@Test(dependsOnMethods = "testCorrectInitialization")
public void testExonByName() {
for (final SimpleInterval loc : nonOverlappingExomeIntervals) {
Assert.assertEquals(exonDB.target(loc.toString()), loc);
}
Assert.assertNull(exonDB.target("no-id"));
}
@Test(dependsOnMethods = {"testCorrectInitialization"})
public void testExomeSize() {
int size = 0;
for (final SimpleInterval loc : nonOverlappingExomeIntervals) {
size += loc.size();
}
Assert.assertEquals(exonDB.exomeSize(), 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;
}
/**
* 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))));
}
}
/**
* 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;
}
/**
* Set expanded window boundaries, subject to cropping at contig boundaries
*
* <p>Allows the client to request a specific number of extra reference bases to include before
* and after the bases within our interval. These extra bases will be returned by calls to {@link
* #getBases} and {@link #iterator} in addition to the bases spanning our actual interval.
*
* <p>Note that the true window size may be smaller than requested due to cropping at contig
* boundaries. Call {@link @numWindowLeadingBases} and {@link @numWindowTrailingBases} to get the
* actual window dimensions.
*
* @param windowLeadingBases Number of extra reference bases to include before the start of our
* interval. Must be >= 0.
* @param windowTrailingBases Number of extra reference bases to include after the end of our
* interval. Must be >= 0.
*/
public void setWindow(final int windowLeadingBases, final int windowTrailingBases) {
if (windowLeadingBases < 0)
throw new GATKException("Reference window starts after the current interval");
if (windowTrailingBases < 0)
throw new GATKException("Reference window ends before the current interval");
if (interval == null || (windowLeadingBases == 0 && windowTrailingBases == 0)) {
// the "windowless" case
window = interval;
} else {
window =
new SimpleInterval(
interval.getContig(),
calculateWindowStart(interval, windowLeadingBases),
calculateWindowStop(interval, windowTrailingBases));
}
// Changing the window size invalidates our cached query result
cachedSequence = null;
}
public static JavaPairRDD<GATKRead, Iterable<GATKVariant>> join(
final JavaRDD<GATKRead> reads, final JavaRDD<GATKVariant> variants) {
final JavaSparkContext ctx = new JavaSparkContext(reads.context());
final IntervalsSkipList<GATKVariant> variantSkipList =
new IntervalsSkipList<>(variants.collect());
final Broadcast<IntervalsSkipList<GATKVariant>> variantsBroadcast =
ctx.broadcast(variantSkipList);
return reads.mapToPair(
r -> {
final IntervalsSkipList<GATKVariant> intervalsSkipList = variantsBroadcast.getValue();
if (SimpleInterval.isValid(r.getContig(), r.getStart(), r.getEnd())) {
return new Tuple2<>(r, intervalsSkipList.getOverlapping(new SimpleInterval(r)));
} else {
// Sometimes we have reads that do not form valid intervals (reads that do not consume
// any ref bases, eg CIGAR 61S90I
// In those cases, we'll just say that nothing overlaps the read
return new Tuple2<>(r, Collections.emptyList());
}
});
}
public static JavaPairRDD<GATKRead, ReferenceBases> addBases(
final ReferenceDataflowSource referenceDataflowSource, final JavaRDD<GATKRead> reads) {
SerializableFunction<GATKRead, SimpleInterval> windowFunction =
referenceDataflowSource.getReferenceWindowFunction();
JavaPairRDD<ReferenceShard, GATKRead> shardRead =
reads.mapToPair(
gatkRead -> {
ReferenceShard shard =
ReferenceShard.getShardNumberFromInterval(windowFunction.apply(gatkRead));
return new Tuple2<>(shard, gatkRead);
});
JavaPairRDD<ReferenceShard, Iterable<GATKRead>> shardiRead = shardRead.groupByKey();
return shardiRead.flatMapToPair(
in -> {
List<Tuple2<GATKRead, ReferenceBases>> out = Lists.newArrayList();
Iterable<GATKRead> iReads = in._2();
// Apply the reference window function to each read to produce a set of intervals
// representing
// the desired reference bases for each read.
final List<SimpleInterval> readWindows =
StreamSupport.stream(iReads.spliterator(), false)
.map(read -> windowFunction.apply(read))
.collect(Collectors.toList());
SimpleInterval interval = SimpleInterval.getSpanningInterval(readWindows);
ReferenceBases bases = referenceDataflowSource.getReferenceBases(null, interval);
for (GATKRead r : iReads) {
final ReferenceBases subset = bases.getSubset(windowFunction.apply(r));
out.add(new Tuple2<>(r, subset));
}
return out;
});
}
/**
* 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);
}
/**
* Determines the start of the expanded reference window, bounded by 1.
*
* @param locus The locus to expand.
* @param windowLeadingBases number of bases to attempt to expand relative to the locus start (>=
* 0)
* @return The start of the expanded window.
*/
private int calculateWindowStart(final SimpleInterval locus, final int windowLeadingBases) {
return Math.max(locus.getStart() - windowLeadingBases, 1);
}
/**
* 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();
}
/**
* Get the number of extra bases of context before the start 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 before the start of our interval
*/
public int numWindowLeadingBases() {
return window == null ? 0 : interval.getStart() - window.getStart();
}
@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()][]);
}