.tdb
new file mode 100644
index 000000000..2b36c5944
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a3_var.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a4.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a4.tdb
new file mode 100644
index 000000000..73ba5a1c4
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a4.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a5.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a5.tdb
new file mode 100644
index 000000000..b36d90faa
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a5.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a6.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a6.tdb
new file mode 100644
index 000000000..95cd0f28e
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a6.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a6_var.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a6_var.tdb
new file mode 100644
index 000000000..8cafb08b0
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/a6_var.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/d0.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/d0.tdb
new file mode 100644
index 000000000..781db0655
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/d0.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/d0_var.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/d0_var.tdb
new file mode 100644
index 000000000..fa86c6564
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/d0_var.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/d1.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/d1.tdb
new file mode 100644
index 000000000..ea3834d4b
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/d1.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/d1_var.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/d1_var.tdb
new file mode 100644
index 000000000..82b9265cc
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/d1_var.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/d2.tdb b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/d2.tdb
new file mode 100644
index 000000000..73ba5a1c4
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__fragments/__1706813524799_1706813524799_4631aede2e67ffd18f9fccba4388a61f_21/d2.tdb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__meta/__1706813523981_1706813523981_04eef2b4b5d860cc67a7aabe10d172d6 b/libtiledbvcf/test/inputs/arrays/largebedarray/__meta/__1706813523981_1706813523981_04eef2b4b5d860cc67a7aabe10d172d6
new file mode 100644
index 000000000..6c6d443db
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__meta/__1706813523981_1706813523981_04eef2b4b5d860cc67a7aabe10d172d6 differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__meta/__1706813524020_1706813524020_8548dea130821acc583c502c832e0a3a b/libtiledbvcf/test/inputs/arrays/largebedarray/__meta/__1706813524020_1706813524020_8548dea130821acc583c502c832e0a3a
new file mode 100644
index 000000000..6685dad15
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__meta/__1706813524020_1706813524020_8548dea130821acc583c502c832e0a3a differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__meta/__1706813525041_1706813525041_23d9a035f5e095708b3a26b7aa4bcecb b/libtiledbvcf/test/inputs/arrays/largebedarray/__meta/__1706813525041_1706813525041_23d9a035f5e095708b3a26b7aa4bcecb
new file mode 100644
index 000000000..6685dad15
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__meta/__1706813525041_1706813525041_23d9a035f5e095708b3a26b7aa4bcecb differ
diff --git a/libtiledbvcf/test/inputs/arrays/largebedarray/__schema/__1706813523980_1706813523980_b5ee8cb6abe457f8f258d22d4db91392 b/libtiledbvcf/test/inputs/arrays/largebedarray/__schema/__1706813523980_1706813523980_b5ee8cb6abe457f8f258d22d4db91392
new file mode 100644
index 000000000..d9ede16a1
Binary files /dev/null and b/libtiledbvcf/test/inputs/arrays/largebedarray/__schema/__1706813523980_1706813523980_b5ee8cb6abe457f8f258d22d4db91392 differ