@Test(dependsOnMethods = {"testCorrectInitialization"})
public void testExomeSize() {
int size = 0;
for (final SimpleInterval loc : nonOverlappingExomeIntervals) {
size += loc.size();
}
Assert.assertEquals(exonDB.exomeSize(), size);
}
/**
* 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))));
}
}