public void set(MouseEvent e, SAMRecord sr) {
if (sr == null) return;
StringBuffer text = new StringBuffer();
text.append("<html>");
if (sr != null) {
text.append(
MessageManager.getString("shortreadtrack.name") + " " + sr.getReadName() + "<br/>");
text.append(
MessageManager.getString("shortreadtrack.len") + " " + sr.getReadLength() + "<br/>");
text.append(
MessageManager.getString("shortreadtrack.cigar") + " " + sr.getCigarString() + "<br/>");
text.append(
MessageManager.getString("shortreadtrack.sequence")
+ " "
+ rerun(sr.getReadString())
+ "<br/>");
text.append(
MessageManager.getString("shortreadtrack.paired")
+ " "
+ sr.getReadPairedFlag()
+ "<br/>");
if (sr.getReadPairedFlag()) {
if (!sr.getMateUnmappedFlag())
text.append(
MessageManager.getString("shortreadtrack.mate")
+ " "
+ sr.getMateReferenceName()
+ ":"
+ sr.getMateAlignmentStart()
+ "<br/>");
else text.append(MessageManager.getString("shortreadtrack.mate_missing") + "<br/>");
text.append(
MessageManager.getString("shortreadtrack.second") + " " + sr.getFirstOfPairFlag());
}
// text.append("<br/>");
}
text.append("</html>");
if (!text.toString().equals(floater.getText())) {
floater.setText(text.toString());
this.pack();
}
setLocation(e.getXOnScreen() + 5, e.getYOnScreen() + 5);
if (!isVisible()) {
setVisible(true);
}
}
public void dump() {
while (!delegateQueue.isEmpty()) {
SAMRecord r = doPoll();
System.out.println(r.getAlignmentStart() + "\t" + r.getReadName());
}
}
@Override
public int doWork(String[] args) {
File refFile = null;
com.github.lindenb.jvarkit.util.cli.GetOpt getopt =
new com.github.lindenb.jvarkit.util.cli.GetOpt();
int c;
while ((c = getopt.getopt(args, "hvL:r:")) != -1) {
switch (c) {
case 'h':
printUsage();
return 0;
case 'v':
System.out.println(getVersion());
return 0;
case 'L':
getLogger().setLevel(java.util.logging.Level.parse(getopt.getOptArg()));
break;
case 'r':
refFile = new File(getopt.getOptArg());
break;
case ':':
System.err.println("Missing argument for option -" + getopt.getOptOpt());
return -1;
default:
System.err.println("Unknown option -" + getopt.getOptOpt());
return -1;
}
}
if (refFile == null) {
error("Undefined REF file");
return -1;
}
File bamFile = null;
if (getopt.getOptInd() + 1 != args.length) {
info("reading from stdin.");
} else {
bamFile = new File(args[getopt.getOptInd()]);
}
IndexedFastaSequenceFile indexedFastaSequenceFile = null;
SAMFileReader samFileReader = null;
try {
GenomicSequence genomicSequence = null;
indexedFastaSequenceFile = new IndexedFastaSequenceFile(refFile);
SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
samFileReader = null;
if (bamFile == null) {
samFileReader = new SAMFileReader(System.in);
} else {
samFileReader = new SAMFileReader(bamFile);
}
XMLOutputFactory xmlfactory = XMLOutputFactory.newInstance();
XMLStreamWriter w = xmlfactory.createXMLStreamWriter(System.out, "UTF-8");
w.writeStartDocument("UTF-8", "1.0");
w.writeStartElement("sam");
w.writeComment(getProgramCommandLine());
w.writeAttribute("ref", (bamFile == null ? "stdin" : bamFile.getPath()));
w.writeAttribute("bam", args[1]);
SAMRecordIterator iter = samFileReader.iterator();
while (iter.hasNext()) {
SAMRecord rec = iter.next();
final byte readbases[] = rec.getReadBases();
w.writeStartElement("read");
w.writeStartElement("name");
w.writeCharacters(rec.getReadName());
w.writeEndElement();
w.writeStartElement("sequence");
w.writeCharacters(new String(readbases));
w.writeEndElement();
w.writeStartElement("flags");
w.writeAttribute("paired", String.valueOf(rec.getReadPairedFlag()));
w.writeAttribute(
"failsVendorQual", String.valueOf(rec.getReadFailsVendorQualityCheckFlag()));
w.writeAttribute("mapped", String.valueOf(!rec.getReadUnmappedFlag()));
w.writeAttribute("strand", (rec.getReadNegativeStrandFlag() ? "-" : "+"));
if (rec.getReadPairedFlag()) {
w.writeAttribute("mate-mapped", String.valueOf(!rec.getMateUnmappedFlag()));
w.writeAttribute("mate-strand", (rec.getMateNegativeStrandFlag() ? "-" : "+"));
w.writeAttribute("proper-pair", String.valueOf(rec.getProperPairFlag()));
}
w.writeCharacters(String.valueOf(rec.getFlags()));
w.writeEndElement();
if (!rec.getReadUnmappedFlag()) {
w.writeStartElement("qual");
w.writeCharacters(String.valueOf(rec.getMappingQuality()));
w.writeEndElement();
w.writeStartElement("chrom");
w.writeAttribute("index", String.valueOf(rec.getReferenceIndex()));
w.writeCharacters(rec.getReferenceName());
w.writeEndElement();
w.writeStartElement("pos");
w.writeCharacters(String.valueOf(rec.getAlignmentStart()));
w.writeEndElement();
w.writeStartElement("cigar");
w.writeCharacters(rec.getCigarString());
w.writeEndElement();
}
if (!rec.getMateUnmappedFlag()) {
w.writeStartElement("mate-chrom");
w.writeAttribute("index", String.valueOf(rec.getMateReferenceIndex()));
w.writeCharacters(rec.getMateReferenceName());
w.writeEndElement();
w.writeStartElement("mate-pos");
w.writeCharacters(String.valueOf(rec.getMateAlignmentStart()));
w.writeEndElement();
}
if (!rec.getReadUnmappedFlag()) {
if (genomicSequence == null
|| genomicSequence.getChrom().equals(rec.getReferenceName())) {
genomicSequence = new GenomicSequence(indexedFastaSequenceFile, rec.getReferenceName());
}
w.writeStartElement("align");
int readIndex = 0;
int refIndex = rec.getAlignmentStart();
for (final CigarElement e : rec.getCigar().getCigarElements()) {
switch (e.getOperator()) {
case H:
break; // ignore hard clips
case P:
break; // ignore pads
case I: // cont.
