GATK ReadsPathDataSource类介绍

GATK（Genome Analysis Toolkit）是一个广泛使用的基因组分析工具包，它的核心库之一是htsjdk，用于处理高通量测序数据。在GATK中，ReadsPathDataSource类是负责管理和提供读取高通量测序数据文件（如BAM、SAM、CRAM）的类。

常见使用场景

• 数据加载：在GATK的基因组分析工具链中，ReadsPathDataSource 经常被用来从指定路径加载测序数据。
• 数据过滤：通过 ReadsPathDataSource，可以方便地在加载数据的同时进行预过滤，如按特定标准选择感兴趣的序列记录。
• 多文件支持：支持同时从多个文件中加载数据，使得分析多个样本的数据更加便捷。

类关系

ReadsPathDataSource源码

package org.broadinstitute.hellbender.engine;import com.google.common.annotations.VisibleForTesting;
import htsjdk.samtools.MergingSamRecordIterator;
import htsjdk.samtools.SAMException;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMSequenceDictionary;
import htsjdk.samtools.SamFileHeaderMerger;
import htsjdk.samtools.SamInputResource;
import htsjdk.samtools.SamReader;
import htsjdk.samtools.SamReaderFactory;
import htsjdk.samtools.util.CloseableIterator;
import htsjdk.samtools.util.IOUtil;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.broadinstitute.hellbender.exceptions.GATKException;
import org.broadinstitute.hellbender.exceptions.UserException;
import org.broadinstitute.hellbender.utils.IntervalUtils;
import org.broadinstitute.hellbender.utils.SimpleInterval;
import org.broadinstitute.hellbender.utils.Utils;
import org.broadinstitute.hellbender.utils.gcs.BucketUtils;
import org.broadinstitute.hellbender.utils.iterators.SAMRecordToReadIterator;
import org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator;
import org.broadinstitute.hellbender.utils.read.GATKRead;
import org.broadinstitute.hellbender.utils.read.ReadConstants;import java.io.IOException;
import java.nio.channels.SeekableByteChannel;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.function.Function;
import java.util.stream.Collectors;/*** Manages traversals and queries over sources of reads which are accessible via {@link Path}s* (for now, SAM/BAM/CRAM files only).** Two basic operations are available:** -Iteration over all reads, optionally restricted to reads that overlap a set of intervals* -Targeted queries by one interval at a time*/
public final class ReadsPathDataSource implements ReadsDataSource {private static final Logger logger = LogManager.getLogger(ReadsPathDataSource.class);/*** Mapping from SamReaders to iterators over the reads from each reader. Only one* iterator can be open from a given reader at a time (this is a restriction* in htsjdk). Iterator is set to null for a reader if no iteration is currently* active on that reader.*/private final Map<SamReader, CloseableIterator<SAMRecord>> readers;/*** Hang onto the input files so that we can print useful errors about them*/private final Map<SamReader, Path> backingPaths;/*** Only reads that overlap these intervals (and unmapped reads, if {@link #traverseUnmapped} is set) will be returned* during a full iteration. Null if iteration is unbounded.** Individual queries are unaffected by these intervals -- only traversals initiated via {@link #iterator} are affected.*/private List<SimpleInterval> intervalsForTraversal;/*** If true, restrict traversals to unmapped reads (and reads overlapping any {@link #intervalsForTraversal}, if set).* False if iteration is unbounded or bounded only by our {@link #intervalsForTraversal}.** Note that this setting covers only unmapped reads that have no position -- unmapped reads that are assigned the* position of their mates will be returned by queries overlapping that position.** Individual queries are unaffected by this setting  -- only traversals initiated via {@link #iterator} are affected.*/private boolean traverseUnmapped;/*** Used to create a merged Sam header when we're dealing with multiple readers. Null if we only have a single reader.*/private final SamFileHeaderMerger headerMerger;/*** Are indices available for all files?*/private boolean indicesAvailable;/*** Has it been closed already.*/private boolean isClosed;/*** Initialize this data source with a single SAM/BAM file and validation stringency SILENT.** @param samFile SAM/BAM file, not null.*/public ReadsPathDataSource( final Path samFile ) {this(samFile != null ? Arrays.asList(samFile) : null, (SamReaderFactory)null);}/*** Initialize this data source with multiple SAM/BAM files and validation stringency SILENT.** @param samFiles SAM/BAM files, not null.*/public ReadsPathDataSource( final List<Path> samFiles ) {this(samFiles, (SamReaderFactory)null);}/*** Initialize this data source with a single SAM/BAM file and a custom SamReaderFactory** @param samPath path to SAM/BAM file, not null.* @param customSamReaderFactory SamReaderFactory to use, if null a default factory with no reference and validation*                               stringency SILENT is used.*/public ReadsPathDataSource( final Path samPath, SamReaderFactory customSamReaderFactory ) {this(samPath != null ? Arrays.asList(samPath) : null, customSamReaderFactory);}/*** Initialize this data source with multiple SAM/BAM files and a custom SamReaderFac