/**
  * 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))));
    }
  }