case S:
{
final int length = e.getLength();
for (int i = 0; i < length; ++i) {
w.writeEmptyElement(e.getOperator().name());
w.writeAttribute("read-index", String.valueOf(readIndex + 1));
if (readIndex >= 0 && readIndex < readbases.length) {
w.writeAttribute("read-base", String.valueOf((char) (readbases[readIndex])));
}
readIndex++;
}
break;
}
case N: // cont. -- reference skip
case D:
{
final int length = e.getLength();
for (int i = 0; i < length; ++i) {
w.writeEmptyElement(e.getOperator().name());
w.writeAttribute("ref-index", String.valueOf(refIndex));
if (refIndex >= 1 && refIndex <= genomicSequence.length()) {
w.writeAttribute(
"ref-base", String.valueOf(genomicSequence.charAt(refIndex - 1)));
}
refIndex++;
}
break;
}
case M:
case EQ:
case X:
{
final int length = e.getLength();
for (int i = 0; i < length; ++i) {
w.writeEmptyElement(e.getOperator().name());
char baseRead = '\0';
if (readIndex >= 0 && readIndex < readbases.length) {
baseRead = (char) (rec.getReadBases()[readIndex]);
w.writeAttribute("read-index", String.valueOf(readIndex + 1));
w.writeAttribute("read-base", String.valueOf(baseRead));
}
w.writeAttribute("ref-index", String.valueOf(refIndex));
if (refIndex >= 1 && refIndex <= genomicSequence.length()) {
char baseRef = genomicSequence.charAt(refIndex - 1);
w.writeAttribute("ref-base", String.valueOf(baseRef));
if (Character.toUpperCase(baseRef) != Character.toUpperCase(baseRead)) {
w.writeAttribute("mismatch", "true");
}
}
refIndex++;
readIndex++;
}
break;
}
default:
throw new IllegalStateException(
"Case statement didn't deal with cigar op: " + e.getOperator());
}
}
}
w.writeEndElement();
w.writeEndElement();
iter.close();
w.writeEndElement();
}
w.writeEndElement();
w.writeEndDocument();
w.flush();
w.close();
} catch (Exception err) {
error(err);
return -1;
} finally {
CloserUtil.close(samFileReader);
CloserUtil.close(indexedFastaSequenceFile);
}
return 0;
}
public void find_coverage(SAMResource sres) {
int start_base = sres.region.range.start;
int end_base = sres.region.range.end;
int coverage_len = (end_base - start_base) + 1;
int i, end, ref_i, read_i, len;
int[] coverage = new int[coverage_len];
Arrays.fill(coverage, 0);
WorkingFile wf = null;
if (outfile != null) {
try {
wf = new WorkingFile(outfile);
ps = wf.getPrintStream();
} catch (Exception e) {
System.err.println("I/O error: " + e); // debug
e.printStackTrace();
System.exit(1);
}
}
try {
//
// gather coverage info:
//
CloseableIterator<SAMRecord> iterator = sres.get_iterator();
int read_count = 0;
int ref_min = -1;
int ref_max = -1;
while (iterator.hasNext()) {
SAMRecord sr = iterator.next();
read_count++;
// System.err.println(sr.getReadName() + ": " + sr.getAlignmentStart() + "-" +
// sr.getAlignmentEnd()); // debug
if (sr.getReadUnmappedFlag()) continue;
if (sr.getDuplicateReadFlag()) {
if (verbose_mode)
System.err.println(
sr.getReadName()
+ "."
+ (sr.getReadNegativeStrandFlag() ? "R" : "F")
+ " ignoring, duplicate");
continue;
}
byte[] read = sr.getReadBases();
byte[] quals = sr.getBaseQualities();
for (AlignmentBlock ab : sr.getAlignmentBlocks()) {
len = ab.getLength();
read_i = ab.getReadStart() - 1;
ref_i = ab.getReferenceStart() - start_base;
if (ref_min == -1 || ref_i < ref_min) ref_min = ref_i;
for (i = read_i, end = read_i + len; i < end; i++, ref_i++) {
if (ref_i >= 0 && ref_i < coverage_len) {
if (quals[i] >= MIN_QUALITY) {
if (verbose_mode)
System.err.println(
sr.getReadName()
+ "."
+ (sr.getReadNegativeStrandFlag() ? "R" : "F")
+ " hit at "
+ (ref_i + start_base)
+ " as="
+ sr.getAlignmentStart()
+ " ae="
+ sr.getAlignmentEnd());
coverage[ref_i]++;
} else if (verbose_mode) {
System.err.println(
sr.getReadName()
+ "."
