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.