/**
* Target information string composer for the genomic coordinate part of the target.
*
* @param index the index of a target within the collection.
* @param collection the containing target collection.
* @return never {@code null}.
*/
private static String coordinateComposer(
final int index, final TargetCollection<Target> collection) {
final SimpleInterval location = collection.location(index);
if (location == null) {
return String.join(COLUMN_SEPARATOR, NO_VALUE_STRING, NO_VALUE_STRING, NO_VALUE_STRING);
} else {
return String.format(
String.join(COLUMN_SEPARATOR, "%s", "%d", "%d"),
location.getContig(),
location.getStart(),
location.getEnd());
}
}
/**
* Checks whether all targets in the input target collection have a designated name.
*
* @param result the query target collection.
* @throws UserException if there are some targets with no name in {@code result}.
*/
private void checkAllTargetsHaveName(TargetCollection<Target> result) {
if (result.targets().stream().anyMatch(t -> t.getName() == null || t.getName().equals(""))) {
throw new UserException(
String.format(
"Target output info requested '%s' requires that each target has a designated unique name/id but there are some with no names: %s",
targetOutInfo.name(),
result
.targets()
.stream()
.filter(t -> t.getName() == null || t.getName().equals(""))
.limit(10)
.map(e -> result.location(e).toString())
.collect(Collectors.joining(", "))));
}
}
/**
* Writes the row in the main matrix output file for a target and, if requested, the corresponding
* row in the row summary output file.
*
* @param countBuffer the counts for the target.
* @param index the index of target within the target collection.
*/
private void writeOutputRows(
final int[] countBuffer, final long[] columnTotals, final int index) {
final String countString =
IntStream.range(0, countBuffer.length)
.mapToObj(i -> transform.apply(countBuffer[i], columnTotals[i]))
.collect(Collectors.joining(COLUMN_SEPARATOR));
final String targetInfoString =
targetOutInfo.composeTargetOutInfoString(index, targetCollection);
outputWriter.println(String.join(COLUMN_SEPARATOR, targetInfoString, countString));
if (rowSummaryOutputWriter != null) {
final long sum = MathUtils.sum(countBuffer);
final SimpleInterval location = targetCollection.location(index);
final int targetSize = location.size();
rowSummaryOutputWriter.println(
String.join(
COLUMN_SEPARATOR,
targetInfoString,
Long.toString(sum),
String.format(
AVERAGE_DOUBLE_FORMAT, sum / ((float) countColumns.columnCount() * targetSize))));
}
}