add support for the variant stats API

Author: DimitrisStaratzis

apis/java/src/main/java/io/tiledb/libvcfnative/LibVCFNative.c

@@ -6,6 +6,32 @@
 #include "LibVCFNative.h"
 #include "tiledbvcf/tiledbvcf.h"
 
+static int set_out_params_size_t(
+    JNIEnv* env, size_t value1, size_t value2, jlongArray valuesOut) {
+  jlong* c_values = (*env)->GetLongArrayElements(env, valuesOut, NULL);
+  if (c_values == NULL) {
+    return -1;
+  }
+
+  // Check that an array of length 2 was passed.
+  if ((*env)->GetArrayLength(env, valuesOut) != 2) {
+    (*env)->ReleaseLongArrayElements(env, valuesOut, c_values, 0);
+    return -1;
+  }
+
+  // Set the values in the result array.
+  c_values[0] = (jlong)value1;
+  c_values[1] = (jlong)value2;
+
+  // Set the modified array back to the Java array.
+  (*env)->SetLongArrayRegion(env, valuesOut, 0, 2, c_values);
+
+  // Release the array elements.
+  (*env)->ReleaseLongArrayElements(env, valuesOut, c_values, 0);
+
+  return TILEDB_VCF_OK;
+}
+
 static int set_out_param_int32(JNIEnv* env, int32_t value, jintArray valueOut) {
   jint* c_value = (*env)->GetIntArrayElements(env, valueOut, NULL);
   if (c_value == NULL) {
@@ -1083,3 +1109,54 @@ Java_io_tiledb_libvcfnative_LibVCFNative_tiledb_1vcf_1bed_1file_1get_1contig_1re
 
   return rc;
 }
+
+JNIEXPORT jint JNICALL
+Java_io_tiledb_libvcfnative_LibVCFNative_tiledb_1vcf_1reader_1get_1variant_1stats_1buffer_1sizes(
+    JNIEnv* env, jclass self, jlong readerPtr, jlongArray resultsOut) {
+  (void)self;
+  tiledb_vcf_reader_t* reader = (tiledb_vcf_reader_t*)readerPtr;
+  if (reader == 0) {
+    return TILEDB_VCF_ERR;
+  }
+
+  size_t num_rows;
+  size_t allele_size;
+  int32_t rc = tiledb_vcf_reader_get_variant_stats_buffer_sizes(
+      reader, &num_rows, &allele_size);
+  if (rc == TILEDB_VCF_OK) {
+    return set_out_params_size_t(
+        env, (size_t)num_rows, (size_t)allele_size, resultsOut);
+  }
+
+  return rc;
+}
+
+JNIEXPORT jint JNICALL
+Java_io_tiledb_libvcfnative_LibVCFNative_tiledb_1vcf_1reader_1prepare_1variant_1stats(
+    JNIEnv* env, jclass self, jlong readerPtr) {
+  (void)self;
+
+  tiledb_vcf_reader_t* reader = (tiledb_vcf_reader_t*)readerPtr;
+
+  if (reader == 0) {
+    return TILEDB_VCF_ERR;
+  }
+
+  int32_t rc = tiledb_vcf_reader_prepare_variant_stats(reader);
+
+  return rc;
+}
+
+JNIEXPORT jint JNICALL
+Java_io_tiledb_libvcfnative_LibVCFNative_tiledb_1vcf_1reader_1read_1from_1variant_1stats(
+    JNIEnv* env,
+    jclass self,
+    jlong readerPtr,
+    jlongArray,
+    jstring,
+    jlongArray,
+    jintArray,
+    jintArray,
+    jfloatArray) {
+  // todo
+}

apis/java/src/main/java/io/tiledb/libvcfnative/LibVCFNative.h

@@ -171,4 +171,18 @@ public static final native int tiledb_vcf_bed_file_get_contig_region(
       byte[] region_contig,
       long[] region_start,
       long[] region_end);
+
+  public static final native int tiledb_vcf_reader_get_variant_stats_buffer_sizes(
+      long readerPtr, long[] results);
+
+  public static final native int tiledb_vcf_reader_prepare_variant_stats(long readerPtr);
+
+  public static final native int tiledb_vcf_reader_read_from_variant_stats(
+      long readerPtr,
+      long[] pos,
+      byte[] allele,
+      long[] allele_offsets,
+      int[] ac,
+      int[] an,
+      float[] af);
 }

apis/java/src/main/java/io/tiledb/libvcfnative/LibVCFNative.java

@@ -1,20 +1,30 @@
-The LibVCFNative bindings are produced with `javah`.
+# The LibVCFNative bindings are produced with `javah`.
 
