htsjdk.samtools.fastq

Class FastqEncoder

java.lang.Object

htsjdk.samtools.fastq.FastqEncoder

public final class FastqEncoder
extends java.lang.Object

Codec for encoding records into FASTQ format.

Method Summary

Modifier and Type	Method and Description
static FastqRecord	asFastqRecord(SAMRecord record) Converts a SAMRecord into a FastqRecord.
static SAMRecord	asSAMRecord(FastqRecord record, SAMFileHeader header) Converts a FastqRecord into a simple unmapped SAMRecord.
static java.lang.String	encode(FastqRecord record) Encodes a FastqRecord in the String FASTQ format.
static java.lang.String	encode(SAMRecord record) Encodes a SAMRecord in the String FASTQ format.
static java.lang.Appendable	write(java.lang.Appendable out, FastqRecord record) Writes a FastqRecord into the Appendable output.

Methods inherited from class java.lang.Object

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

Method Detail

encode

public static java.lang.String encode(FastqRecord record)

Encodes a FastqRecord in the String FASTQ format.

write

public static java.lang.Appendable write(java.lang.Appendable out,
                                         FastqRecord record)

Writes a FastqRecord into the Appendable output.

Throws:

SAMException - if any I/O error occurs.

encode

public static java.lang.String encode(SAMRecord record)

Encodes a SAMRecord in the String FASTQ format.

See Also:

encode(FastqRecord), asSAMRecord(FastqRecord, SAMFileHeader)

asFastqRecord

public static FastqRecord asFastqRecord(SAMRecord record)

Converts a SAMRecord into a FastqRecord.

asSAMRecord

public static SAMRecord asSAMRecord(FastqRecord record,
                                    SAMFileHeader header)

Converts a FastqRecord into a simple unmapped SAMRecord.