public void setSequencingCenter(final String center) { setAttribute(SEQUENCING_CENTER_TAG, center); }
public void setPlatformUnit(final String pu) { setAttribute(PLATFORM_UNIT_TAG, pu); }
public void setDescription(final String description) { setAttribute(DESCRIPTION_TAG, description); }
public void setSample(final String value) { setAttribute(READ_GROUP_SAMPLE_TAG, value); }
public void setLibrary(final String value) { setAttribute(LIBRARY_TAG, value); }
public void setKeySequence(final String keySequence) { setAttribute(KEY_SEQUENCE_TAG, keySequence); }
public void setPlatformModel(final String platformModel) { setAttribute(PLATFORM_MODEL_TAG, platformModel); }
public void setLibrary(final String value) { setAttribute(LIBRARY_TAG, value); }
public void setPredictedMedianInsertSize(final Integer predictedMedianInsertSize) { setAttribute(PREDICTED_MEDIAN_INSERT_SIZE_TAG, (predictedMedianInsertSize == null? null: predictedMedianInsertSize.toString())); }
public void setPredictedMedianInsertSize(final Integer predictedMedianInsertSize) { setAttribute(PREDICTED_MEDIAN_INSERT_SIZE_TAG, (predictedMedianInsertSize == null? null: predictedMedianInsertSize.toString())); }
public void setPredictedMedianInsertSize(final Integer predictedMedianInsertSize) { setAttribute(PREDICTED_MEDIAN_INSERT_SIZE_TAG, (predictedMedianInsertSize == null? null: predictedMedianInsertSize.toString())); }
/** * Set the barcodes associated with this ReadGroup. * Note that an input of null results in unsetting the attribute while an empty list is set as a tag with an empty value. * @param barcodes a list of barcodes to associate with this read group */ public void setBarcodes(final List<String> barcodes) { if (barcodes == null) { setAttribute(BARCODE_TAG, null); } else { if (barcodes.stream().anyMatch(String::isEmpty)) { throw new IllegalArgumentException("A barcode must not be an empty String"); } setAttribute(BARCODE_TAG, String.join(SamConstants.BARCODE_SEQUENCE_DELIMITER, barcodes)); } }
public SAMReadGroupRecord(final String id, final SAMReadGroupRecord srcProgramRecord) { mReadGroupId = id; for (final Map.Entry<String, String> entry : srcProgramRecord.getAttributes()) { setAttribute(entry.getKey(), entry.getValue()); } }
/** * Converts to Iso8601Date if not already in that form. */ public void setRunDate(Date runDate) { if (runDate != null && !(runDate instanceof Iso8601Date)) { runDate = new Iso8601Date(runDate); } setAttribute(DATE_RUN_PRODUCED_TAG, runDate != null ? runDate.toString() : null); }
public SAMReadGroupRecord(final String id, final SAMReadGroupRecord srcProgramRecord) { mReadGroupId = id; for (final Map.Entry<String, String> entry : srcProgramRecord.getAttributes()) { setAttribute(entry.getKey(), entry.getValue()); } }
public SAMReadGroupRecord(final String id, final SAMReadGroupRecord srcProgramRecord) { mReadGroupId = id; for (final Map.Entry<String, String> entry : srcProgramRecord.getAttributes()) { setAttribute(entry.getKey(), entry.getValue()); } }
/** * Converts to Iso8601Date if not already in that form. */ public void setRunDate(Date runDate) { if (runDate != null && !(runDate instanceof Iso8601Date)) { runDate = new Iso8601Date(runDate); } setAttribute(DATE_RUN_PRODUCED_TAG, runDate != null ? runDate.toString() : null); }
/** * Converts to Iso8601Date if not already in that form. */ public void setRunDate(Date runDate) { if (runDate != null && !(runDate instanceof Iso8601Date)) { runDate = new Iso8601Date(runDate); } setAttribute(DATE_RUN_PRODUCED_TAG, runDate != null ? runDate.toString() : null); }
private SAMReadGroupRecord createSAMReadGroupRecord(String id) { SAMReadGroupRecord readGroupRecord = new SAMReadGroupRecord(id); readGroupRecord.setAttribute(SAMTag.SM.name(), Double.toString(Math.random())); return readGroupRecord; }
@Override AbstractSAMHeaderRecord newGroup(String id) { SAMReadGroupRecord group = new SAMReadGroupRecord(id); group.setAttribute(SAMTag.SM.name(), id); return group; }