/** Reads the next key/value pair from the input for processing. */
public boolean next(Text key, SequencedFragment value) throws IOException {
if (pos >= end) return false; // past end of slice
int bytesRead = 0;
boolean goodRecord;
do {
bytesRead = lowLevelQseqRead(key, value); // if bytesRead <= 0 EOF has been reached
goodRecord =
(bytesRead > 0)
&& (!filterFailedQC || value.getFilterPassed() == null || value.getFilterPassed());
} while (bytesRead > 0 && !goodRecord);
if (goodRecord) // post process the record only if it's going to be used
{
try {
postProcessSequencedFragment(value);
} catch (FormatException e) {
throw new FormatException(
e.getMessage()
+ " Position: "
+ makePositionMessage(this.pos - bytesRead)
+ "; line: "
+ buffer); // last line read is still in the buffer
}
}
return goodRecord;
}
/*
* This method applies some transformations to the read and quality data.
*
* <ul>
* <li>'.' in the read are converted to 'N'</li>
* <li>the base quality encoding is converted to 'sanger', unless otherwise
* requested by the configuration.</li>
* </ul>
*
* @exception FormatException Thrown if the record contains base quality scores
* outside the range allowed by the format.
*/
private void postProcessSequencedFragment(SequencedFragment fragment) {
byte[] bytes = fragment.getSequence().getBytes();
// replace . with N
for (int i = 0; i < fieldLengths[8]; ++i) if (bytes[i] == '.') bytes[i] = 'N';
if (qualityEncoding == BaseQualityEncoding.Illumina) {
// convert illumina to sanger scale
SequencedFragment.convertQuality(
fragment.getQuality(), BaseQualityEncoding.Illumina, BaseQualityEncoding.Sanger);
} else // sanger qualities.
{
int outOfRangeElement =
SequencedFragment.verifyQuality(fragment.getQuality(), BaseQualityEncoding.Sanger);
if (outOfRangeElement >= 0) {
throw new FormatException(
"qseq base quality score out of range for Sanger Phred+33 format (found "
+ (fragment.getQuality().getBytes()[outOfRangeElement]
- FormatConstants.SANGER_OFFSET)
+ ").\n"
+ "Although Sanger format has been requested, maybe qualities are in Illumina Phred+64 format?\n");
}
}
}
private void scanQseqLine(Text line, Text key, SequencedFragment fragment) {
setFieldPositionsAndLengths(line);
// Build the key. We concatenate all fields from 0 to 5 (machine to y-pos)
// and then the read number, replacing the tabs with colons.
key.clear();
// append up and including field[5]
key.append(line.getBytes(), 0, fieldPositions[5] + fieldLengths[5]);
// replace tabs with :
byte[] bytes = key.getBytes();
int temporaryEnd = key.getLength();
for (int i = 0; i < temporaryEnd; ++i) if (bytes[i] == '\t') bytes[i] = ':';
// append the read number
key.append(
line.getBytes(),
fieldPositions[7] - 1,
fieldLengths[7] + 1); // +/- 1 to catch the preceding tab.
// convert the tab preceding the read number into a :
key.getBytes()[temporaryEnd] = ':';
// now the fragment
try {
fragment.clear();
fragment.setInstrument(Text.decode(line.getBytes(), fieldPositions[0], fieldLengths[0]));
fragment.setRunNumber(
Integer.parseInt(Text.decode(line.getBytes(), fieldPositions[1], fieldLengths[1])));
// fragment.setFlowcellId();
fragment.setLane(
Integer.parseInt(Text.decode(line.getBytes(), fieldPositions[2], fieldLengths[2])));
fragment.setTile(
Integer.parseInt(Text.decode(line.getBytes(), fieldPositions[3], fieldLengths[3])));
fragment.setXpos(
Integer.parseInt(Text.decode(line.getBytes(), fieldPositions[4], fieldLengths[4])));
fragment.setYpos(
Integer.parseInt(Text.decode(line.getBytes(), fieldPositions[5], fieldLengths[5])));
fragment.setRead(
Integer.parseInt(Text.decode(line.getBytes(), fieldPositions[7], fieldLengths[7])));
fragment.setFilterPassed(line.getBytes()[fieldPositions[10]] != '0');
// fragment.setControlNumber();
if (fieldLengths[6] > 0
&& line.getBytes()[fieldPositions[6]] == '0') // 0 is a null index sequence
fragment.setIndexSequence(null);
else
fragment.setIndexSequence(
Text.decode(line.getBytes(), fieldPositions[6], fieldLengths[6]).replace('.', 'N'));
} catch (CharacterCodingException e) {
throw new FormatException(
"Invalid character format at "
+ makePositionMessage(this.pos - line.getLength())
+ "; line: "
+ line);
}
fragment.getSequence().append(line.getBytes(), fieldPositions[8], fieldLengths[8]);
fragment.getQuality().append(line.getBytes(), fieldPositions[9], fieldLengths[9]);
}
