Package htsjdk.samtools.fastq
Class FastqEncoder
- java.lang.Object
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- htsjdk.samtools.fastq.FastqEncoder
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public final class FastqEncoder extends Object
Codec for encoding records into FASTQ format.
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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 inasSAMRecord(FastqRecord, SAMFileHeader, BiConsumer)
.
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static FastqRecord
asFastqRecord(SAMRecord record)
Converts aSAMRecord
into aFastqRecord
.static SAMRecord
asSAMRecord(FastqRecord record, SAMFileHeader header)
Converts aFastqRecord
into a simple unmappedSAMRecord
.static SAMRecord
asSAMRecord(FastqRecord record, SAMFileHeader header, BiConsumer<FastqRecord,SAMRecord> custom)
Converts aFastqRecord
into a simple unmappedSAMRecord
.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.
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Field Detail
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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 inasSAMRecord(FastqRecord, SAMFileHeader, BiConsumer)
.Note that all tabs present in the quality header are replaced by spaces.
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QUALITY_HEADER_PARSE_SAM_TAGS
public static final BiConsumer<FastqRecord,SAMRecord> QUALITY_HEADER_PARSE_SAM_TAGS
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Method Detail
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encode
public static String encode(FastqRecord record)
Encodes a FastqRecord in the String FASTQ format.
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write
public static Appendable write(Appendable out, FastqRecord record)
Writes a FastqRecord into the Appendable output.- Throws:
SAMException
- if any I/O error occurs.
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encode
public static String encode(SAMRecord record)
Encodes a SAMRecord in the String FASTQ format.
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asFastqRecord
public static FastqRecord asFastqRecord(SAMRecord record)
Converts aSAMRecord
into aFastqRecord
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asSAMRecord
public static SAMRecord asSAMRecord(FastqRecord record, SAMFileHeader header)
Converts aFastqRecord
into a simple unmappedSAMRecord
.
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asSAMRecord
public static SAMRecord asSAMRecord(FastqRecord record, SAMFileHeader header, BiConsumer<FastqRecord,SAMRecord> custom)
Converts aFastqRecord
into a simple unmappedSAMRecord
.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.
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