/htsjdk

Permalink
Browse files

Add a size method to SamLocusIterator.LocusInfo. 

This is useful if we want to quickly know how many records overlap this
position but do not want to get all those records.
  • Loading branch information...
1 parent d683012 commit fa519a33be16ced519721c8b3e590701dad5ada2 @nh13 nh13 committed May 30, 2016
View
2 src/main/java/htsjdk/samtools/util/SamLocusIterator.java
@@ -116,6 +116,8 @@ public void addInserted(final SAMRecord read, int firstPosition) {
public List<RecordAndOffset> getInsertedInRecord() {
return (insertedInRecord == null) ? Collections.emptyList() : Collections.unmodifiableList(insertedInRecord);
}
+ /** @return the number of records overlapping the position, with deletions included if they are being tracked. */
+ public int size() { return this.recordAndOffsets.size() + ((deletedInRecord == null) ? 0 : deletedInRecord.size()); }
/**
* @return <code>true</code> if all the RecordAndOffset lists are empty;
View
24 src/test/java/htsjdk/samtools/util/SamLocusIteratorTest.java
@@ -86,6 +86,7 @@ public void testBasicIterator() {
for (final SamLocusIterator.LocusInfo li : sli) {
Assert.assertEquals(li.getPosition(), pos++);
Assert.assertEquals(li.getRecordAndPositions().size(), coverage);
+ Assert.assertEquals(li.size(), coverage);
// make sure that we are not accumulating indels
Assert.assertEquals(li.getDeletedInRecord().size(), 0);
Assert.assertEquals(li.getInsertedInRecord().size(), 0);
@@ -108,10 +109,10 @@ public void testMissingQualityString() {
// make sure we accumulated depth of 2 for each position
int pos = 165;
for (final SamLocusIterator.LocusInfo li : sli) {
- Assert.assertEquals(pos++, li.getPosition());
- Assert.assertEquals(2, li.getRecordAndPositions().size());
+ Assert.assertEquals(li.getPosition(), pos++);
+ Assert.assertEquals(li.getRecordAndPositions().size(), 2);
+ Assert.assertEquals(li.size(), 2);
}
-
}
/**
@@ -146,6 +147,7 @@ public void testEmitUncoveredLoci() {
expectedReads = 0;
}
Assert.assertEquals(li.getRecordAndPositions().size(), expectedReads);
+ Assert.assertEquals(li.size(), expectedReads);
// make sure that we are not accumulating indels
Assert.assertEquals(li.getDeletedInRecord().size(), 0);
Assert.assertEquals(li.getInsertedInRecord().size(), 0);
@@ -183,6 +185,7 @@ public void testQualityFilter() {
int pos = startPosition;
for (final SamLocusIterator.LocusInfo li : sli) {
Assert.assertEquals(li.getRecordAndPositions().size(), (pos % 2 == 0) ? coverage / 2 : coverage);
+ Assert.assertEquals(li.size(), (pos % 2 == 0) ? coverage / 2 : coverage);
Assert.assertEquals(li.getPosition(), pos++);
// make sure that we are not accumulating indels
Assert.assertEquals(li.getDeletedInRecord().size(), 0);
@@ -221,12 +224,16 @@ public void testSimpleDeletion() {
if (isDeletedPosition) {
// make sure there are no reads without indels
Assert.assertEquals(li.getRecordAndPositions().size(), 0);
+ Assert.assertEquals(li.size(), coverage); // should include deletions
+
// make sure that we are accumulating indels
Assert.assertEquals(li.getDeletedInRecord().size(), coverage);
Assert.assertEquals(li.getInsertedInRecord().size(), 0);
} else {
// make sure we are accumulating normal coverage
Assert.assertEquals(li.getRecordAndPositions().size(), coverage);
+ Assert.assertEquals(li.size(), coverage);
+
// make sure that we are not accumulating indels
Assert.assertEquals(li.getDeletedInRecord().size(), 0);
Assert.assertEquals(li.getInsertedInRecord().size(), 0);
@@ -258,6 +265,8 @@ public void testSimpleInsertion() {
Assert.assertEquals(li.getPosition(), pos++);
// make sure we are accumulating normal coverage
Assert.assertEquals(li.getRecordAndPositions().size(), coverage);
+ Assert.assertEquals(li.size(), coverage);
+
// make sure that we are not accumulating deletions