+ (sr.getReadNegativeStrandFlag() ? "R" : "F")
+ " qual_reject at "
+ (ref_i + start_base)
+ " as="
+ sr.getAlignmentStart()
+ " ae="
+ sr.getAlignmentEnd());
}
}
}
if (ref_max == -1 || ref_i > ref_max) ref_max = ref_i;
}
}
sres.close();
System.err.println(
"records:"
+ read_count
+ " ref_min:"
+ (ref_min + start_base)
+ " ref_max:"
+ (ref_max + start_base)); // debug
//
// report coverage info:
//
for (i = 0; i < coverage.length; i++) {
if (name != null) ps.print(name + ",");
ps.println((i + start_base) + "," + coverage[i]); // debug
}
if (wf != null) wf.finish();
} catch (Exception e) {
System.err.println("ERROR: " + e); // debug
e.printStackTrace();
}
}
public void run(URL url) throws SocketException, IOException {
FTPSeekableStream fss = new FTPSeekableStream(url);
File index = fss.getIndexFile();
SAMFileReader reader = new SAMFileReader(fss, index, false);
reader.getFileHeader();
reader.setValidationStringency(ValidationStringency.SILENT);
logger.info("attributes");
for (Map.Entry<String, String> entry : reader.getFileHeader().getAttributes()) {
logger.info(String.format("%s : %s", entry.getKey(), entry.getValue()));
}
logger.info("sequences");
for (SAMSequenceRecord ssr : reader.getFileHeader().getSequenceDictionary().getSequences()) {
logger.info(String.format("%s : %s ", ssr.getSequenceName(), ssr.getSequenceLength()));
}
logger.info("sequences");
for (SAMSequenceRecord ssr : reader.getFileHeader().getSequenceDictionary().getSequences()) {
// if (! ssr.getSequenceName().equals("NT_166325")) {
// continue;
// }
int length = ssr.getSequenceLength();
int min = 1000;
int max = 100000;
if (min >= length) {
min = 0;
}
// logger.warn((max >= length));
if (max >= length) {
max = length;
}
if (min >= max) {
min = 0;
}
logger.info(
String.format("Sequence: %s (%s) %s-%s", ssr.getSequenceName(), length, min, max));
SAMRecordIterator i = reader.query(ssr.getSequenceName(), min, max, false);
while (i.hasNext()) {
SAMRecord record = i.next();
logger.info(
String.format(
"Read: %s (%s (%s-%s) %s) / %s",
record.getReadName(),
min,
record.getAlignmentStart(),
record.getAlignmentEnd(),
max,
record.getFlags()));
assertTrue(record.getAlignmentStart() >= min);
}
i.close();
logger.info("_________________________________________________");
}
logger.info("Done");
}
private static void updateSAM(
SAMRecord rec,
ReferenceSequence sequence,
SAMProgramRecord programRecord,
AlignHeapNode bestAlignHeapNode,
SRMAUtil.Space space,
String read,
String qualities,
String softClipStartBases,
String softClipStartQualities,
String softClipEndBases,
String softClipEndQualities,
boolean strand,
boolean correctBases)
throws Exception {
AlignHeapNode curAlignHeapNode = null;
AlignHeapNode prevAlignHeapNode = null;
int alignmentStart = 0;
int readIndex = -1;
byte readBases[] = null;
byte baseQualities[] = null;
byte colorErrors[] = null;
int i;
int numEdits = 0;
List<String> optFieldTags = new LinkedList<String>();
List<Object> optFieldValues = new LinkedList<Object>();
Object attr;
// Debugging stuff
String readName = rec.getReadName();
if (null == bestAlignHeapNode) {
// Do not modify the alignment
return;
}
// To generate a new CIGAR
List<CigarElement> cigarElements = null;
CigarOperator prevCigarOperator = null, curCigarOperator = null;
int prevCigarOperatorLength = 0;
// TODO
// setInferredInsertSize (invalidates paired end reads)
// setMappingQuality (?)
// setFlag
// update base qualities for color space reads
// clear attributes, but save some
Align.clearAttributes(rec, optFieldTags, optFieldValues);
readBases = new byte[read.length()];
baseQualities = new byte[qualities.length()];
for (i = 0; i < qualities.length(); i++) {
// Must subtract 33 for PHRED scaling
baseQualities[i] = (byte) (qualities.charAt(i) - 33);
}
if (strand) {
readIndex = 0;
} else {
readIndex = read.length() - 1;
}
cigarElements = new LinkedList<CigarElement>();
if (strand) { // reverse strand is the current position
alignmentStart = bestAlignHeapNode.node.position;
} else {
alignmentStart = bestAlignHeapNode.startPosition;
}
assert null != bestAlignHeapNode;
curAlignHeapNode = bestAlignHeapNode;
while (null != curAlignHeapNode) {
// Get the current cigar operator
if (null != prevAlignHeapNode
&& CigarOperator.DELETION != prevCigarOperator
&& 1 < Math.abs(curAlignHeapNode.node.position - prevAlignHeapNode.node.position)) {
curCigarOperator = CigarOperator.DELETION;
} else {
switch (curAlignHeapNode.node.type) {
case Node.MISMATCH: // Fall through
