/**
* Read in a list of ExactCall objects from reader, keeping only those with starts in startsToKeep
* or all sites (if this is empty)
*
* @param reader a just-opened reader sitting at the start of the file
* @param startsToKeep a list of start position of the calls to keep, or empty if all calls should
* be kept
* @param parser a genome loc parser to create genome locs
* @return a list of ExactCall objects in reader
* @throws IOException
*/
public static List<ExactCall> readExactLog(
final BufferedReader reader, final List<Integer> startsToKeep, GenomeLocParser parser)
throws IOException {
if (reader == null) throw new IllegalArgumentException("reader cannot be null");
if (startsToKeep == null) throw new IllegalArgumentException("startsToKeep cannot be null");
if (parser == null) throw new IllegalArgumentException("GenomeLocParser cannot be null");
List<ExactCall> calls = new LinkedList<ExactCall>();
// skip the header line
reader.readLine();
// skip the first "type" line
reader.readLine();
while (true) {
final VariantContextBuilder builder = new VariantContextBuilder();
final List<Allele> alleles = new ArrayList<Allele>();
final List<Genotype> genotypes = new ArrayList<Genotype>();
final double[] posteriors = new double[2];
final double[] priors = MathUtils.normalizeFromLog10(new double[] {0.5, 0.5}, true);
final List<Integer> mle = new ArrayList<Integer>();
final Map<Allele, Double> log10pNonRefByAllele = new HashMap<Allele, Double>();
long runtimeNano = -1;
GenomeLoc currentLoc = null;
while (true) {
final String line = reader.readLine();
if (line == null) return calls;
final String[] parts = line.split("\t");
final GenomeLoc lineLoc = parser.parseGenomeLoc(parts[0]);
final String variable = parts[1];
final String key = parts[2];
final String value = parts[3];
if (currentLoc == null) currentLoc = lineLoc;
if (variable.equals("type")) {
if (startsToKeep.isEmpty() || startsToKeep.contains(currentLoc.getStart())) {
builder.alleles(alleles);
final int stop = currentLoc.getStart() + alleles.get(0).length() - 1;
builder.chr(currentLoc.getContig()).start(currentLoc.getStart()).stop(stop);
builder.genotypes(genotypes);
final int[] mleInts = ArrayUtils.toPrimitive(mle.toArray(new Integer[] {}));
final AFCalcResult result =
new AFCalcResult(mleInts, 1, alleles, posteriors, priors, log10pNonRefByAllele);
calls.add(new ExactCall(builder.make(), runtimeNano, result));
}
break;
} else if (variable.equals("allele")) {
final boolean isRef = key.equals("0");
alleles.add(Allele.create(value, isRef));
} else if (variable.equals("PL")) {
final GenotypeBuilder gb = new GenotypeBuilder(key);
gb.PL(GenotypeLikelihoods.fromPLField(value).getAsPLs());
genotypes.add(gb.make());
} else if (variable.equals("log10PosteriorOfAFEq0")) {
posteriors[0] = Double.valueOf(value);
} else if (variable.equals("log10PosteriorOfAFGt0")) {
posteriors[1] = Double.valueOf(value);
} else if (variable.equals("MLE")) {
mle.add(Integer.valueOf(value));
} else if (variable.equals("pNonRefByAllele")) {
final Allele a = Allele.create(key);
log10pNonRefByAllele.put(a, Double.valueOf(value));
} else if (variable.equals("runtime.nano")) {
runtimeNano = Long.valueOf(value);
} else {
