/** Writes the column summary output table. */
private void writeColumnSummaryOutput() {
if (columnSummaryOutputWriter == null) {
return;
}
final long totalSize = targetCollection.totalSize();
final List<String> columnNames = countColumns.columnNames();
for (int i = 0; i < columnNames.size(); i++) {
final long sum = IntStream.of(counts[i]).sum();
columnSummaryOutputWriter.println(
String.join(
COLUMN_SEPARATOR,
columnNames.get(i),
String.valueOf(sum),
String.format(AVERAGE_DOUBLE_FORMAT, sum / (double) totalSize)));
}
}
@Override
public void onTraversalStart() {
sampleCollection = new SampleCollection(getHeaderForReads());
logger.log(Level.INFO, "Reading targets locations from intervals...");
targetCollection = resolveTargetCollection();
// Initializing count and count column management member fields:
countColumns = groupBy.countColumns(this);
final int columnCount = countColumns.columnCount();
counts = new int[columnCount][targetCollection.targetCount()];
// Open output files and write headers:
outputWriter =
openOutputWriter(
output,
composeMatrixOutputHeader(
getCommandLine(), targetOutInfo, groupBy, countColumns.columnNames()));
if (columnSummaryOutput != null) {
columnSummaryOutputWriter =
openOutputWriter(
columnSummaryOutput,
composeColumnSummaryHeader(
getCommandLine(),
groupBy,
targetCollection.targetCount(),
targetCollection.totalSize()));
}
if (rowSummaryOutput != null) {
rowSummaryOutputWriter =
openOutputWriter(
rowSummaryOutput,
composeRowOutputHeader(
getCommandLine(), targetOutInfo, groupBy, countColumns.columnCount()));
}
// Next we start the traversal:
logger.log(Level.INFO, "Collecting read counts ...");
}