case Node.MATCH:
curCigarOperator = CigarOperator.MATCH_OR_MISMATCH;
break;
case Node.INSERTION:
// System.out.println("INS");
curCigarOperator = CigarOperator.INSERTION;
break;
default:
throw new Exception("Unknown node type");
}
if (space == SRMAUtil.Space.COLORSPACE || correctBases) {
readBases[readIndex] = (byte) curAlignHeapNode.node.base;
if (strand) {
readIndex++;
} else {
readIndex--;
}
// count the number of mismatches
switch (curAlignHeapNode.node.type) {
case Node.MISMATCH:
case Node.INSERTION:
numEdits++;
break;
default:
break;
}
} else {
// count the number of mismatches
switch (curAlignHeapNode.node.type) {
case Node.MATCH:
if (read.charAt(curAlignHeapNode.readOffset) != curAlignHeapNode.node.base) {
numEdits++;
}
break;
case Node.MISMATCH: // Fall through
if (read.charAt(curAlignHeapNode.readOffset)
!= sequence.getBases()[curAlignHeapNode.node.position - 1]) {
numEdits++;
}
break;
case Node.INSERTION:
numEdits++;
break;
default:
break;
}
}
}
if (prevCigarOperator != curCigarOperator) {
// different cigar operator
// add the previous cigar operator
if (null != prevCigarOperator) {
if (strand) { // reverse
// append
cigarElements.add(new CigarElement(prevCigarOperatorLength, prevCigarOperator));
} else {
// prepend
cigarElements.add(0, new CigarElement(prevCigarOperatorLength, prevCigarOperator));
}
}
// update prevCigarOperator
prevCigarOperator = curCigarOperator;
if (curCigarOperator == CigarOperator.DELETION) {
// length of deletion
prevCigarOperatorLength =
Math.abs(curAlignHeapNode.node.position - prevAlignHeapNode.node.position) - 1;
numEdits += prevCigarOperatorLength; // deletions
} else {
prevCigarOperatorLength = 1;
}
} else {
// same cigar operator
prevCigarOperatorLength++;
}
// Update
if (CigarOperator.DELETION != curCigarOperator) {
prevAlignHeapNode = curAlignHeapNode;
curAlignHeapNode = curAlignHeapNode.prev;
}
}
if (0 < prevCigarOperatorLength) {
if (null == prevCigarOperator || CigarOperator.DELETION == prevCigarOperator) {
throw new Exception("Ended with a null cigar operator or a deletion cigar operator");
}
if (strand) { // reverse
// append
cigarElements.add(new CigarElement(prevCigarOperatorLength, prevCigarOperator));
} else {
// prepend
cigarElements.add(0, new CigarElement(prevCigarOperatorLength, prevCigarOperator));
}
}
if (space == SRMAUtil.Space.COLORSPACE) { // color space, read bases already inferred
// Get color error string
colorErrors = new byte[read.length()];
char prevBase = SRMAUtil.COLORSPACE_ADAPTOR;
if (strand) { // reverse
for (i = 0; i < read.length(); i++) {
char nextBase = SRMAUtil.colorSpaceNextBase(prevBase, read.charAt(i));
if (nextBase == SRMAUtil.getCompliment((char) readBases[read.length() - i - 1])) {
colorErrors[i] = (byte) Alignment.GAP;
} else {
colorErrors[i] = (byte) read.charAt(i);
}
if (0 < i) {
// qualities are assumed to be always in the same direction as the color errors
baseQualities[read.length() - i] =
getColorQuality(
colorErrors[i - 1],
colorErrors[i],
(byte) (qualities.charAt(i - 1) - 33),
(byte) (qualities.charAt(i) - 33));
}
prevBase = SRMAUtil.getCompliment((char) readBases[read.length() - i - 1]);
}
// last color
baseQualities[0] = (byte) (qualities.charAt(read.length() - 1) - 33);
} else {
for (i = 0; i < read.length(); i++) {
char nextBase = SRMAUtil.colorSpaceNextBase(prevBase, read.charAt(i));
if (nextBase == readBases[i]) {
colorErrors[i] = (byte) Alignment.GAP;
} else {
colorErrors[i] = (byte) read.charAt(i);
}
if (0 < i) {
baseQualities[i - 1] =
getColorQuality(
colorErrors[i - 1],
colorErrors[i],
(byte) (qualities.charAt(i - 1) - 33),
(byte) (qualities.charAt(i) - 33));
}
prevBase = (char) readBases[i];
}
// last color
baseQualities[read.length() - 1] = (byte) (qualities.charAt(read.length() - 1) - 33);
}
} else if (correctBases) { // bases were corrected
if (strand) {
for (i = 0; i < read.length(); i++) {
if (readBases[i] == (byte) read.charAt(read.length() - i - 1)) {
baseQualities[i] = (byte) (qualities.charAt(read.length() - i - 1) - 33);
} else {
// TODO: how much to down-weight ?
baseQualities[i] =
(byte)
(SRMAUtil.QUAL2CHAR(
SRMAUtil.CHAR2QUAL(qualities.charAt(read.length() - i - 1))
- CORRECT_BASE_QUALITY_PENALTY)
- 33);
if (baseQualities[i] <= 0) {
baseQualities[i] = 1;
}
}
}
} else {
for (i = 0; i < read.length(); i++) {
if (readBases[i] == (byte) read.charAt(i)) {
baseQualities[i] = (byte) (qualities.charAt(i) - 33);
} else {
// TODO: how much to down-weight ?
