ADAM APIs

import org.bdgenomics.adam.api.java.JavaADAMContext;
import org.bdgenomics.adam.rdd.ADAMContext;
import org.apache.spark.api.java.JavaSparkContext;
import htsjdk.samtools.ValidationStringency;

import org.bdgenomics.adam.rdd.read.AlignmentRecordRDD;
import org.bdgenomics.adam.rdd.contig.NucleotideContigFragmentRDD;
import org.bdgenomics.adam.rdd.fragment.FragmentRDD;
import org.bdgenomics.adam.rdd.feature.FeatureRDD;
import org.bdgenomics.adam.rdd.feature.CoverageRDD;
import org.bdgenomics.adam.rdd.variant.GenotypeRDD;
import org.bdgenomics.adam.rdd.variant.VariantRDD;
import org.bdgenomics.adam.rdd.variant.VariantContextRDD;
import org.bdgenomics.adam.util.ReferenceFile;

import org.bdgenomics.adam.api.java.*;

import org.bdgenomics.adam.api.python.DataFrameConversionWrapper;

import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.bdgenomics.adam.api.java.JavaADAMContext;
import org.bdgenomics.adam.rdd.ADAMContext;
import org.bdgenomics.adam.rdd.read.AlignmentRecordRDD;

// Create Spark context
SparkConf conf = new SparkConf().setAppName("ADAM API Example");
JavaSparkContext jsc = new JavaSparkContext(conf);

// Create ADAM context
ADAMContext ac = new ADAMContext(jsc.sc());
JavaADAMContext jac = new JavaADAMContext(ac);

// Load genomic data
AlignmentRecordRDD alignments = jac.loadAlignments("sample.bam");
System.out.println("Loaded " + alignments.jrdd().count() + " alignment records");

// Load other genomic data types
jac.loadVariants("variants.vcf");
jac.loadFeatures("annotations.bed");
jac.loadContigFragments("reference.fa");

// Main context class
class JavaADAMContext {
    JavaADAMContext(ADAMContext ac);
    JavaSparkContext getSparkContext();
    
    // Load alignment data (BAM/CRAM/SAM/FASTA/FASTQ)
    AlignmentRecordRDD loadAlignments(String pathName);
    AlignmentRecordRDD loadAlignments(String pathName, ValidationStringency stringency);
    
    // Load reference sequences
    NucleotideContigFragmentRDD loadContigFragments(String pathName);
    ReferenceFile loadReferenceFile(String pathName);
    ReferenceFile loadReferenceFile(String pathName, Long maximumLength);
    
    // Load fragments (paired-end sequencing data)
    FragmentRDD loadFragments(String pathName);
    FragmentRDD loadFragments(String pathName, ValidationStringency stringency);
    
    // Load genomic features (annotations)
    FeatureRDD loadFeatures(String pathName);
    FeatureRDD loadFeatures(String pathName, ValidationStringency stringency);
    
    // Load coverage data
    CoverageRDD loadCoverage(String pathName);
    CoverageRDD loadCoverage(String pathName, ValidationStringency stringency);
    
    // Load variant data
    GenotypeRDD loadGenotypes(String pathName);
    GenotypeRDD loadGenotypes(String pathName, ValidationStringency stringency);
    VariantRDD loadVariants(String pathName);
    VariantRDD loadVariants(String pathName, ValidationStringency stringency);
}

// Base conversion interface
interface SameTypeConversion<T, U extends GenomicRDD<T, U>> extends Function2<U, RDD<T>, U> {
    U call(U v1, RDD<T> v2);
}

// Example converter classes
class ContigsToAlignmentRecordsConverter extends Function2<NucleotideContigFragmentRDD, RDD<AlignmentRecord>, AlignmentRecordRDD>;
class AlignmentRecordsToVariantsConverter extends Function2<AlignmentRecordRDD, RDD<Variant>, VariantRDD>;
class VariantsToGenotypesConverter extends Function2<VariantRDD, RDD<Genotype>, GenotypeRDD>;

// Base dataset conversion traits
interface ToAlignmentRecordDatasetConversion<T extends Product, U extends GenomicDataset<?, T, U>> 
    extends GenomicDatasetConversion<T, U, AlignmentRecord, AlignmentRecordRDD>;

// Example dataset converter classes  
class ContigsToAlignmentRecordsDatasetConverter extends ToAlignmentRecordDatasetConversion<NucleotideContigFragment, NucleotideContigFragmentRDD>;
class VariantsToGenotypesDatasetConverter extends ToGenotypeDatasetConversion<Variant, VariantRDD>;

class DataFrameConversionWrapper implements JFunction<DataFrame, DataFrame> {
    DataFrameConversionWrapper(DataFrame newDf);
    DataFrame call(DataFrame v1);
}

// Genomic RDD wrapper types with metadata preservation
interface GenomicRDD<T, U extends GenomicRDD<T, U>> {
    RDD<T> jrdd();
    // Additional metadata methods...
}

class AlignmentRecordRDD extends GenomicRDD<AlignmentRecord, AlignmentRecordRDD> {}
class NucleotideContigFragmentRDD extends GenomicRDD<NucleotideContigFragment, NucleotideContigFragmentRDD> {}
class FragmentRDD extends GenomicRDD<Fragment, FragmentRDD> {}
class FeatureRDD extends GenomicRDD<Feature, FeatureRDD> {}
class CoverageRDD extends GenomicRDD<Coverage, CoverageRDD> {}
class GenotypeRDD extends GenomicRDD<Genotype, GenotypeRDD> {}
class VariantRDD extends GenomicRDD<Variant, VariantRDD> {}
class VariantContextRDD extends GenomicRDD<VariantContext, VariantContextRDD> {}

// HTSJDK validation strictness control
enum ValidationStringency {
    STRICT,   // Fail on any format violations
    LENIENT,  // Warn on format issues but continue processing  
    SILENT    // Ignore format violations silently
}

// Broadcastable reference sequences
class ReferenceFile {
    // Methods for efficient reference lookups across cluster
}

// Spark integration types
class JavaSparkContext {
    // Standard Spark Java API context
}

class DataFrame {
    // Spark SQL DataFrame for Python integration
}