-To build the binding you must first compile the java file to a class file:
+## To build the LibVCFNative header run:
+```
+javac -cp .:commons-io-2.14.0.jar  *.java -h dstara  
+```
+
+This will generate io_tiledb_libvcfnative_LibVCFNative.h as a separate file.
 
+## Format the new header file:
 ```
-cd api/spark/src/main/java/io/tiledb/libvcfnative
-javac LibVCFNative.java
+clang-format -i io_tiledb_libvcfnative_LibVCFNative.h
 ```
 
-Next you can use `javah` to rebuild the LibVCFNative header:
+## Replace the old header file with the new:
 ```
-# Navigate back to top level spark src directory
-cd ../../../
-javah -v -cp $PWD -o io/tiledb/libvcfnative/LibVCFNative.h io.tiledb.libvcfnative.LibVCFNative
+mv io_tiledb_libvcfnative_LibVCFNative.h LibVCFNative.h 
 ```
 
-It is safe to delete the class file now:
+## It is safe to delete the class files now:
 ```
-rm io/tiledb/libvcfnative/LibVCFNative.class
+rm io/tiledb/libvcfnative/*.class
 ```
+
+
+
+
+
+
+

apis/java/src/main/java/io/tiledb/libvcfnative/README.md

@@ -584,6 +584,25 @@ public String stats() {
     return stats;
   }
 
+  public VCFReader prepareVariantStats() {
+    int rc = LibVCFNative.tiledb_vcf_reader_prepare_variant_stats(this.readerPtr);
+    if (rc != 0) {
+      String msg = getLastErrorMessage();
+      throw new RuntimeException("Error preparing variant stats: " + msg);
+    }
+    return this;
+  }
+
+  public long[] getVariantStatsBufferSizes() {
+    long[] results = new long[2];
+    int rc = LibVCFNative.tiledb_vcf_reader_get_variant_stats_buffer_sizes(this.readerPtr, results);
+    if (rc != 0) {
+      String msg = getLastErrorMessage();
+      throw new RuntimeException("Error getting variant stats buffer sizes: " + msg);
+    }
+    return results;
+  }
+
   public String version() {
     return LibVCFNative.tiledb_vcf_version();
   }

apis/java/src/main/java/io/tiledb/libvcfnative/VCFReader.java

@@ -0,0 +1,4 @@
+javac - cp. : commons - io - 2.14.0.jar *.java - h.;
+clang - format - i io_tiledb_libvcfnative_LibVCFNative.h;
+mv io_tiledb_libvcfnative_LibVCFNative.h LibVCFNative.h;
+rm*.class;

apis/java/src/main/java/io/tiledb/libvcfnative/generateJNI.sh

@@ -378,6 +378,20 @@ public void testStats() throws IOException {
     Assert.assertNotNull(reader.stats());
   }
 
+  @Test
+  public void testVariantStatsPrepare() throws IOException {
+    VCFReader reader = getVFCReader(Optional.empty(), Optional.of(constructBEDURI()));
+    reader.prepareVariantStats();
+  }
+
+  @Test
+  public void testVariantStatsBufferSizes() throws IOException {
+    VCFReader reader = getVFCReader(Optional.empty(), Optional.of(constructBEDURI()));
+    reader.prepareVariantStats();
+    long[] a = reader.getVariantStatsBufferSizes();
+    System.out.println(a[0] + " ---->>>>>>>> " + a[1]);
+  }
+
   /**
    * * Checks that the reader attribute details are initialized in constructor
    *