private VariantContext getMatchingSnpEffRecord(
List<VariantContext> snpEffRecords, VariantContext vc) {
for (VariantContext snpEffRecord : snpEffRecords) {
if (snpEffRecord.hasSameAlternateAllelesAs(vc)
&& snpEffRecord.getReference().equals(vc.getReference())) {
return snpEffRecord;
}
}
return null;
}
private byte[] generateHaplotype(
final List<VariantContext> sourceVCs, final ReferenceContext refContext) {
final StringBuilder sb = new StringBuilder();
final int startPos = refContext.getWindow().getStart();
int currentPos = startPos;
final byte[] reference = refContext.getBases();
for (final VariantContext vc : sourceVCs) {
// add any missing reference context
int vcStart = vc.getStart();
final int refAlleleLength = vc.getReference().length();
if (refAlleleLength
== vc.getEnd()
- vc.getStart()) // this is a deletion (whereas for other events the padding base
// isn't part of the position)
vcStart++;
while (currentPos < vcStart) sb.append((char) reference[currentPos++ - startPos]);
// add the alt allele
sb.append(vc.getAlternateAllele(0).getBaseString());
// skip the reference allele
currentPos += refAlleleLength;
}
// add any missing reference context
final int stopPos = refContext.getWindow().getStop();
while (currentPos < stopPos) sb.append((char) reference[currentPos++ - startPos]);
return sb.toString().getBytes();
}
@Override
public void accumulate(final VariantContext ctx) {
logger.record(ctx.getContig(), ctx.getStart());
final String variantChrom = ctx.getContig();
final int variantPos = ctx.getStart();
// Skip anything a little too funky
if (ctx.isFiltered()) return;
if (!ctx.isVariant()) return;
if (SKIP_CHROMS.contains(variantChrom)) return;
for (final MendelianViolationMetrics trio : trios) {
final Genotype momGt = ctx.getGenotype(trio.MOTHER);
final Genotype dadGt = ctx.getGenotype(trio.FATHER);
final Genotype kidGt = ctx.getGenotype(trio.OFFSPRING);
// if any genotype:
// - has a non-snp allele; or
// - lacks a reference allele
//
// then ignore this trio
if (CollectionUtil.makeList(momGt, dadGt, kidGt)
.stream()
.anyMatch(
gt ->
gt.isHetNonRef()
|| Stream.concat(Stream.of(ctx.getReference()), gt.getAlleles().stream())
.anyMatch(a -> a.length() != 1 || a.isSymbolic()))) {
continue;
}
// if between the trio there are more than 2 alleles including the reference, continue
if (Stream.concat(
Collections.singleton(ctx.getReference()).stream(),
CollectionUtil.makeList(momGt, dadGt, kidGt)
.stream()
.flatMap(gt -> gt.getAlleles().stream()))
.collect(Collectors.toSet())
.size()
> 2) continue;
// Test to make sure:
// 1) That the site is in fact variant in the trio
// 2) that the offspring doesn't have a really wacky het allele balance
if (!isVariant(momGt, dadGt, kidGt)) continue;
if (kidGt.isHet()) {
final int[] ad = kidGt.getAD();
if (ad == null) continue;
final List<Integer> adOfAlleles =
kidGt
.getAlleles()
.stream()
.map(a -> ad[ctx.getAlleleIndex(a)])
.collect(Collectors.toList());
final double minAlleleFraction =
Math.min(adOfAlleles.get(0), adOfAlleles.get(1))
/ (double) (adOfAlleles.get(0) + adOfAlleles.get(1));
if (minAlleleFraction < MIN_HET_FRACTION) continue;
}
///////////////////////////////////////////////////////////////
// Determine whether the offspring should be haploid at this
// locus and which is the parental donor of the haploid genotype
///////////////////////////////////////////////////////////////
boolean haploid = false;
Genotype haploidParentalGenotype = null;
if (FEMALE_CHROMS.contains(variantChrom) && trio.OFFSPRING_SEX != Sex.Unknown) {
if (trio.OFFSPRING_SEX == Sex.Female) {
// famale
haploid = false;
} else if (isInPseudoAutosomalRegion(variantChrom, variantPos)) {
// male but in PAR on X, so diploid
haploid = false;
} else {
// male, out of PAR on X, haploid
haploid = true;
haploidParentalGenotype = momGt;
}
}
// the PAR on the male chromosome should be masked so that reads
// align to the female chromosomes instead, so there's no point
// of worrying about that here.
