本文整理汇总了Java中htsjdk.samtools.util.SortingCollection.Codec方法的典型用法代码示例。如果您正苦于以下问题:Java SortingCollection.Codec方法的具体用法?Java SortingCollection.Codec怎么用?Java SortingCollection.Codec使用的例子?那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类htsjdk.samtools.util.SortingCollection
的用法示例。
在下文中一共展示了SortingCollection.Codec方法的11个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的Java代码示例。
示例1: IlluminaBasecallsConverter
import htsjdk.samtools.util.SortingCollection; //导入方法依赖的package包/类
/**
* @param basecallsDir Where to read basecalls from.
* @param lane What lane to process.
* @param readStructure How to interpret each cluster.
* @param barcodeRecordWriterMap Map from barcode to CLUSTER_OUTPUT_RECORD writer. If demultiplex is false, must contain
* one writer stored with key=null.
* @param demultiplex If true, output is split by barcode, otherwise all are written to the same output stream.
* @param maxReadsInRamPerTile Configures number of reads each tile will store in RAM before spilling to disk.
* @param tmpDirs For SortingCollection spilling.
* @param numProcessors Controls number of threads. If <= 0, the number of threads allocated is
* available cores - numProcessors.
* @param forceGc Force explicit GC periodically. This is good for causing memory maps to be released.
* @param firstTile (For debugging) If non-null, start processing at this tile.
* @param tileLimit (For debugging) If non-null, process no more than this many tiles.
* @param outputRecordComparator For sorting output records within a single tile.
* @param codecPrototype For spilling output records to disk.
* @param outputRecordClass Inconveniently needed to create SortingCollections.
* @param includeNonPfReads If true, will include ALL reads (including those which do not have PF set)
* @param ignoreUnexpectedBarcodes If true, will ignore reads whose called barcode is not found in barcodeRecordWriterMap,
* otherwise will throw an exception
*/
public IlluminaBasecallsConverter(final File basecallsDir, final int lane, final ReadStructure readStructure,
final Map<String, ? extends ConvertedClusterDataWriter<CLUSTER_OUTPUT_RECORD>> barcodeRecordWriterMap,
final boolean demultiplex,
final int maxReadsInRamPerTile,
final List<File> tmpDirs,
final int numProcessors, final boolean forceGc,
final Integer firstTile, final Integer tileLimit,
final Comparator<CLUSTER_OUTPUT_RECORD> outputRecordComparator,
final SortingCollection.Codec<CLUSTER_OUTPUT_RECORD> codecPrototype,
final Class<CLUSTER_OUTPUT_RECORD> outputRecordClass,
final BclQualityEvaluationStrategy bclQualityEvaluationStrategy,
final boolean applyEamssFiltering,
final boolean includeNonPfReads,
final boolean ignoreUnexpectedBarcodes
) {
this(basecallsDir, null, lane, readStructure,
barcodeRecordWriterMap, demultiplex, maxReadsInRamPerTile,
tmpDirs, numProcessors, forceGc, firstTile, tileLimit,
outputRecordComparator, codecPrototype, outputRecordClass,
bclQualityEvaluationStrategy, applyEamssFiltering,
includeNonPfReads, ignoreUnexpectedBarcodes);
}
示例2: clone
import htsjdk.samtools.util.SortingCollection; //导入方法依赖的package包/类
@Override
public SortingCollection.Codec<SortableRecord> clone() {
try {
return (SortingCollection.Codec<SortableRecord>) super.clone();
} catch (CloneNotSupportedException e) {
throw new SortingException(e);
}
}
示例3: BasecallsConverter
import htsjdk.samtools.util.SortingCollection; //导入方法依赖的package包/类
/**
* @param barcodeRecordWriterMap Map from barcode to CLUSTER_OUTPUT_RECORD writer. If demultiplex is false, must contain
* one writer stored with key=null.
* @param demultiplex If true, output is split by barcode, otherwise all are written to the same output stream.
* @param maxReadsInRamPerTile Configures number of reads each tile will store in RAM before spilling to disk.
