public final class FastqEncoder
extends java.lang.Object
| Modifier and Type | Field and Description |
|---|---|
static java.util.function.BiConsumer<FastqRecord,SAMRecord> |
QUALITY_HEADER_PARSE_SAM_TAGS |
static java.util.function.BiConsumer<FastqRecord,SAMRecord> |
QUALITY_HEADER_TO_COMMENT_TAG
Encodes the quality header into the comment tag (use in
asSAMRecord(FastqRecord, SAMFileHeader, BiConsumer). |
| 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 SAMRecord |
asSAMRecord(FastqRecord record,
SAMFileHeader header,
java.util.function.BiConsumer<FastqRecord,SAMRecord> custom)
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.
|
public static final java.util.function.BiConsumer<FastqRecord,SAMRecord> QUALITY_HEADER_TO_COMMENT_TAG
asSAMRecord(FastqRecord, SAMFileHeader, BiConsumer).
Note that all tabs present in the quality header are replaced by spaces.
public static final java.util.function.BiConsumer<FastqRecord,SAMRecord> QUALITY_HEADER_PARSE_SAM_TAGS
public static java.lang.String encode(FastqRecord record)
public static java.lang.Appendable write(java.lang.Appendable out,
FastqRecord record)
SAMException - if any I/O error occurs.public static java.lang.String encode(SAMRecord record)
public static FastqRecord asFastqRecord(SAMRecord record)
SAMRecord into a FastqRecord.public static SAMRecord asSAMRecord(FastqRecord record, SAMFileHeader header)
FastqRecord into a simple unmapped SAMRecord.public static SAMRecord asSAMRecord(FastqRecord record, SAMFileHeader header, java.util.function.BiConsumer<FastqRecord,SAMRecord> custom)
FastqRecord into a simple unmapped SAMRecord.
This method allows to pass a BiConsumer to add the information from the record in
a customizable manner.
record - object to encode.header - header for the returned object.custom - function to customize encoding. Note that default information might be overriden.