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public class BigBedFile.Companion
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Field Summary
Fields Modifier and Type Field Description public final static BigBedFile.CompanionINSTANCE
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Method Summary
Modifier and Type Method Description final BigBedFileread(Path path, Function0<Unit> cancelledChecker)final BigBedFileread(String src, Integer prefetch, Function0<Unit> cancelledChecker, Function2<String, ByteOrder, RomBufferFactory> factoryProvider)final Unitwrite(Iterable<BedEntry> bedEntries, Iterable<Pair<String, Integer>> chromSizes, Path outputPath, Integer itemsPerSlot, Integer zoomLevelCount, CompressionType compression, ByteOrder order, Function0<Unit> cancelledChecker)Creates a BigBED file from given entries. -
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Method Detail
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read
final BigBedFile read(Path path, Function0<Unit> cancelledChecker)
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read
final BigBedFile read(String src, Integer prefetch, Function0<Unit> cancelledChecker, Function2<String, ByteOrder, RomBufferFactory> factoryProvider)
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write
@JvmOverloads() final Unit write(Iterable<BedEntry> bedEntries, Iterable<Pair<String, Integer>> chromSizes, Path outputPath, Integer itemsPerSlot, Integer zoomLevelCount, CompressionType compression, ByteOrder order, Function0<Unit> cancelledChecker)
Creates a BigBED file from given entries.
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bedEntries- entries sorted by chromosome and start offset.chromSizes- chromosome names and sizes, e.g.outputPath- BigBED file path.itemsPerSlot- number of items to store in a single R+ tree index node.zoomLevelCount- number of zoom levels to pre-compute.compression- method for data sections, see CompressionType.order- byte order used, see java.nio.ByteOrder.cancelledChecker- Throw cancelled exception to abort operation @@throws IOException if any of the read or write operations failed.
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