@DataProvider(name = "indexRangeData")
public Object[][] indexRangeData() {
final List<Object[]> result = new ArrayList<>();
final Random rdn = new Random(131313);
for (int i = 0; i < nonOverlappingExomeIntervals.size(); i++) {
result.add(new Object[] {nonOverlappingExomeIntervals.get(i), new IndexRange(i, i + 1)});
result.add(
new Object[] {
ExomeToolsTestUtils.createInterval(
nonOverlappingExomeIntervals.get(i).getContig(),
nonOverlappingExomeIntervals.get(i).getStart() - 1),
new IndexRange(i, i)
});
int j;
for (j = i + 1; j < nonOverlappingExomeIntervals.size() && rdn.nextBoolean(); j++) {
if (!nonOverlappingExomeIntervals
.get(j)
.getContig()
.equals(nonOverlappingExomeIntervals.get(i).getContig())) {
break;
}
}
result.add(
new Object[] {
ExomeToolsTestUtils.createInterval(
nonOverlappingExomeIntervals.get(i).getContig(),
nonOverlappingExomeIntervals.get(i).getStart(),
nonOverlappingExomeIntervals.get(j - 1).getEnd()),
new IndexRange(i, j)
});
}
return result.toArray(new Object[result.size()][]);
}
@DataProvider(name = "wrongExonLookUpData")
public Object[][] wrongExonLookUpData() {
return new Object[][] {
{null},
{ExomeToolsTestUtils.createOverEntireContig(nonOverlappingExomeIntervals.get(0).getContig())},
{
ExomeToolsTestUtils.createInterval(
nonOverlappingExomeIntervals.get(0).getContig(),
nonOverlappingExomeIntervals.get(0).getEnd(),
nonOverlappingExomeIntervals.get(1).getStart())
}
};
}
@BeforeClass
public void setUp() {
nonOverlappingExomeIntervals = new ArrayList<>(100);
final Random rdn =
new Random(13); // some "random" but fixed seed to make sure errors are deterministic.
for (int i = 0; i < ExomeToolsTestUtils.REFERENCE_DICTIONARY.size(); i++) {
int current = 0;
final SAMSequenceRecord sequence = ExomeToolsTestUtils.REFERENCE_DICTIONARY.getSequence(i);
while (current < sequence.getSequenceLength()) {
int start =
current
+ Math.max(
minimumExonIntergapSize,
(int)
Math.round(
rdn.nextGaussian() * sdExonIntergapSize + averageExonIntergapSize));
if (start >= sequence.getSequenceLength()) {
break;
}
int size =
Math.max(
minimumExonSize,
(int) Math.round(rdn.nextGaussian() * sdExonSize + averageExonSize));
int stop = start + size - 1;
if (stop >= sequence.getSequenceLength()) {
break;
}
nonOverlappingExomeIntervals.add(
ExomeToolsTestUtils.createInterval(sequence.getSequenceName(), start, stop));
current = stop + 1;
}
}
Collections.sort(nonOverlappingExomeIntervals, IntervalUtils.LEXICOGRAPHICAL_ORDER_COMPARATOR);
exonDB = new HashedListTargetCollection<>(nonOverlappingExomeIntervals);
}
@DataProvider(name = "exonLookUpData")
public Object[][] exonLookUpData() {
final List<Object[]> result = new ArrayList<>();
for (int i = 0; i < nonOverlappingExomeIntervals.size(); i++) {
result.add(
new Object[] {
nonOverlappingExomeIntervals.get(i), nonOverlappingExomeIntervals.get(i), i
});
}
for (int i = 0; i < nonOverlappingExomeIntervals.size(); i++) {
final SimpleInterval interval = nonOverlappingExomeIntervals.get(i);
result.add(
new Object[] {
new SimpleInterval(interval.getContig(), interval.getStart(), interval.getStart()),
interval,
i
});
}
for (int i = 0; i < nonOverlappingExomeIntervals.size(); i++) {
final SimpleInterval interval = nonOverlappingExomeIntervals.get(i);
result.add(
new Object[] {
new SimpleInterval(interval.getContig(), interval.getEnd(), interval.getEnd()),
interval,
i
});
}
for (int i = 1; i < nonOverlappingExomeIntervals.size(); i++) {
final SimpleInterval previous = nonOverlappingExomeIntervals.get(i - 1);
final SimpleInterval next = nonOverlappingExomeIntervals.get(i);
final SimpleInterval query =
previous.getContig().equals(next.getContig())
? ExomeToolsTestUtils.createInterval(
previous.getContig(), previous.getEnd() + 1, next.getStart() - 1)
: ExomeToolsTestUtils.createInterval(next.getContig(), 1, next.getStart() - 1);
result.add(new Object[] {query, null, -i - 1});
}
return result.toArray(new Object[result.size()][]);
}