* @param tmpDirs For SortingCollection spilling.
* @param numProcessors Controls number of threads. If <= 0, the number of threads allocated is
* available cores - numProcessors.
* @param outputRecordComparator For sorting output records within a single tile.
* @param codecPrototype For spilling output records to disk.
* @param outputRecordClass Inconveniently needed to create SortingCollections.
* @param ignoreUnexpectedBarcodes If true, will ignore reads whose called barcode is not found in barcodeRecordWriterMap,
*/
BasecallsConverter(final Map<String, ? extends ConvertedClusterDataWriter<CLUSTER_OUTPUT_RECORD>> barcodeRecordWriterMap,
final int maxReadsInRamPerTile,
final List<File> tmpDirs,
final SortingCollection.Codec<CLUSTER_OUTPUT_RECORD> codecPrototype,
final boolean ignoreUnexpectedBarcodes,
final boolean demultiplex,
final Comparator<CLUSTER_OUTPUT_RECORD> outputRecordComparator,
final BclQualityEvaluationStrategy bclQualityEvaluationStrategy,
final Class<CLUSTER_OUTPUT_RECORD> outputRecordClass,
final int numProcessors,
final IlluminaDataProviderFactory factory) {
this.barcodeRecordWriterMap = barcodeRecordWriterMap;
this.maxReadsInRamPerTile = maxReadsInRamPerTile;
this.tmpDirs = tmpDirs;
this.codecPrototype = codecPrototype;
this.ignoreUnexpectedBarcodes = ignoreUnexpectedBarcodes;
this.demultiplex = demultiplex;
this.outputRecordComparator = outputRecordComparator;
this.bclQualityEvaluationStrategy = bclQualityEvaluationStrategy;
this.outputRecordClass = outputRecordClass;
this.factory = factory;
if (numProcessors == 0) {
this.numThreads = Runtime.getRuntime().availableProcessors();
} else if (numProcessors < 0) {
this.numThreads = Runtime.getRuntime().availableProcessors() + numProcessors;
} else {
this.numThreads = numProcessors;
}
}
示例4: clone
import htsjdk.samtools.util.SortingCollection; //导入方法依赖的package包/类
public SortingCollection.Codec<SortableRecord> clone() {
SortableRecordCodec other = new SortableRecordCodec();
return other;
}
示例5: clone
import htsjdk.samtools.util.SortingCollection; //导入方法依赖的package包/类
@Override
public SortingCollection.Codec<SAMRecordsForCluster> clone() {
return new Codec(numRecords, bamCodec.clone());
}
示例6: clone
import htsjdk.samtools.util.SortingCollection; //导入方法依赖的package包/类
@Override
public SortingCollection.Codec<FastqRecordsForCluster> clone() {
return new FastqRecordsForClusterCodec(numTemplates, numSampleBarcodes, numMolecularBarcodes);
}
示例7: getCodec
import htsjdk.samtools.util.SortingCollection; //导入方法依赖的package包/类
public static SortingCollection.Codec<PairedReadSequence> getCodec() {
return new PairedReadCodec();
}
示例8: clone
import htsjdk.samtools.util.SortingCollection; //导入方法依赖的package包/类
@Override
public SortingCollection.Codec<PairedReadSequence> clone() { return new PairedReadCodec(); }
示例9: clone
import htsjdk.samtools.util.SortingCollection; //导入方法依赖的package包/类
@Override
public SortingCollection.Codec<ReadEndsForMarkDuplicates> clone() {
return new ReadEndsForMarkDuplicatesWithBarcodesCodec();
}
示例10: clone
import htsjdk.samtools.util.SortingCollection; //导入方法依赖的package包/类
public SortingCollection.Codec<ReadEndsForMarkDuplicates> clone() {
return new ReadEndsForMarkDuplicatesCodec();
}
示例11: clone
import htsjdk.samtools.util.SortingCollection; //导入方法依赖的package包/类
public SortingCollection.Codec<RepresentativeReadIndexer> clone() {
return new RepresentativeReadIndexerCodec();
}