Package htsjdk.samtools.fastq

Class FastqEncoder

java.lang.Object

htsjdk.samtools.fastq.FastqEncoder

public final class FastqEncoder
extends Object

Codec for encoding records into FASTQ format.

Field Summary

Fields

Modifier and Type	Field	Description
static final BiConsumer<FastqRecord,SAMRecord>	QUALITY_HEADER_PARSE_SAM_TAGS
static final BiConsumer<FastqRecord,SAMRecord>	QUALITY_HEADER_TO_COMMENT_TAG	Encodes the quality header into the comment tag (use in asSAMRecord(FastqRecord, SAMFileHeader, BiConsumer).

Method Summary

Modifier and Type	Method	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 SAMRecord	asSAMRecord(FastqRecord record, SAMFileHeader header, BiConsumer<FastqRecord,SAMRecord> custom)	Converts a FastqRecord into a simple unmapped SAMRecord.
static String	encode(FastqRecord record)	Encodes a FastqRecord in the String FASTQ format.
static String	encode(SAMRecord record)	Encodes a SAMRecord in the String FASTQ format.
static Appendable	write(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

Field Details

QUALITY_HEADER_TO_COMMENT_TAG

public static final BiConsumer<FastqRecord,SAMRecord> QUALITY_HEADER_TO_COMMENT_TAG

Encodes the quality header into the comment tag (use in asSAMRecord(FastqRecord, SAMFileHeader, BiConsumer).

Note that all tabs present in the quality header are replaced by spaces.

QUALITY_HEADER_PARSE_SAM_TAGS

public static final BiConsumer<FastqRecord,SAMRecord> QUALITY_HEADER_PARSE_SAM_TAGS

Method Details

encode

public static String encode(FastqRecord record)

Encodes a FastqRecord in the String FASTQ format.

write

public static Appendable write(Appendable out,
 FastqRecord record)

Writes a FastqRecord into the Appendable output.

Throws:

SAMException - if any I/O error occurs.

encode

public static 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.

asSAMRecord

public static SAMRecord asSAMRecord(FastqRecord record,
 SAMFileHeader header,
 BiConsumer<FastqRecord,SAMRecord> custom)

Converts a FastqRecord into a simple unmapped SAMRecord.

This method allows to pass a BiConsumer to add the information from the record in a customizable manner.

Parameters:

record - object to encode.

header - header for the returned object.

custom - function to customize encoding. Note that default information might be overriden.