baseQualities[i] =
(byte)
(SRMAUtil.QUAL2CHAR(
SRMAUtil.CHAR2QUAL(qualities.charAt(i)) - CORRECT_BASE_QUALITY_PENALTY)
- 33);
if (baseQualities[i] <= 0) {
baseQualities[i] = 1;
}
}
}
}
rec.setAttribute("XO", read);
rec.setAttribute("XQ", qualities);
} else { // bases not corrected
readBases = new byte[read.length()];
baseQualities = new byte[qualities.length()]; // qualities.length() == read.length()
if (strand) { // reverse
for (i = 0; i < read.length(); i++) {
readBases[i] = (byte) read.charAt(read.length() - i - 1);
baseQualities[i] = (byte) (qualities.charAt(read.length() - i - 1) - 33);
}
} else {
for (i = 0; i < read.length(); i++) {
readBases[i] = (byte) read.charAt(i);
baseQualities[i] = (byte) (qualities.charAt(i) - 33);
}
}
}
// Add in soft-clipping
if (null != softClipStartBases) { // prepend
cigarElements.add(0, new CigarElement(softClipStartBases.length(), CigarOperator.S));
byte tmpBases[] = new byte[readBases.length + softClipStartBases.length()];
System.arraycopy(readBases, 0, tmpBases, softClipStartBases.length(), readBases.length);
readBases = tmpBases;
for (i = 0; i < softClipStartBases.length(); i++) {
readBases[i] = (byte) softClipStartBases.charAt(i);
}
byte tmpQualities[] = new byte[baseQualities.length + softClipStartQualities.length()];
System.arraycopy(
baseQualities, 0, tmpQualities, softClipStartQualities.length(), baseQualities.length);
baseQualities = tmpQualities;
for (i = 0; i < softClipStartQualities.length(); i++) {
baseQualities[i] = (byte) softClipStartQualities.charAt(i);
}
}
if (null != softClipEndBases) { // append
cigarElements.add(new CigarElement(softClipEndBases.length(), CigarOperator.S));
byte tmpBases[] = new byte[readBases.length + softClipEndBases.length()];
System.arraycopy(readBases, 0, tmpBases, 0, readBases.length);
for (i = 0; i < softClipEndBases.length(); i++) {
tmpBases[i + readBases.length] = (byte) softClipEndBases.charAt(i);
}
readBases = tmpBases;
byte tmpQualities[] = new byte[baseQualities.length + softClipEndQualities.length()];
System.arraycopy(baseQualities, 0, tmpQualities, 0, baseQualities.length);
for (i = 0; i < softClipEndQualities.length(); i++) {
tmpQualities[i + baseQualities.length] = (byte) softClipEndQualities.charAt(i);
}
baseQualities = tmpQualities;
}
// Update SAM record
rec.setCigar(new Cigar(cigarElements));
rec.setAlignmentStart(alignmentStart);
rec.setReadBases(readBases);
rec.setBaseQualities(baseQualities);
// Reset saved attributes
Align.resetAttributes(rec, optFieldTags, optFieldValues);
// Set new attributes
if (space == SRMAUtil.Space.COLORSPACE) {
// set the XE attribute for colorError string
rec.setAttribute("XE", new String(colorErrors));
}
rec.setAttribute("AS", bestAlignHeapNode.score);
rec.setAttribute("XC", bestAlignHeapNode.alleleCoverageSum);
rec.setAttribute("PG", programRecord.getId());
rec.setAttribute("NM", numEdits);
}
public static void align(
Graph graph,
SAMRecord rec,
Node recNode,
ReferenceSequence sequence,
SAMProgramRecord programRecord,
int offset,
AlleleCoverageCutoffs alleleCoverageCutoffs,
boolean correctBases,
boolean useSequenceQualities,
int MAXIMUM_TOTAL_COVERAGE,
int MAX_HEAP_SIZE)
throws Exception {
int i;
AlignHeapNode curAlignHeapNode = null;
AlignHeapNode nextAlignHeapNode = null;
AlignHeapNode bestAlignHeapNode = null;
AlignHeap heap = null;
String read = null; // could be cs
String readBases = null; // always nt
String qualities = null; // could be cq
SRMAUtil.Space space = SRMAUtil.Space.NTSPACE;
ListIterator<NodeRecord> iter = null;
AlignHeapNodeComparator comp = null;
int alignmentStart = -1;
int numStartNodesAdded = 0;
boolean strand = rec.getReadNegativeStrandFlag(); // false -> forward, true -> reverse
String softClipStartBases = null;
String softClipStartQualities = null;
String softClipEndBases = null;
String softClipEndQualities = null;
// Debugging stuff
String readName = rec.getReadName();
assert SRMAUtil.Space.COLORSPACE != space;
// Get space
read = (String) rec.getAttribute("CS");
if (null == read) {
// Use base space
space = SRMAUtil.Space.NTSPACE;
} else {
// assumes CS and CQ are always in sequencing order
space = SRMAUtil.Space.COLORSPACE;
}
// Get read and qualities
if (space == SRMAUtil.Space.NTSPACE) {
byte tmpRead[] = rec.getReadString().getBytes();
byte tmpQualities[] = rec.getBaseQualityString().getBytes();
// Reverse once
if (strand) { // reverse
SAMRecordUtil.reverseArray(tmpRead);
SAMRecordUtil.reverseArray(tmpQualities);
}
read = new String(tmpRead);
readBases = new String(tmpRead);
qualities = new String(tmpQualities);
// Reverse again
if (strand) { // reverse
SAMRecordUtil.reverseArray(tmpRead);
SAMRecordUtil.reverseArray(tmpQualities);
}
} else {
byte tmpRead[] = rec.getReadString().getBytes();
// Reverse once
if (strand) { // reverse
SAMRecordUtil.reverseArray(tmpRead);
}
