public StudyEntry addSampleData(String sampleName, String format, String value, String defaultValue) { requireSamplesPosition(); Integer formatIdx = getFormatPositions().get(format); Integer samplePosition = getSamplesPosition().get(sampleName); return addSampleData(samplePosition, formatIdx, value, defaultValue); }
private String variantToString(Variant v) { StringBuilder sb = new StringBuilder(v.getChromosome()); sb.append(":").append(v.getStart()).append("-").append(v.getEnd()); sb.append(v.getReference().isEmpty() ? "-" : v.getReference()); sb.append(":").append(v.getAlternate().isEmpty() ? "-" : v.getAlternate()).append("["); StudyEntry se = getStudy(v); List<List<String>> sd = se.getSamplesData(); for(String sn : se.getSamplesName()){ Integer pos = se.getSamplesPosition().get(sn); if (pos >= sd.size()) { sb.append(sn).append(":S;"); } else if (null == sd.get(pos) || sd.get(pos).size() < 1) { sb.append(sn).append(":G;"); } else { String gt = sd.get(pos).get(0); // GT sb.append(sn).append(":").append(gt).append(";"); } } sb.append("]"); return sb.toString(); }
LinkedHashMap<String, Integer> samplesPosition = study.getSamplesPosition();
newSamplesPosition = new LinkedHashMap<>(currentStudy.getSamplesPosition()); varToAlts.stream() .map(Pair::getKey) "No GT [%s] found for sample %s in \nVariant: %s\nOtherSe:%s\nOtherSp:%s", getGtKey(), sampleName, other.getImpl(), otherStudy.getSamplesData(), otherStudy.getSamplesPosition()));
StudyEntry se = new StudyEntry(); se.setStudyId(vse.getStudyId()); if (null != vse.getSamplesPosition()) { se.setSamplesPosition(new HashMap<>(vse.getSamplesPosition())); } else { se.setSamplesPosition(new HashMap<>());
LinkedHashMap<String, Integer> samplesPosition = study.getSamplesPosition();
normalizedEntry.setSamplesPosition(entry.getSamplesPosition()); normalizedEntry.setFormat(entry.getFormat());
if (MapUtils.isNotEmpty(studyEntry.getSamplesPosition()) && ListUtils.isNotEmpty(studyEntry.getOrderedSamplesName())) { List<String> sampleNames = studyEntry.getOrderedSamplesName();
samplesPosition1 = variant1.getStudy(studyConfiguration.getStudyName()).getSamplesPosition(); samplesPosition2 = variant2.getStudy(studyConfiguration.getStudyName()).getSamplesPosition(); assertEquals(samplesName, new ArrayList<>(samplesPosition2.keySet())); assertSame(samplesPosition1, variant1.getStudy(studyConfiguration.getStudyName()).getSamplesPosition()); assertSame(samplesPosition2, variant2.getStudy(studyConfiguration.getStudyName()).getSamplesPosition()); for (String sampleName : samplesName) { String gt1 = variant1.getStudy(studyConfiguration.getStudyName()).getSampleData(sampleName, "GT");