Assert.assertEquals(li.getDeletedInRecord().size(), 0);
if (incIndels && li.getPosition() == insStart) {
@@ -293,6 +302,8 @@ public void testStartWithInsertion() {
Assert.assertEquals(li.getPosition(), pos);
// accumulation of coverage
Assert.assertEquals(li.getRecordAndPositions().size(), (indelPosition) ? 0 : coverage);
+ Assert.assertEquals(li.size(), (indelPosition) ? 0 : coverage);
+
// no accumulation of deletions
Assert.assertEquals(li.getDeletedInRecord().size(), 0);
// accumulation of insertion
@@ -332,6 +343,7 @@ public void testStartWithSoftClipAndInsertion() {
Assert.assertEquals(li.getPosition(), pos);
// accumulation of coverage
Assert.assertEquals(li.getRecordAndPositions().size(), (indelPosition) ? 0 : coverage);
+ Assert.assertEquals(li.size(), (indelPosition) ? 0 : coverage);
// no accumulation of deletions
Assert.assertEquals(li.getDeletedInRecord().size(), 0);
// accumulation of insertion
@@ -376,6 +388,7 @@ public void testNBeforeInsertion() {
Assert.assertEquals(li.getPosition(), pos);
// accumulation of coverage
Assert.assertEquals(li.getRecordAndPositions().size(), (pos == endN) ? 0 : coverage);
+ Assert.assertEquals(li.size(), (pos == endN) ? 0 : coverage);
// no accumulation of deletions
Assert.assertEquals(li.getDeletedInRecord().size(), 0);
// accumulation of insertion
@@ -427,6 +440,7 @@ public void testNBeforeDeletion() {
Assert.assertEquals(li.getPosition(), pos);
// accumulation of coverage
Assert.assertEquals(li.getRecordAndPositions().size(), (insideDeletion) ? 0 : coverage);
+ Assert.assertEquals(li.size(), coverage); // either will be all deletions, or all non-deletions, but always of size `coverage`.
// accumulation of deletions
Assert.assertEquals(li.getDeletedInRecord().size(), (insideDeletion) ? coverage : 0);
// no accumulation of insertion
@@ -515,12 +529,14 @@ public void testSimpleGappedAlignment() {
// check the coverage for insertion and normal records
Assert.assertEquals(li.getDeletedInRecord().size(), coverage);
Assert.assertEquals(li.getRecordAndPositions().size(), 0);
+ Assert.assertEquals(li.size(), coverage); // includes deletions
// check the offset for the deletion
Assert.assertEquals(li.getDeletedInRecord().get(0).getOffset(), expectedReadOffsets[i]);
Assert.assertEquals(li.getDeletedInRecord().get(1).getOffset(), expectedReadOffsets[i]);
} else {
// if it is not a deletion, perform the same test as before
Assert.assertEquals(li.getRecordAndPositions().size(), coverage);
+ Assert.assertEquals(li.size(), coverage);
// Assert.assertEquals(li.getDeletedInRecord().size(), 0);
Assert.assertEquals(li.getRecordAndPositions().get(0).getOffset(), expectedReadOffsets[i]);
Assert.assertEquals(li.getRecordAndPositions().get(1).getOffset(), expectedReadOffsets[i]);
@@ -582,6 +598,7 @@ public void testOverlappingGappedAlignmentsWithoutIndels() {
i = 0;
for (final SamLocusIterator.LocusInfo li : sli) {
Assert.assertEquals(li.getRecordAndPositions().size(), expectedDepths[i]);
+ Assert.assertEquals(li.size(), expectedDepths[i]);
Assert.assertEquals(li.getPosition(), expectedReferencePositions[i]);
Assert.assertEquals(li.getRecordAndPositions().size(), expectedReadOffsets[i].length);
for (int j = 0; j < expectedReadOffsets[i].length; ++j) {
@@ -657,6 +674,7 @@ public void testOverlappingGappedAlignmentsWithIndels() {
for (final SamLocusIterator.LocusInfo li : sli) {
// checking the same as without indels
Assert.assertEquals(li.getRecordAndPositions().size(), expectedDepths[i]);
+ Assert.assertEquals(li.size(), expectedDepths[i] + expectedDelDepths[i]); // include deletions
Assert.assertEquals(li.getPosition(), expectedReferencePositions[i]);
Assert.assertEquals(li.getRecordAndPositions().size(), expectedReadOffsets[i].length);
for (int j = 0; j < expectedReadOffsets[i].length; ++j) {

0 comments on commit fa519a3

Please sign in to comment.