@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 ...");
}
@Override
public Object onTraversalSuccess() {
logger.log(Level.INFO, "Collecting read counts done.");
logger.log(Level.INFO, "Writing counts ...");
final long[] columnTotals = calculateColumnTotals();
IntStream.range(0, targetCollection.targetCount())
.forEach(
target -> {
final int[] countBuffer =
IntStream.range(0, counts.length).map(column -> counts[column][target]).toArray();
writeOutputRows(countBuffer, columnTotals, target);
});
logger.log(Level.INFO, "Writing counts done.");
writeColumnSummaryOutput();
return "SUCCESS";
}
/**
* Composes the target information output string.
*
* @param index of the target in the collection.
* @param collection the target containing collection.
* @throws IllegalArgumentException if either {@code target} or {@code collection} is {@code
* null}.
*/
protected String composeTargetOutInfoString(
final int index, final TargetCollection<Target> collection) {
Utils.nonNull(collection, "the collection cannot be null");
Utils.validIndex(index, collection.targetCount());
return composer.apply(index, collection);
}