@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()][]);
}
/**
* 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());
}
}
// returns all the intervals that overlap with the query.
// (use the optimized version instead, unless you're testing it and need something to compare
// against)
protected ArrayList<T> getOverlappingIgnoringIndex(SimpleInterval query) {
if (!contig.equals(query.getContig())) {
// different contig, so we know no one'll overlap.
return new ArrayList<T>();
}
ArrayList<T> ret = new ArrayList<T>();
for (T v : vs) {
// they are sorted by start location, so if this one starts too late
// then all of the others will, too.
if (v.getStart() > query.getEnd()) {
break;
}
if (query.overlaps(v)) {
ret.add(v);
}
}
return ret;
}
/**
* Returns all the intervals that overlap with the query. The query doesn't *have* to be in the
* same contig as the intervals we hold, but of course if it isn't you'll get an empty result. You
* may modify the returned list.
*/
public ArrayList<T> getOverlapping(SimpleInterval query) {
if (!contig.equals(query.getContig())) {
// different contig, so we know no one'll overlap.
return new ArrayList<T>();
}
ArrayList<T> ret = new ArrayList<T>();
// use index to skip early non-overlapping entries.
int idx = firstPotentiallyReaching(query.getStart());
if (idx < 0) {
idx = 0;
}
for (; idx < vs.size(); idx++) {
T v = vs.get(idx);
// they are sorted by start location, so if this one starts too late
// then all of the others will, too.
if (v.getStart() > query.getEnd()) {
break;
}
if (query.overlaps(v)) {
ret.add(v);
}
}
return ret;
}
/**
* Determines the stop of the expanded reference window, bounded if necessary by the contig.
*
* @param locus The locus to expand.
* @param windowTrailingBases number of bases to attempt to expand relative to the locus end (>=
* 0)
* @return The end of the expanded window.
*/
private int calculateWindowStop(final SimpleInterval locus, final int windowTrailingBases) {
final int sequenceLength =
dataSource.getSequenceDictionary().getSequence(locus.getContig()).getSequenceLength();
return Math.min(locus.getEnd() + windowTrailingBases, sequenceLength);
}
/**
* Get the number of extra bases of context after the end of our interval, as configured by a call
* to {@link #setWindow} or at construction time.
*
* <p>Actual number of bases may be less than originally requested if the interval is near a
* contig boundary.
*
* @return number of extra bases of context after the end of our interval
*/
public int numWindowTrailingBases() {
return window == null ? 0 : window.getEnd() - interval.getEnd();
}