readBases = new String(tmpRead);
// Reverse again
if (strand) { // reverse
SAMRecordUtil.reverseArray(tmpRead);
}
read = SRMAUtil.normalizeColorSpaceRead(read);
qualities = (String) rec.getAttribute("CQ");
// Some aligners include a quality value for the adapter. A quality value
// IMHO should not be given for an unobserved (assumed) peice of data. Trim
// the first quality in this case
if (qualities.length() == 1 + read.length()) { // trim the first quality
qualities = qualities.substring(1);
}
}
// Reverse back
if (readBases.length() <= 0) {
throw new Exception("Error. The current alignment has no bases.");
}
if (read.length() <= 0) {
throw new Exception("Error. The current alignment has no bases.");
}
if (qualities.length() <= 0) {
throw new Exception("Error. The current alignment has no qualities.");
}
if (readBases.length() != read.length()) {
if (space == SRMAUtil.Space.COLORSPACE) {
throw new Exception(
"Error. The current alignment's read bases length does not match the length of the colors in the CS tag ["
+ rec.getReadName()
+ "].");
} else {
throw new Exception("Error. Internal error: readBases.length() != read.length()");
}
}
// Deal with soft-clipping
// - save the soft clipped sequence for latter
{
List<CigarElement> cigarElements = null;
cigarElements = rec.getCigar().getCigarElements();
CigarElement e1 = cigarElements.get(0); // first
CigarElement e2 = cigarElements.get(cigarElements.size() - 1); // last
// Soft-clipped
if (CigarOperator.S == e1.getOperator()) {
if (space == SRMAUtil.Space.COLORSPACE) {
throw new Exception(
"Error. Soft clipping with color-space data not currently supported.");
}
int l = e1.getLength();
if (strand) { // reverse
softClipStartBases = readBases.substring(readBases.length() - l);
softClipStartQualities = qualities.substring(qualities.length() - l);
readBases = readBases.substring(0, readBases.length() - l);
read = read.substring(0, read.length() - l);
qualities = qualities.substring(0, qualities.length() - l);
} else {
softClipStartBases = readBases.substring(0, l - 1);
softClipStartQualities = qualities.substring(0, l - 1);
readBases = readBases.substring(l);
read = read.substring(l);
qualities = qualities.substring(l);
}
}
if (CigarOperator.S == e2.getOperator()) {
if (space == SRMAUtil.Space.COLORSPACE) {
throw new Exception(
"Error. Soft clipping with color-space data not currently supported.");
}
int l = e2.getLength();
if (strand) { // reverse
softClipEndBases = readBases.substring(0, l - 1);
softClipEndQualities = qualities.substring(0, l - 1);
readBases = readBases.substring(l);
read = read.substring(l);
qualities = qualities.substring(l);
} else {
softClipEndBases = readBases.substring(readBases.length() - l);
softClipEndQualities = qualities.substring(qualities.length() - l);
readBases = readBases.substring(0, readBases.length() - l);
read = read.substring(0, read.length() - l);
qualities = qualities.substring(0, qualities.length() - l);
}
}
}
// Remove mate pair information
Align.removeMateInfo(rec);
comp =
new AlignHeapNodeComparator(
(strand) ? AlignHeap.HeapType.MAXHEAP : AlignHeap.HeapType.MINHEAP);
// Bound by original alignment if possible
bestAlignHeapNode =
Align.boundWithOriginalAlignment(
rec,
graph,
recNode,
comp,
strand,
read,
qualities,
readBases,
space,
sequence,
alleleCoverageCutoffs,
useSequenceQualities,
MAXIMUM_TOTAL_COVERAGE,
MAX_HEAP_SIZE);
/*
System.err.println("readName="+rec.getReadName());
if(null != bestAlignHeapNode) {
System.err.println("\nFOUND BEST:" + rec.toString());
}
else {
System.err.println("\nNOT FOUND (BEST): " + rec.toString());
}
Align.updateSAM(rec, programRecord, bestAlignHeapNode, space, read, qualities, softClipStartBases, softClipStartQualities, softClipEndBases, softClipEndQualities, strand, correctBases);
return;
*/
heap = new AlignHeap((strand) ? AlignHeap.HeapType.MAXHEAP : AlignHeap.HeapType.MINHEAP);
// Add start nodes
if (strand) { // reverse
alignmentStart = rec.getAlignmentEnd();
for (i = alignmentStart + offset; alignmentStart - offset <= i; i--) {
int position = graph.getPriorityQueueIndexAtPositionOrBefore(i);
PriorityQueue<Node> startNodeQueue = graph.getPriorityQueue(position);
if (0 != position && null != startNodeQueue) {
Iterator<Node> startNodeQueueIter = startNodeQueue.iterator();
while (startNodeQueueIter.hasNext()) {
Node startNode = startNodeQueueIter.next();
int f = passFilters(graph, startNode, alleleCoverageCutoffs, MAXIMUM_TOTAL_COVERAGE);
if (0 == f) {
heap.add(
new AlignHeapNode(
null,
startNode,
startNode.coverage,
read.charAt(0),
qualities.charAt(0),
useSequenceQualities,
space));
} else if (f < 0) {
return;
}
if (startNode.position < i) {
i = startNode.position;
}
numStartNodesAdded++;
}
}
}
} else {
alignmentStart = rec.getAlignmentStart();
for (i = alignmentStart - offset; i <= alignmentStart + offset; i++) {