if (MALE_CHROMS.contains(variantChrom)) {
if (trio.OFFSPRING_SEX == Sex.Male) {
haploid = true;
haploidParentalGenotype = dadGt;
} else {
continue;
}
}
// We only want to look at sites where we have high enough confidence that the genotypes we
// are looking at are
// interesting. We want to ensure that parents are always GQ>=MIN_GQ, and that the kid is
// either GQ>=MIN_GQ or in the
// case where kid is het that the phred-scaled-likelihood of being reference is >=MIN_GQ.
if (haploid
&& (haploidParentalGenotype.isNoCall() || haploidParentalGenotype.getGQ() < MIN_GQ))
continue;
if (!haploid
&& (momGt.isNoCall()
|| momGt.getGQ() < MIN_GQ
|| dadGt.isNoCall()
|| dadGt.getGQ() < MIN_GQ)) continue;
if (kidGt.isNoCall()) continue;
if (momGt.isHomRef() && dadGt.isHomRef() && !kidGt.isHomRef()) {
if (kidGt.getPL()[0] < MIN_GQ) continue;
} else if (kidGt.getGQ() < MIN_GQ) continue;
// Also filter on the DP for each of the samples - it's possible to miss hets when DP is too
// low
if (haploid && (kidGt.getDP() < MIN_DP || haploidParentalGenotype.getDP() < MIN_DP)) continue;
if (!haploid && (kidGt.getDP() < MIN_DP || momGt.getDP() < MIN_DP || dadGt.getDP() < MIN_DP))
continue;
trio.NUM_VARIANT_SITES++;
///////////////////////////////////////////////////////////////
// First test for haploid violations
///////////////////////////////////////////////////////////////
MendelianViolation type = null;
if (haploid) {
if (kidGt.isHet()) continue; // Should not see heterozygous calls at haploid regions
if (!haploidParentalGenotype.getAlleles().contains(kidGt.getAllele(0))) {
if (kidGt.isHomRef()) {
type = MendelianViolation.Haploid_Other;
trio.NUM_HAPLOID_OTHER++;
} else {
type = MendelianViolation.Haploid_Denovo;
trio.NUM_HAPLOID_DENOVO++;
}
}
}
///////////////////////////////////////////////////////////////
// Then test for diploid mendelian violations
///////////////////////////////////////////////////////////////
else if (isMendelianViolation(momGt, dadGt, kidGt)) {
if (momGt.isHomRef() && dadGt.isHomRef() && !kidGt.isHomRef()) {
trio.NUM_DIPLOID_DENOVO++;
type = MendelianViolation.Diploid_Denovo;
} else if (momGt.isHomVar() && dadGt.isHomVar() && kidGt.isHet()) {
trio.NUM_HOMVAR_HOMVAR_HET++;
type = MendelianViolation.HomVar_HomVar_Het;
} else if (kidGt.isHom()
&& ((momGt.isHomRef() && dadGt.isHomVar()) || (momGt.isHomVar() && dadGt.isHomRef()))) {
trio.NUM_HOMREF_HOMVAR_HOM++;
type = MendelianViolation.HomRef_HomVar_Hom;
} else if (kidGt.isHom()
&& ((momGt.isHom() && dadGt.isHet()) || (momGt.isHet() && dadGt.isHom()))) {
trio.NUM_HOM_HET_HOM++;
type = MendelianViolation.Hom_Het_Hom;
} else {
trio.NUM_OTHER++;
type = MendelianViolation.Other;
}
}
// Output a record into the family's violation VCF
if (type != null) {
// Create a new Context subsetted to the three samples
final VariantContextBuilder builder = new VariantContextBuilder(ctx);
builder.genotypes(
ctx.getGenotypes()
.subsetToSamples(CollectionUtil.makeSet(trio.MOTHER, trio.FATHER, trio.OFFSPRING)));
builder.attribute(MENDELIAN_VIOLATION_KEY, type.name());
// Copy over some useful attributes from the full context
if (ctx.hasAttribute(VCFConstants.ALLELE_COUNT_KEY))
builder.attribute(ORIGINAL_AC, ctx.getAttribute(VCFConstants.ALLELE_COUNT_KEY));
if (ctx.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY))
builder.attribute(ORIGINAL_AF, ctx.getAttribute(VCFConstants.ALLELE_FREQUENCY_KEY));
