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();
}
}
/**
* Asserts that files are readable and writable and then fires off an HsMetricsCalculator instance
* to do the real work.
*/
protected int doWork() {
IoUtil.assertFileIsReadable(getProbeIntervals());
IoUtil.assertFileIsReadable(TARGET_INTERVALS);
IoUtil.assertFileIsReadable(INPUT);
IoUtil.assertFileIsWritable(OUTPUT);
if (PER_TARGET_COVERAGE != null) IoUtil.assertFileIsWritable(PER_TARGET_COVERAGE);
final SAMFileReader samReader = new SAMFileReader(INPUT);
final File probeIntervals = getProbeIntervals();
// Validate that the targets and baits have the same references as the reads file
SequenceUtil.assertSequenceDictionariesEqual(
samReader.getFileHeader().getSequenceDictionary(),
IntervalList.fromFile(TARGET_INTERVALS).getHeader().getSequenceDictionary(),
INPUT,
TARGET_INTERVALS);
SequenceUtil.assertSequenceDictionariesEqual(
samReader.getFileHeader().getSequenceDictionary(),
IntervalList.fromFile(probeIntervals).getHeader().getSequenceDictionary(),
INPUT,
probeIntervals);
ReferenceSequenceFile ref = null;
if (REFERENCE_SEQUENCE != null) {
IoUtil.assertFileIsReadable(REFERENCE_SEQUENCE);
ref = ReferenceSequenceFileFactory.getReferenceSequenceFile(REFERENCE_SEQUENCE);
SequenceUtil.assertSequenceDictionariesEqual(
samReader.getFileHeader().getSequenceDictionary(),
ref.getSequenceDictionary(),
INPUT,
REFERENCE_SEQUENCE);
}
final TargetMetricsCollector collector =
makeCollector(
METRIC_ACCUMULATION_LEVEL,
samReader.getFileHeader().getReadGroups(),
ref,
PER_TARGET_COVERAGE,
TARGET_INTERVALS,
probeIntervals,
getProbeSetName());
// Add each record to the requested collectors
final Iterator<SAMRecord> records = samReader.iterator();
final ProgressLogger progress = new ProgressLogger(log);
while (records.hasNext()) {
final SAMRecord sam = records.next();
collector.acceptRecord(sam, null);
progress.record(sam);
}
// Write the output file
final MetricsFile<HsMetrics, Integer> metrics = getMetricsFile();
collector.finish();
collector.addAllLevelsToFile(metrics);
metrics.write(OUTPUT);
return 0;
}
static VariantContext reallyMergeIntoMNP(
VariantContext vc1, VariantContext vc2, ReferenceSequenceFile referenceFile) {
int startInter = vc1.getEnd() + 1;
int endInter = vc2.getStart() - 1;
byte[] intermediateBases = null;
if (startInter <= endInter) {
intermediateBases =
referenceFile.getSubsequenceAt(vc1.getChr(), startInter, endInter).getBases();
StringUtil.toUpperCase(intermediateBases);
}
MergedAllelesData mergeData =
new MergedAllelesData(
intermediateBases, vc1, vc2); // ensures that the reference allele is added
GenotypesContext mergedGenotypes = GenotypesContext.create();
for (final Genotype gt1 : vc1.getGenotypes()) {
Genotype gt2 = vc2.getGenotype(gt1.getSampleName());
List<Allele> site1Alleles = gt1.getAlleles();
List<Allele> site2Alleles = gt2.getAlleles();
List<Allele> mergedAllelesForSample = new LinkedList<Allele>();
/* NOTE: Since merged alleles are added to mergedAllelesForSample in the SAME order as in the input VC records,
we preserve phase information (if any) relative to whatever precedes vc1:
*/
Iterator<Allele> all2It = site2Alleles.iterator();
for (Allele all1 : site1Alleles) {
Allele all2 = all2It.next(); // this is OK, since allSamplesAreMergeable()
Allele mergedAllele = mergeData.ensureMergedAllele(all1, all2);
mergedAllelesForSample.add(mergedAllele);
}
double mergedGQ = Math.max(gt1.getLog10PError(), gt2.getLog10PError());
Set<String> mergedGtFilters =
new HashSet<
String>(); // Since gt1 and gt2 were unfiltered, the Genotype remains unfiltered
Map<String, Object> mergedGtAttribs = new HashMap<String, Object>();
PhaseAndQuality phaseQual = calcPhaseForMergedGenotypes(gt1, gt2);
if (phaseQual.PQ != null) mergedGtAttribs.put(ReadBackedPhasingWalker.PQ_KEY, phaseQual.PQ);
Genotype mergedGt =
new Genotype(
gt1.getSampleName(),
mergedAllelesForSample,
mergedGQ,
mergedGtFilters,
mergedGtAttribs,
phaseQual.isPhased);
mergedGenotypes.add(mergedGt);
}
String mergedName = mergeVariantContextNames(vc1.getSource(), vc2.getSource());
double mergedLog10PError = Math.min(vc1.getLog10PError(), vc2.getLog10PError());
Set<String> mergedFilters =
new HashSet<
String>(); // Since vc1 and vc2 were unfiltered, the merged record remains unfiltered
Map<String, Object> mergedAttribs = mergeVariantContextAttributes(vc1, vc2);
// ids
List<String> mergedIDs = new ArrayList<String>();
if (vc1.hasID()) mergedIDs.add(vc1.getID());
if (vc2.hasID()) mergedIDs.add(vc2.getID());
String mergedID =
mergedIDs.isEmpty()
? VCFConstants.EMPTY_ID_FIELD
: Utils.join(VCFConstants.ID_FIELD_SEPARATOR, mergedIDs);
VariantContextBuilder mergedBuilder =
new VariantContextBuilder(
mergedName,
vc1.getChr(),
vc1.getStart(),
vc2.getEnd(),
mergeData.getAllMergedAlleles())
.id(mergedID)
.genotypes(mergedGenotypes)
.log10PError(mergedLog10PError)
.filters(mergedFilters)
.attributes(mergedAttribs);
VariantContextUtils.calculateChromosomeCounts(mergedBuilder, true);
return mergedBuilder.make();
}