int position = graph.getPriorityQueueIndexAtPositionOrGreater(i);
PriorityQueue<Node> startNodeQueue = graph.getPriorityQueue(position);
if (0 != position && null != startNodeQueue) {
Iterator<Node> startNodeQueueIter = startNodeQueue.iterator();
while (startNodeQueueIter.hasNext()) {
Node startNode = startNodeQueueIter.next();
int f = passFilters(graph, startNode, alleleCoverageCutoffs, MAXIMUM_TOTAL_COVERAGE);
if (0 == f) {
heap.add(
new AlignHeapNode(
null,
startNode,
startNode.coverage,
read.charAt(0),
qualities.charAt(0),
useSequenceQualities,
space));
} else if (f < 0) {
return;
}
if (i < startNode.position) {
i = startNode.position;
}
numStartNodesAdded++;
}
}
}
}
if (numStartNodesAdded == 0) {
throw new Exception("Did not add any start nodes!");
}
// Get first node off the heap
curAlignHeapNode = heap.poll();
while (null != curAlignHeapNode) {
if (MAX_HEAP_SIZE <= heap.size()) {
// too many to consider
return;
}
// System.err.println("strand:" + strand + "\tsize:" + heap.size() + "\talignmentStart:" +
// alignmentStart + "\toffset:" + offset + "\treadOffset:" + curAlignHeapNode.readOffset);
// System.err.print("size:" + heap.size() + ":" + curAlignHeapNode.readOffset + ":" +
// curAlignHeapNode.score + ":" + curAlignHeapNode.alleleCoverageSum + ":" +
// curAlignHeapNode.startPosition + "\t");
// curAlignHeapNode.node.print(System.err);
// System.err.print("\rposition:" + curAlignHeapNode.node.position + "\treadOffset:" +
// curAlignHeapNode.readOffset);
// Remove all non-insertions with the same contig/pos/read-offset/type/base and lower score
nextAlignHeapNode = heap.peek();
while (Node.INSERTION != curAlignHeapNode.node.type
&& null != nextAlignHeapNode
&& 0 == comp.compare(curAlignHeapNode, nextAlignHeapNode)) {
if (curAlignHeapNode.score < nextAlignHeapNode.score
|| (curAlignHeapNode.score == nextAlignHeapNode.score
&& curAlignHeapNode.alleleCoverageSum < nextAlignHeapNode.alleleCoverageSum)) {
// Update current node
curAlignHeapNode = heap.poll();
} else {
// Ignore next node
heap.poll();
}
nextAlignHeapNode = heap.peek();
}
nextAlignHeapNode = null;
// Check if the alignment is complete
if (curAlignHeapNode.readOffset == read.length() - 1) {
// All read bases examined, store if has the best alignment.
// System.err.print(curAlignHeapNode.alleleCoverageSum + ":" + curAlignHeapNode.score +
// ":");
// System.err.print(curAlignHeapNode.startPosition + ":");
// curAlignHeapNode.node.print(System.err);
if (null == bestAlignHeapNode
|| bestAlignHeapNode.score < curAlignHeapNode.score
|| (bestAlignHeapNode.score == curAlignHeapNode.score
&& bestAlignHeapNode.alleleCoverageSum < curAlignHeapNode.alleleCoverageSum)) {
bestAlignHeapNode = curAlignHeapNode;
}
} else if (null != bestAlignHeapNode && curAlignHeapNode.score < bestAlignHeapNode.score) {
// ignore, under the assumption that scores can only become more negative.
} else {
if (strand) { // reverse
// Go to all the "prev" nodes
iter = curAlignHeapNode.node.prev.listIterator();
} else { // forward
// Go to all "next" nodes
iter = curAlignHeapNode.node.next.listIterator();
}
while (iter.hasNext()) {
NodeRecord next = iter.next();
int f =
passFilters(
graph, next.node, next.coverage, alleleCoverageCutoffs, MAXIMUM_TOTAL_COVERAGE);
if (0 == f) {
heap.add(
new AlignHeapNode(
curAlignHeapNode,
next.node,
next.coverage,
read.charAt(curAlignHeapNode.readOffset + 1),
qualities.charAt(curAlignHeapNode.readOffset + 1),
useSequenceQualities,
space));
} else if (f < 0) {
return;
}
}
iter = null;
}
// Get next node
curAlignHeapNode = heap.poll();
}
// Recover alignment
Align.updateSAM(
rec,
sequence,
programRecord,
bestAlignHeapNode,
space,
read,
qualities,
softClipStartBases,
softClipStartQualities,
softClipEndBases,
softClipEndQualities,
strand,
correctBases);
}
@Override
public int doWork(String[] args) {
boolean repair_missing_read = false;
SortingCollectionFactory<MappedFastq> sortingFactory =
new SortingCollectionFactory<MappedFastq>();
File forwardFile = null;
File reverseFile = null;
com.github.lindenb.jvarkit.util.cli.GetOpt opt =
new com.github.lindenb.jvarkit.util.cli.GetOpt();
int c;
sortingFactory.setComponentType(MappedFastq.class);
sortingFactory.setCodec(new MappedFastqCodec());
sortingFactory.setComparator(new MappedFastqComparator());
while ((c = opt.getopt(args, super.getGetOptDefault() + "F:R:N:r")) != -1) {
switch (c) {
case 'F':
forwardFile = new File(opt.getOptArg());
break;
case 'R':
reverseFile = new File(opt.getOptArg());
break;
case 't':
addTmpDirectory(new File(opt.getOptArg()));
break;
case 'N':
sortingFactory.setMaxRecordsInRAM(Math.max(Integer.parseInt(opt.getOptArg()), 100));
break;
case 'r':
repair_missing_read = true;
break;
case ':':
System.err.println("Missing argument for option -" + opt.getOptOpt());
return -1;
default:
{
switch (handleOtherOptions(c, opt, args)) {
