@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 static void main(String[] args) {
args =
new String[] {
"/commun/data/users/cfaucheron/aln_20120329/S0529/data_S0529/S0529_sort.nodup.bam"
};
ReferenceSequenceFile rsf =
ReferenceSequenceFileFactory.getReferenceSequenceFile(
new File("/commun/data/pubdb/ucsc/hg19/chromosomes/hg19.fa"));
int count = 0;
for (String filename : args) {
File file = new File(filename);
SAMFileReader samIn = new SAMFileReader(file);
SAMRecordIterator r = samIn.iterator();
while (r.hasNext()) {
SAMRecord rec = r.next();
if (rec.getReadUnmappedFlag()) continue;
if (++count > 10000) break;
if (rec.getAlignmentStart() > rec.getAlignmentEnd()) throw new IllegalStateException();
byte bases[] =
rsf.getSubsequenceAt(
rec.getReferenceName(),
rec.getAlignmentStart(),
Math.max(
rec.getAlignmentEnd(),
rec.getAlignmentStart() + rec.getCigar().getPaddedReferenceLength()))
.getBases();
Iterator<CigarAlignment> i = CigarAlignment.iterator(rec);
/*System.err.println(rec.getCigarString());
System.err.println(bases.length);
System.err.println("start:"+rec.getAlignmentStart());*/
StringBuilder s1 = new StringBuilder();
StringBuilder s2 = new StringBuilder();
while (i.hasNext()) {
CigarAlignment caln = i.next();
/*
System.err.println(rec.getCigarString());
System.err.println("bases.length:"+bases.length);
System.err.println("refpos:"+caln.getReferencePosition1());
System.err.println("readpos:"+rec.getAlignmentStart());
*/
if (caln.getReferencePosition1() - rec.getAlignmentStart() >= bases.length) {
System.out.println("SHORT!");
System.out.println("op:" + caln.getCigarOperator());
System.out.println("read start:" + rec.getAlignmentStart());
System.out.println("clan.pos1:" + caln.getReferencePosition1());
System.out.println("read end:" + rec.getAlignmentEnd());
System.out.println("bases.length:" + bases.length);
System.out.println(
"getPaddedReferenceLength:" + rec.getCigar().getPaddedReferenceLength());
System.out.println("getReferenceLength:" + rec.getCigar().getReferenceLength());
System.out.println("getReadLength:" + rec.getCigar().getReadLength());
System.out.println(
"cigar.read.length:" + Cigar.getReadLength(rec.getCigar().getCigarElements()));
count = 2000;
break;
}
if (caln.isInsertRef()) {
s2.append("-");
s1.append(caln.getReadBase());
} else if (caln.isDeletionRef()) {
s2.append((char) bases[caln.getReferencePosition1() - rec.getAlignmentStart()]);
s1.append("-");
} else {
s2.append((char) bases[caln.getReferencePosition1() - rec.getAlignmentStart()]);
s1.append(caln.getReadBase());
}
// System.out.println(s1);
// System.out.println(s2);
// System.out.println();
}
System.out.println(
rec.getCigarString() + " " + rec.getReferenceName() + ":" + rec.getAlignmentStart());
System.out.println("ref :" + new String(bases));
System.out.println("read:" + new String(rec.getReadBases()));
System.out.println();
System.out.println(s1);
System.out.println(s2);
System.out.println();
}
samIn.close();
}
}