if (ctx.hasAttribute(VCFConstants.ALLELE_NUMBER_KEY))
builder.attribute(ORIGINAL_AN, ctx.getAttribute(VCFConstants.ALLELE_NUMBER_KEY));
// Write out the variant record
familyToViolations.get(trio.FAMILY_ID).add(builder.make());
}
}
}
@Override
public void runCommand() {
logger.info("MergeVCFColumnsCommand");
/*
* Assumptions
* (1) Only two vcfs that are sorted with the same contig order
* (2) if contigs on it same order, then we will just skip that contig
* (3) No overlapping samples allowed
*
* Output:
* A vcf where intersecting sites are merged together and will only return biallelic markers
* the info field will be cleared
* the only GT FORMAT field will be there
*/
Collection<File> vcfs = applicationOptions.getVcfs();
String outfile = applicationOptions.getOutFile();
if (vcfs.size() != 2) {
throw new IllegalArgumentException("This function requires exactly two vcfs");
}
Iterator<File> vcfFileIter = vcfs.iterator();
File vcf1 = vcfFileIter.next();
File vcf2 = vcfFileIter.next();
VCFFileReader reader1 = new VCFFileReader(vcf1, false);
VCFFileReader reader2 = new VCFFileReader(vcf2, false);
Iterator<VariantContext> iter1 = reader1.iterator();
Iterator<VariantContext> iter2 = reader2.iterator();
VariantContextComparator comparator = new VariantContextComparator();
/*
* Merge headers
*/
VCFHeader header1 = reader1.getFileHeader();
VCFHeader header2 = reader2.getFileHeader();
List<String> samples1 = header1.getGenotypeSamples();
List<String> samples2 = header2.getGenotypeSamples();
List<String> mergedSamples = new ArrayList<>(samples1.size() + samples2.size());
mergedSamples.addAll(samples1);
mergedSamples.addAll(samples2);
// Validate that there are no duplicates
HashSet<String> sampleSet = new HashSet<String>();
for (String id : mergedSamples) {
if (sampleSet.contains(id)) {
throw new IllegalArgumentException("Duplicate id found: " + id);
} else {
sampleSet.add(id);
}
}
HashSet<VCFHeaderLine> meta = new HashSet<>();
meta.add(new VCFFormatHeaderLine("GT", 1, VCFHeaderLineType.String, "GT"));
meta.addAll(header1.getContigLines());
VCFHeader mergedHeader = new VCFHeader(meta, mergedSamples);
/*
* Create encoder
*/
VCFEncoder encoder = new VCFEncoder(mergedHeader, false, false);
BufferedWriter writer = null;
try {
if (outfile.endsWith(".gz")) {
BlockCompressedOutputStream outstream = new BlockCompressedOutputStream(new File(outfile));
writer = new BufferedWriter(new OutputStreamWriter(outstream));
} else {
writer =
Files.newBufferedWriter(
Paths.get(outfile),
Charset.defaultCharset(),
StandardOpenOption.CREATE,
StandardOpenOption.TRUNCATE_EXISTING);
}
/*
* Write header
*/
VCFHeaderWriter.writeHeader(writer, mergedHeader);
logger.info("Wrote header");
VariantContext previous1 = null;
VariantContext previous2 = null;
int count = 0;
int countFile1 = 0;
int countFile2 = 0;
boolean usePrevious1 = false;
boolean usePrevious2 = false;
while (iter1.hasNext() || iter2.hasNext()) {
if ((iter1.hasNext() || usePrevious1) && (iter2.hasNext() || usePrevious2)) {
VariantContext variant1 = null;
VariantContext variant2 = null;
// if(usePrevious1 == true && usePrevious2 == true &&
// comparator.compare(previous1,previous2) != 0) {
// //then skip both
// usePrevious1 = false;
// usePrevious2 = false;
// }
if (usePrevious1) {
variant1 = previous1;
} else {
variant1 = iter1.next();
countFile1++;
}
if (usePrevious2) {
