htsjdk.samtools

Class SAMFileTruncatedReader

java.lang.Object

htsjdk.samtools.SAMFileReader

htsjdk.samtools.SAMFileTruncatedReader

All Implemented Interfaces:

SamReader, SamReader.Indexing, java.io.Closeable, java.lang.AutoCloseable, java.lang.Iterable<SAMRecord>

Deprecated.

@Deprecated
public class SAMFileTruncatedReader
extends SAMFileReader

A truncated form of a SAMFileReader that iterates over a limited number of records.

Nested Class Summary

Nested classes/interfaces inherited from interface htsjdk.samtools.SamReader

SamReader.AssertingIterator, SamReader.Indexing, SamReader.PrimitiveSamReader, SamReader.PrimitiveSamReaderToSamReaderAdapter, SamReader.ReaderImplementation, SamReader.Type

Constructor Summary

Constructors

Constructor and Description
SAMFileTruncatedReader(java.io.File input, long max) Deprecated.

Method Summary

Methods

Modifier and Type	Method and Description
SAMRecordIterator	iterator() Deprecated. Iterate through file in order.
SAMRecordIterator	iterator(SAMFileSpan chunks) Deprecated. Iterate through the given chunks in the file.

Methods inherited from class htsjdk.samtools.SAMFileReader

close, enableCrcChecking, enableFileSource, enableIndexCaching, enableIndexMemoryMapping, getBrowseableIndex, getDefaultValidationStringency, getFileHeader, getFilePointerSpanningReads, getIndex, getResourceDescription, getSequenceDictionary, hasBrowseableIndex, hasIndex, indexing, isBinary, makeQueryInterval, makeQueryInterval, query, query, queryAlignmentStart, queryContained, queryContained, queryMate, queryOverlapping, queryOverlapping, queryUnmapped, setDefaultValidationStringency, setSAMRecordFactory, setValidationStringency, toString, type

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

SAMFileTruncatedReader

public SAMFileTruncatedReader(java.io.File input,
                      long max)

Deprecated.

Parameters:

input - The SAM file

max - The maximum number of records to read from the file via iterator() methods

Method Detail

iterator

public SAMRecordIterator iterator()

Deprecated.

Description copied from class: SAMFileReader

Iterate through file in order. For a SAMFileReader constructed from an InputStream, and for any SAM file, a 2nd iteration starts where the 1st one left off. For a BAM constructed from a File, each new iteration starts at the first record.

Only a single open iterator on a SAM or BAM file may be extant at any one time. If you want to start a second iteration, the first one must be closed first.

Specified by:

iterator in interface SamReader

Specified by:

iterator in interface java.lang.Iterable<SAMRecord>

Overrides:

iterator in class SAMFileReader

iterator

public SAMRecordIterator iterator(SAMFileSpan chunks)

Deprecated.

Description copied from class: SAMFileReader

Iterate through the given chunks in the file.

Specified by:

iterator in interface SamReader.Indexing

Overrides:

iterator in class SAMFileReader

Parameters:

chunks - List of chunks for which to retrieve data.

Returns:

An iterator over the given chunks.