@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);
}