variant2 = previous2;
} else {
variant2 = iter2.next();
countFile2++;
}
// check that variants are ordered correctly
if (previous1 != null
&& previous1 != variant1
&& comparator.compare(previous1, variant1) > 0) {
throw new IllegalStateException(
previous1.getContig()
+ ":"
+ previous1.getStart()
+ " > "
+ variant1.getContig()
+ ":"
+ variant1.getStart());
}
if (previous2 != null
&& previous2 != variant2
&& comparator.compare(previous2, variant2) > 0) {
throw new IllegalStateException(
previous2.getContig()
+ ":"
+ previous2.getStart()
+ " > "
+ variant2.getContig()
+ ":"
+ variant2.getStart());
}
int cmp = comparator.compare(variant1, variant2);
if (cmp < 0) {
// logger.info("Skipping VCF1: " + variant1.getContig() + ":" + variant1.getStart() +
// "\t" + variant1.getReference().toString() + "\t" + variant1.getAlternateAlleles());
if (usePrevious1 == true && usePrevious2 == true) {
// variant1 < variant2
// we need to go to next variant in vcf1
usePrevious1 = false;
}
usePrevious2 = true;
} else if (cmp > 0) {
if (usePrevious1 == true && usePrevious2 == true) {
// variant1 > variant2
// we need to go to next variant in vcf2
usePrevious2 = false;
}
usePrevious1 = true;
// logger.info("Skipping VCF2: " + variant2.getContig() + ":" + variant2.getStart() +
// "\t" + variant2.getReference().toString() + "\t" + variant2.getAlternateAlleles());
} else {
// they equal position
usePrevious1 = false;
usePrevious2 = false;
if (variant1.isBiallelic()
&& variant2.isBiallelic()
&& variant1.getReference().equals(variant2.getReference())
&& variant1.getAlternateAllele(0).equals(variant2.getAlternateAllele(0))) {
// TODO: Finish merging
// both variants are bialleleic and the reference and alternative alleles match
count++;
if (count % 10000 == 0) {
logger.info(count + " mergeable variants found");
}
VariantContext merged = VariantContextMerger.merge(variant1, variant2);
writer.write(encoder.encode(merged));
writer.write("\n");
} else {
// skip if they do not equal
// logger.info("Skipping: " + variant1.getContig() + ":" + variant1.getStart() +
// "\t" + variant1.getReference().toString() + "\t" +
// variant1.getAlternateAlleles());
// logger.info("Skipping: " + variant2.getContig() + ":" + variant2.getStart() +
// "\t" + variant2.getReference().toString() + "\t" +
// variant2.getAlternateAlleles());
}
}
previous1 = variant1;
previous2 = variant2;
} else if (iter1.hasNext()) {
// just skip remaining variants
VariantContext current = iter1.next();
countFile1++;
if (previous1 != null && current != null && comparator.compare(previous1, current) > 0) {
throw new IllegalStateException(
previous1.getContig()
+ ":"
+ previous1.getStart()
+ " > "
+ current.getContig()
+ ":"
+ current.getStart());
}
previous1 = current;
// logger.info("Skipping: " + previous1.getContig() + ":" + previous1.getStart() + "\t" +
// previous1.getReference().toString() + "\t" + previous1.getAlternateAlleles());
} else if (iter2.hasNext()) {
// just skip remaining variants
// fixed bug/ was iter1 changed to iter2
VariantContext current = iter2.next();
countFile2++;
if (previous2 != null && current != null && comparator.compare(previous2, current) > 0) {
throw new IllegalStateException(
previous2.getContig()
+ ":"
+ previous2.getStart()
+ " > "
+ current.getContig()
+ ":"
+ current.getStart());
}
previous2 = current;