case EXIT_FAILURE:
return -1;
case EXIT_SUCCESS:
return 0;
default:
break;
}
}
}
}
SAMFileReader sfr = null;
SortingCollection<MappedFastq> fastqCollection = null;
try {
sortingFactory.setTmpDirs(this.getTmpDirectories());
fastqCollection = sortingFactory.make();
fastqCollection.setDestructiveIteration(true);
boolean found_single = false;
boolean found_paired = false;
long non_primary_alignmaned_flag = 0L;
if (opt.getOptInd() == args.length) {
info("Reading from stdin");
sfr = new SAMFileReader(System.in);
} else if (opt.getOptInd() + 1 == args.length) {
String filename = args[opt.getOptInd()];
sfr = new SAMFileReader(new File(filename));
} else {
error(getMessageBundle("illegal.number.of.arguments"));
return -1;
}
sfr.setValidationStringency(ValidationStringency.LENIENT);
SAMRecordIterator iter = sfr.iterator();
SAMSequenceDictionaryProgress progress =
new SAMSequenceDictionaryProgress(sfr.getFileHeader().getSequenceDictionary());
while (iter.hasNext()) {
SAMRecord rec = iter.next();
progress.watch(rec);
if (rec.isSecondaryOrSupplementary()) {
if (non_primary_alignmaned_flag == 0) {
warning("SKIPPING NON-PRIMARY " + (non_primary_alignmaned_flag + 1) + " ALIGNMENTS");
}
non_primary_alignmaned_flag++;
continue;
}
MappedFastq m = new MappedFastq();
m.name = rec.getReadName();
if (m.name == null) m.name = "";
m.hash = m.name.hashCode();
m.seq = rec.getReadString();
if (m.seq.equals(SAMRecord.NULL_SEQUENCE_STRING)) m.seq = "";
m.qual = rec.getBaseQualityString();
if (m.qual.equals(SAMRecord.NULL_QUALS_STRING)) m.qual = "";
if (!rec.getReadUnmappedFlag() && rec.getReadNegativeStrandFlag()) {
m.seq = AcidNucleics.reverseComplement(m.seq);
m.qual = new StringBuilder(m.qual).reverse().toString();
}
if (m.seq.length() != m.qual.length()) {
error("length(seq)!=length(qual) in " + m.name);
continue;
}
if (m.seq.isEmpty() && m.qual.isEmpty()) {
m.seq = "N";
m.qual = "#";
}
if (rec.getReadPairedFlag()) {
found_paired = true;
if (found_single) {
sfr.close();
throw new PicardException("input is a mix of paired/singled reads");
}
m.side = (byte) (rec.getSecondOfPairFlag() ? 2 : 1);
} else {
found_single = true;
if (found_paired) {
sfr.close();
throw new PicardException("input is a mix of paired/singled reads");
}
m.side = (byte) 0;
}
fastqCollection.add(m);
}
iter.close();
CloserUtil.close(iter);
CloserUtil.close(sfr);
progress.finish();
fastqCollection.doneAdding();
info("Done reading.");
if (found_paired) {
FastqWriter fqw1 = null;
FastqWriter fqw2 = null;
if (forwardFile != null) {
info("Writing to " + forwardFile);
fqw1 = new BasicFastqWriter(forwardFile);
} else {
info("Writing to stdout");
fqw1 = new BasicFastqWriter(new PrintStream(System.out));
}
if (reverseFile != null) {
info("Writing to " + reverseFile);
fqw2 = new BasicFastqWriter(reverseFile);
} else {
info("Writing to interlaced stdout");
fqw2 = fqw1;
}
List<MappedFastq> row = new ArrayList<MappedFastq>();
CloseableIterator<MappedFastq> r = fastqCollection.iterator();
for (; ; ) {
MappedFastq curr = null;
if (r.hasNext()) curr = r.next();
if (curr == null || (!row.isEmpty() && !row.get(0).name.equals(curr.name))) {
if (!row.isEmpty()) {
if (row.size() > 2) {
warning("WTF :" + row);
}
boolean found_F = false;
boolean found_R = false;
for (MappedFastq m : row) {
switch ((int) m.side) {
case 1:
if (found_F)
throw new PicardException("two forward reads found for " + row.get(0).name);
found_F = true;
echo(fqw1, m);
break;
case 2:
if (found_R)
throw new PicardException("two reverse reads found for " + row.get(0).name);
found_R = true;
echo(fqw2, m);
break;
default:
throw new IllegalStateException("uh???");
}
}
if (!found_F) {
if (repair_missing_read) {
warning("forward not found for " + row.get(0));
MappedFastq pad = new MappedFastq();
pad.side = (byte) 1;
pad.name = row.get(0).name;
pad.seq = "N";
pad.qual = "#";
echo(fqw1, pad);
} else {
throw new PicardException("forward not found for " + row);
}
}
if (!found_R) {
if (repair_missing_read) {
warning("reverse not found for " + row.get(0));
MappedFastq pad = new MappedFastq();
pad.side = (byte) 2;
pad.name = row.get(0).name;
pad.seq = "N";
pad.qual = "#";
echo(fqw2, pad);
} else {
throw new PicardException("reverse not found for " + row);
}
}
}
if (curr == null) break;
row.clear();
}
row.add(curr);
}
r.close();
fqw1.close();
fqw2.close();
} else if (found_single) {
FastqWriter fqw1 = null;
if (forwardFile != null) {
info("Writing to " + forwardFile);
fqw1 = new BasicFastqWriter(forwardFile);
} else {
info("Writing to stdout");
fqw1 = new BasicFastqWriter(new PrintStream(System.out));
}
CloseableIterator<MappedFastq> r = fastqCollection.iterator();
while (r.hasNext()) {
echo(fqw1, r.next());
}
r.close();
fqw1.close();
}
return 0;
} catch (Exception err) {
error(err);
return -1;
} finally {
if (fastqCollection != null) fastqCollection.cleanup();
}
}