// nothing to do
}
}
}
}
private final double getRefBinomialProb(final int depth) {
if (depth < binomialProbabilityDepthCache.length) return binomialProbabilityDepthCache[depth];
else return MathUtils.binomialProbability(0, depth, 0.5);
}
/**
* query='dbConn.((0 as i close by (i + 100 where i <= max(Trener.getPremia())) as i join
* count((Trener where getPremia() >= i and getPremia() < i + 100)) as c).(c + " Trenerow uzyskuje
* premie pomiedzy " + i + " i " + i + 100) as message)' '
*/
public java.util.List<java.lang.String> executeQuery(
final ObjectContainerBase ocb, final Transaction t) {
final LocalTransaction transLocal = (LocalTransaction) t;
java.lang.Integer _asResult_i = 0;
java.util.List<java.lang.Integer> _closeByResult = new ArrayList<java.lang.Integer>();
_closeByResult.add(_asResult_i);
int _i3 = 0;
while (_i3 < _closeByResult.size()) {
java.lang.Integer _closeByEl = _closeByResult.get(_i3);
if (_closeByEl != null) {
ocb.activate(_closeByEl, 1);
}
java.lang.Integer _ident_i = _closeByEl;
java.lang.Integer _plusResult = _ident_i + 100;
if (_plusResult != null) {
ocb.activate(_plusResult, 2);
}
java.lang.Integer _whereEl = _plusResult;
java.lang.Integer _ident_i1 = _closeByEl;
final java.util.Collection<pl.wcislo.sbql4j.javac.test.football.model.Trener> _ident_Trener =
new java.util.ArrayList<pl.wcislo.sbql4j.javac.test.football.model.Trener>();
ClassMetadata _classMeta31 =
ocb.classCollection()
.getClassMetadata("pl.wcislo.sbql4j.javac.test.football.model.Trener");
long[] _ids31 = _classMeta31.getIDs(transLocal);
for (long _id31 : _ids31) {
LazyObjectReference _ref31 = transLocal.lazyReferenceFor((int) _id31);
_ident_Trener.add((pl.wcislo.sbql4j.javac.test.football.model.Trener) _ref31.getObject());
}
java.util.Collection<java.lang.Integer> _dotResult =
new java.util.ArrayList<java.lang.Integer>();
int _dotIndex = 0;
if (_ident_Trener != null) {
for (pl.wcislo.sbql4j.javac.test.football.model.Trener _dotEl : _ident_Trener) {
if (_dotEl == null) {
continue;
}
if (_dotEl != null) {
ocb.activate(_dotEl, 1);
}
java.lang.Integer _mth_getPremiaResult = _dotEl.getPremia();
if (_mth_getPremiaResult != null) {
ocb.activate(_mth_getPremiaResult, 1);
}
if (_mth_getPremiaResult != null) {
ocb.activate(_mth_getPremiaResult, 1);
}
_dotResult.add(_mth_getPremiaResult);
_dotIndex++;
}
}
Number _max7 = null;
for (Number _maxEl7 : _dotResult) {
_max7 = MathUtils.max(_max7, _maxEl7);
}
java.lang.Integer _maxResult = (java.lang.Integer) _max7;
Boolean _less_or_equalResult = _ident_i1 <= _maxResult;
java.lang.Integer _whereResult = null;
if (_less_or_equalResult) {
_whereResult = _plusResult;
}
java.lang.Integer _asResult_i1 = _whereResult;
if (_asResult_i1 != null) {
_closeByResult.add(_asResult_i1);
}
_i3++;
}
java.util.List<pl.wcislo.sbql4j.java.model.runtime.Struct> _joinResult =
new java.util.ArrayList<pl.wcislo.sbql4j.java.model.runtime.Struct>();
int _joinIndex = 0;
for (java.lang.Integer _joinEl : _closeByResult) {
if (_joinEl != null) {
ocb.activate(_joinEl, 1);
}
final java.util.Collection<pl.wcislo.sbql4j.javac.test.football.model.Trener> _ident_Trener1 =
new java.util.ArrayList<pl.wcislo.sbql4j.javac.test.football.model.Trener>();