// logger.info("Skipping: " + previous2.getContig() + ":" + previous2.getStart() + "\t" +
// previous2.getReference().toString() + "\t" + previous2.getAlternateAlleles());
} else {
throw new IllegalStateException("Error should not of reached this point");
}
}
reader1.close();
reader2.close();
logger.info(count + " merged variants");
logger.info(countFile1 + " variants in " + vcf1.getAbsolutePath());
logger.info(countFile2 + " variants in " + vcf2.getAbsolutePath());
} catch (Exception e) {
e.printStackTrace();
} finally {
if (writer != null) {
try {
logger.info("Flushing writer");
writer.close();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
}
logger.info("finished merging vcfs");
}
@Override
protected void doWork(VcfIterator r, VariantContextWriter w) throws IOException {
AbstractVCFCodec codeIn3 = VCFUtils.createDefaultVCFCodec();
String line;
StringWriter sw = new StringWriter();
LOG.info("opening tabix file: " + this.TABIX);
TabixReader tabix = new TabixReader(this.TABIX);
while ((line = tabix.readLine()) != null) {
if (!line.startsWith(VCFHeader.HEADER_INDICATOR)) {
break;
}
sw.append(line).append("\n");
}
VCFHeader header3 =
(VCFHeader)
codeIn3.readActualHeader(
new LineIteratorImpl(
LineReaderUtil.fromBufferedStream(
new ByteArrayInputStream(sw.toString().getBytes()))));
VCFHeader header1 = r.getHeader();
VCFHeader h2 =
new VCFHeader(header1.getMetaDataInInputOrder(), header1.getSampleNamesInOrder());
for (String infoId : this.INFO_IDS) {
VCFInfoHeaderLine vihl = header3.getInfoHeaderLine(infoId);
if (vihl == null) {
LOG.warn("Not INFO=" + infoId + " in " + TABIX);
continue;
}
if (h2.getInfoHeaderLine(infoId) != null) {
LOG.warn("Input already contains INFO=" + vihl);
}
h2.addMetaDataLine(vihl);
}
if (ALT_CONFLICT_FLAG != null) {
h2.addMetaDataLine(
new VCFInfoHeaderLine(
ALT_CONFLICT_FLAG,
1,
VCFHeaderLineType.Flag,
"conflict ALT allele with " + this.TABIX));
}
w.writeHeader(h2);
while (r.hasNext()) {
VariantContext ctx1 = r.next();
VariantContextBuilder vcb = new VariantContextBuilder(ctx1);
String line2;
String BEST_ID = null;
boolean best_id_match_alt = false;
List<VariantContext> variantsList = new ArrayList<VariantContext>();
int[] array = tabix.parseReg(ctx1.getChr() + ":" + (ctx1.getStart()) + "-" + (ctx1.getEnd()));
TabixReader.Iterator iter = null;
if (array != null && array.length == 3 && array[0] != -1 && array[1] >= 0 && array[2] >= 0) {
iter = tabix.query(array[0], array[1], array[2]);
} else {
LOG.info("Cannot get " + ctx1.getChr() + ":" + (ctx1.getStart()) + "-" + (ctx1.getEnd()));
}
while (iter != null && (line2 = iter.next()) != null) {
VariantContext ctx3 = codeIn3.decode(line2);
if (ctx3.getStart() != ctx1.getStart()) continue;
if (ctx3.getEnd() != ctx1.getEnd()) continue;
if (ctx1.getReference().equals(ctx3.getReference())
&& ctx1.getAlternateAlleles().equals(ctx3.getAlternateAlleles())) {
variantsList.clear();
variantsList.add(ctx3);
break;
} else {
variantsList.add(ctx3);
}
}
for (VariantContext ctx3 : variantsList) {
if (this.REF_ALLELE_MATTERS && !ctx1.getReference().equals(ctx3.getReference())) {
continue;
}
if (this.ALT_ALLELES_MATTERS
&& !ctx1.getAlternateAlleles().equals(ctx3.getAlternateAlleles())) {
continue;
}
if (ctx3.getID() != null && this.REPLACE_ID) {
if (BEST_ID != null && best_id_match_alt) {
// nothing
} else {
BEST_ID = ctx3.getID();
best_id_match_alt = ctx1.getAlternateAlleles().equals(ctx3.getAlternateAlleles());
