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 BiConsumer<FastqRecord,SAMRecord>`	`QUALITY_HEADER_PARSE_SAM_TAGS`
`static BiConsumer<FastqRecord,SAMRecord>`	`QUALITY_HEADER_TO_COMMENT_TAG`	Encodes the quality header into the comment tag (use in `asSAMRecord(FastqRecord, SAMFileHeader, BiConsumer)`.

Method Summary

All Methods Static Methods Concrete Methods
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 Detail
  - 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 Detail
  - 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.

Class FastqEncoder

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

QUALITY_HEADER_TO_COMMENT_TAG

QUALITY_HEADER_PARSE_SAM_TAGS

Method Detail

encode

write

encode

asFastqRecord

asSAMRecord

asSAMRecord