ClassMetadata _classMeta32 =
ocb.classCollection()
.getClassMetadata("pl.wcislo.sbql4j.javac.test.football.model.Trener");
long[] _ids32 = _classMeta32.getIDs(transLocal);
for (long _id32 : _ids32) {
LazyObjectReference _ref32 = transLocal.lazyReferenceFor((int) _id32);
_ident_Trener1.add((pl.wcislo.sbql4j.javac.test.football.model.Trener) _ref32.getObject());
}
java.util.Collection<pl.wcislo.sbql4j.javac.test.football.model.Trener> _whereResult1 =
new java.util.ArrayList<pl.wcislo.sbql4j.javac.test.football.model.Trener>();
int _whereLoopIndex1 = 0;
for (pl.wcislo.sbql4j.javac.test.football.model.Trener _whereEl1 : _ident_Trener1) {
if (_whereEl1 == null) {
continue;
}
if (_whereEl1 != null) {
ocb.activate(_whereEl1, 1);
}
java.lang.Integer _mth_getPremiaResult1 = _whereEl1.getPremia();
if (_mth_getPremiaResult1 != null) {
ocb.activate(_mth_getPremiaResult1, 1);
}
java.lang.Integer _ident_i2 = _joinEl;
if (_ident_i2 != null) {
ocb.activate(_ident_i2, 1);
}
Boolean _more_or_equalResult = _mth_getPremiaResult1 >= _ident_i2;
java.lang.Boolean _andResult;
if (!_more_or_equalResult) {
_andResult = false;
} else {
java.lang.Integer _mth_getPremiaResult2 = _whereEl1.getPremia();
if (_mth_getPremiaResult2 != null) {
ocb.activate(_mth_getPremiaResult2, 1);
}
java.lang.Integer _ident_i3 = _joinEl;
if (_ident_i3 != null) {
ocb.activate(_ident_i3, 1);
}
java.lang.Integer _plusResult1 = _ident_i3 + 100;
Boolean _lessResult = _mth_getPremiaResult2 < _plusResult1;
_andResult = _lessResult;
}
if (_andResult) {
_whereResult1.add(_whereEl1);
}
_whereLoopIndex1++;
}
java.lang.Integer _countResult = _whereResult1.size();
java.lang.Integer _asResult_c = _countResult;
_joinResult.add(OperatorUtils.cartesianProductSS(_joinEl, _asResult_c, "i", "c"));
_joinIndex++;
}
java.util.List<java.lang.String> _dotResult1 = new java.util.ArrayList<java.lang.String>();
int _dotIndex1 = 0;
if (_joinResult != null) {
for (pl.wcislo.sbql4j.java.model.runtime.Struct _dotEl1 : _joinResult) {
if (_dotEl1 == null) {
continue;
}
if (_dotEl1 != null) {
ocb.activate(_dotEl1, 1);
}
java.lang.Integer _ident_c = (java.lang.Integer) _dotEl1.get("c");
if (_ident_c != null) {
ocb.activate(_ident_c, 1);
}
java.lang.String _plusResult2 = _ident_c + " Trenerow uzyskuje premie pomiedzy ";
java.lang.Integer _ident_i4 = (java.lang.Integer) _dotEl1.get("i");
if (_ident_i4 != null) {
ocb.activate(_ident_i4, 1);
}
java.lang.String _plusResult3 = _plusResult2 + _ident_i4;
java.lang.String _plusResult4 = _plusResult3 + " i ";
java.lang.Integer _ident_i5 = (java.lang.Integer) _dotEl1.get("i");
if (_ident_i5 != null) {
ocb.activate(_ident_i5, 1);
}
java.lang.Integer _plusResult5 = _ident_i5 + 100;
java.lang.String _plusResult6 = _plusResult4 + _plusResult5;
if (_plusResult6 != null) {
ocb.activate(_plusResult6, 1);
}
_dotResult1.add(_plusResult6);
_dotIndex1++;
}
}
java.util.List<java.lang.String> _asResult_message = _dotResult1;
pl.wcislo.sbql4j.db4o.utils.DerefUtils.activateResult(_asResult_message, ocb);
return _asResult_message;
}
static {
for (int i = 1; i < binomialProbabilityDepthCache.length; i++) {
binomialProbabilityDepthCache[i] = MathUtils.binomialProbability(0, i, 0.5);
}
}