}
}
for (String id : this.INFO_IDS) {
Object info3 = ctx3.getAttribute(id);
if (info3 == null) {
continue;
}
Object info1 = ctx1.getAttribute(id);
if (info1 != null && !this.REPLACE_INFO_FIELD) {
continue;
}
vcb.attribute(id, info3);
}
if (ALT_CONFLICT_FLAG != null
&& !ctx1.getAlternateAlleles().equals(ctx3.getAlternateAlleles())) {
vcb.attribute(ALT_CONFLICT_FLAG, true);
}
}
if (BEST_ID != null) {
vcb.id(BEST_ID);
}
w.add(vcb.make());
}
tabix.close();
}
@Override
protected void doWork(VcfIterator r, VariantContextWriter w) throws IOException {
long nChanged = 0L;
final String TAG = "INDELFIXED";
VCFHeader header = r.getHeader();
VCFHeader h2 = new VCFHeader(header.getMetaDataInInputOrder(), header.getSampleNamesInOrder());
h2.addMetaDataLine(
new VCFInfoHeaderLine(TAG, 1, VCFHeaderLineType.String, "Fix Indels for @SolenaLS."));
w.writeHeader(h2);
final Pattern dna = Pattern.compile("[ATGCatgc]+");
while (r.hasNext()) {
VariantContext ctx = r.next();
VariantContextBuilder b = new VariantContextBuilder(ctx);
List<Allele> alleles = ctx.getAlternateAlleles();
if (alleles.size() != 1
|| !dna.matcher(ctx.getReference().getBaseString()).matches()
|| !dna.matcher(alleles.get(0).getBaseString()).matches()) {
w.add(ctx);
continue;
}
StringBuffer ref = new StringBuffer(ctx.getReference().getBaseString().toUpperCase());
StringBuffer alt = new StringBuffer(alleles.get(0).getBaseString().toUpperCase());
int start = ctx.getStart();
int end = ctx.getEnd();
boolean changed = false;
/** ** we trim on the right side *** */
// REF=TGCTGCGGGGGCCGCTGCGGGGG ALT=TGCTGCGGGGG
while (alt.length() > 1
&& alt.length() < ref.length()
&& ref.charAt(ref.length() - 1) == alt.charAt(alt.length() - 1)) {
changed = true;
ref.setLength(ref.length() - 1);
alt.deleteCharAt(alt.length() - 1);
end--;
}
// REF=TGCTGCGGGGG ALT= TGCTGCGGGGGCCGCTGCGGGGG
while (ref.length() > 1
&& alt.length() > ref.length()
&& ref.charAt(ref.length() - 1) == alt.charAt(alt.length() - 1)) {
changed = true;
ref.setLength(ref.length() - 1);
alt.deleteCharAt(alt.length() - 1);
end--;
}
/** ** we trim on the left side *** */
// REF=TGCTGCGGGGGCCGCTGCGGGGG ALT=TGCTGCGGGGG
while (alt.length() > 1 && alt.length() < ref.length() && ref.charAt(0) == alt.charAt(0)) {
changed = true;
ref.deleteCharAt(0);
alt.deleteCharAt(0);
start++;
}
// REF=TGCTGCGGGGG ALT= TGCTGCGGGGGCCGCTGCGGGGG
while (ref.length() > 1 && alt.length() > ref.length() && ref.charAt(0) == alt.charAt(0)) {
changed = true;
ref.deleteCharAt(0);
alt.deleteCharAt(0);
start++;
}
if (!changed) {
w.add(ctx);
continue;
}
/*
LOG.info(line);
LOG.info("ctx.getStart() "+ctx.getStart());
LOG.info("ctx.getEnd() "+ ctx.getEnd());
LOG.info("start " + start);
LOG.info("end "+end);
LOG.info("ref " + ref.toString());
LOG.info("alt "+alt.toString());
*/
Allele newRef = Allele.create(ref.toString(), true);
Allele newAlt = Allele.create(alt.toString(), false);
Allele newalleles[] = new Allele[] {newRef, newAlt};
b.attribute(
TAG,
ctx.getReference().getBaseString()
+ "|"
+ alleles.get(0).getBaseString()
+ "|"
+ ctx.getStart());
b.start(start);
b.stop(end);
b.alleles(Arrays.asList(newalleles));
nChanged++;
VariantContext ctx2 = b.make();
try {
w.add(ctx2);
} catch (TribbleException err) {
error(err, "Cannot convert new context:" + ctx2 + " old context:" + ctx);
w.add(ctx);
}
}
info("indels changed:" + nChanged);
}