/** * Encodes a SAMRecord in the String FASTQ format. * @see #encode(FastqRecord) * @see #asSAMRecord(FastqRecord, SAMFileHeader) */ public static String encode(final SAMRecord record) { return encode(asFastqRecord(record)); }
/** * Encodes a SAMRecord in the String FASTQ format. * @see #encode(FastqRecord) * @see #asSAMRecord(FastqRecord, SAMFileHeader) */ public static String encode(final SAMRecord record) { return encode(asFastqRecord(record)); }
@Test public void testAsFastqRecord() throws Exception { final SAMRecord record = new SAMRecordSetBuilder().addFrag("test", 0, 1, false, false, "10M", null, 2); record.setReadPairedFlag(true); // test first of pair encoding record.setFirstOfPairFlag(true); testRecord(record.getReadName() + FastqConstants.FIRST_OF_PAIR, FastqEncoder.asFastqRecord(record), record); record.setFirstOfPairFlag(false); record.setSecondOfPairFlag(true); testRecord(record.getReadName() + FastqConstants.SECOND_OF_PAIR, FastqEncoder.asFastqRecord(record), record); record.setSecondOfPairFlag(false); testRecord(record.getReadName(), FastqEncoder.asFastqRecord(record), record); record.setAttribute(SAMTag.CO.name(), "Comment in SAM tag"); testRecord(record.getReadName(), FastqEncoder.asFastqRecord(record), record); }