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StudyEntry.setFormatAsString
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How to use
setFormatAsString
method
in
org.opencb.biodata.models.variant.StudyEntry

Best Java code snippets using org.opencb.biodata.models.variant.StudyEntry.setFormatAsString (Showing top 3 results out of 315)

origin: org.opencb.biodata/biodata-formats

@Override
protected void setOtherFields(Variant variant, StudyEntry studyEntry, VariantFileMetadata fileMetadata, List<String> ids,
               float quality, String filter, String info, String format, String[] alternateAlleles, String line) {
  // Fields not affected by the structure of REF and ALT fields
  variant.setIds(ids);
  if (quality > -1) {
    studyEntry.addAttribute(fileMetadata.getId(), StudyEntry.QUAL, String.valueOf(quality));
  }
  if (!filter.isEmpty()) {
    studyEntry.addAttribute(fileMetadata.getId(), StudyEntry.FILTER, filter);
  }
  Map<String, String> infoMap = getInfoMap(info);
  studyEntry.setFormatAsString(format);
  studyEntry.addAttribute(fileMetadata.getId(), StudyEntry.SRC, line);
  studyEntry.addAttributes(fileMetadata.getId(), infoMap);
}
origin: opencb/opencga

fileEntry.getAttributes().put("do.we.accept.attribute.with.dots?", "yes");
studyEntry.setFiles(Collections.singletonList(fileEntry));
studyEntry.setFormatAsString("GT");
origin: opencb/opencga

fileEntry.getAttributes().put("AN", "2");
fileEntry.setCall(null);
studyEntry.setFormatAsString("GT:DP");
org.opencb.biodata.models.variantStudyEntrysetFormatAsString

Popular methods of StudyEntry

  • getSamplesData
  • getFiles
  • <init>
  • getSampleData
  • getFile
  • getStudyId
  • getOrderedSamplesName
  • getSamplesName
  • setFiles
  • setFormat
  • setSamplesData
  • setSamplesPosition
  • setSamplesData,
  • setSamplesPosition,
  • getFormat,
  • getFormatPositions,
  • getStats,
  • setStats,
  • addSampleData,
  • getSamplesPosition,
  • getSecondaryAlternates,
  • setSecondaryAlternates

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