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better method names for read based reference ordered data access. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3069 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-03-24 16:13:31 +00:00
parent 49117819f5
commit 5079f35e40
3 changed files with 47 additions and 47 deletions
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34
java/src/org/broadinstitute/sting/gatk/refdata/ReadMetaDataTracker.java
View File

@ -47,8 +47,8 @@ public class ReadMetaDataTracker {
/**
* create a read meta data tracker, given the read and a queue of RODatum positions
*
* @param record the read to create offset from
* @param mapping the mapping of reference ordered datum
* @param record the read to create offset from
* @param mapping the mapping of reference ordered datum
*/
public ReadMetaDataTracker(SAMRecord record, TreeMap<Long, RODMetaDataContainer> mapping) {
this.record = record;
@ -59,10 +59,10 @@ public class ReadMetaDataTracker {
* create an alignment of read position to reference ordered datum
*
* @param record the SAMRecord
* @param queue the queue (as a tree set)
* @param cl the class name, null if not filtered by classname
* @param name the datum track name, null if not filtered by name
*
* @param queue the queue (as a tree set)
* @param cl the class name, null if not filtered by classname
* @param name the datum track name, null if not filtered by name
*
* @return a mapping from the position in the read to the reference ordered datum
*/
private Map<Long, Collection<ReferenceOrderedDatum>> createReadAlignment(SAMRecord record, TreeMap<Long, RODMetaDataContainer> queue, Class cl, String name) {
@ -79,11 +79,11 @@ public class ReadMetaDataTracker {
else
set = queue.get(loc).getSet(name);
if (set != null && set.size() > 0)
ret.put(position,set);
ret.put(position, set);
}
}
return ret;
}
/**
@ -98,9 +98,9 @@ public class ReadMetaDataTracker {
for (Long location : mapping.keySet()) {
if (location >= start && location <= stop)
if (cl != null)
ret.put(location,mapping.get(location).getSet(cl));
else
ret.put(location,mapping.get(location).getSet(name));
ret.put(location, mapping.get(location).getSet(cl));
else
ret.put(location, mapping.get(location).getSet(name));
}
return ret;
}
@ -110,7 +110,7 @@ public class ReadMetaDataTracker {
*
* @return a mapping of read offset to ROD(s)
*/
public Map<Long, Collection<ReferenceOrderedDatum>> getPositionMapping() {
public Map<Long, Collection<ReferenceOrderedDatum>> getReadOffsetMapping() {
return createReadAlignment(record, mapping, null, null);
}
@ -119,7 +119,7 @@ public class ReadMetaDataTracker {
*
* @return a mapping of genome loc position to ROD(s)
*/
public Map<Long, Collection<ReferenceOrderedDatum>> getGenomeLocMapping() {
public Map<Long, Collection<ReferenceOrderedDatum>> getContigOffsetMapping() {
return createGenomeLocAlignment(record, mapping, null, null);
}
@ -128,7 +128,7 @@ public class ReadMetaDataTracker {
*
* @return a mapping of read offset to ROD(s)
*/
public Map<Long, Collection<ReferenceOrderedDatum>> getPositionMapping(String name) {
public Map<Long, Collection<ReferenceOrderedDatum>> getReadOffsetMapping(String name) {
return createReadAlignment(record, mapping, null, name);
}
@ -137,7 +137,7 @@ public class ReadMetaDataTracker {
*
* @return a mapping of genome loc position to ROD(s)
*/
public Map<Long, Collection<ReferenceOrderedDatum>> getGenomeLocMapping(String name) {
public Map<Long, Collection<ReferenceOrderedDatum>> getContigOffsetMapping(String name) {
return createGenomeLocAlignment(record, mapping, null, name);
}
@ -146,7 +146,7 @@ public class ReadMetaDataTracker {
*
* @return a mapping of read offset to ROD(s)
*/
public Map<Long, Collection<ReferenceOrderedDatum>> getPositionMapping(Class cl) {
public Map<Long, Collection<ReferenceOrderedDatum>> getReadOffsetMapping(Class cl) {
return createReadAlignment(record, mapping, cl, null);
}
@ -155,7 +155,7 @@ public class ReadMetaDataTracker {
*
* @return a mapping of genome loc position to ROD(s)
*/
public Map<Long, Collection<ReferenceOrderedDatum>> getGenomeLocMapping(Class cl) {
public Map<Long, Collection<ReferenceOrderedDatum>> getContigOffsetMapping(Class cl) {
return createGenomeLocAlignment(record, mapping, cl, null);
}
}

31
java/test/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedViewTest.java
View File

@ -43,12 +43,11 @@ import java.util.*;
/**
*
* @author aaron
*
* Class ReadBasedReferenceOrderedViewTest
*
* test out the ReadBasedReferenceOrderedView class
* @author aaron
* <p/>
* Class ReadBasedReferenceOrderedViewTest
* <p/>
* test out the ReadBasedReferenceOrderedView class
*/
public class ReadBasedReferenceOrderedViewTest extends BaseTest {
@ -73,20 +72,20 @@ public class ReadBasedReferenceOrderedViewTest extends BaseTest {
// make ten reads,
List<SAMRecord> records = new ArrayList<SAMRecord>();
for (int x = 1; x < 11; x++) {
SAMRecord rec = ArtificialSAMUtils.createArtificialRead(header, "name", 0, x, 10);
SAMRecord rec = ArtificialSAMUtils.createArtificialRead(header, "name", 0, x, 10);
}
GenomeLoc start = GenomeLocParser.createGenomeLoc(0,0,0);
GenomeLoc start = GenomeLocParser.createGenomeLoc(0, 0, 0);
List<RMDDataState> list = new ArrayList<RMDDataState>();
list.add(new RMDDataState(null, new FakePeekingRODIterator(start,"fakeName")));
list.add(new RMDDataState(null, new FakePeekingRODIterator(start, "fakeName")));
ReadBasedReferenceOrderedView view = new ReadBasedReferenceOrderedView(new WindowedData(list));
for (SAMRecord rec : records) {
ReadMetaDataTracker tracker = view.getReferenceOrderedDataForRead(rec);
Map<Long, Collection<ReferenceOrderedDatum>> map = tracker.getPositionMapping();
Map<Long, Collection<ReferenceOrderedDatum>> map = tracker.getReadOffsetMapping();
for (Long i : map.keySet()) {
Assert.assertEquals(1,map.get(i).size());
Assert.assertEquals(1, map.get(i).size());
}
Assert.assertEquals(10,map.keySet().size());
Assert.assertEquals(10, map.keySet().size());
}
}
@ -100,9 +99,11 @@ class FakePeekingRODIterator implements LocationAwareSeekableRODIterator {
private GenomeLoc location;
private ReadMetaDataTrackerTest.FakeRODatum curROD;
private final String name;
public FakePeekingRODIterator(GenomeLoc startingLoc, String name) {
this.name = name;
this.location = GenomeLocParser.createGenomeLoc(startingLoc.getContigIndex(),startingLoc.getStart()+1,startingLoc.getStop()+1);;
this.location = GenomeLocParser.createGenomeLoc(startingLoc.getContigIndex(), startingLoc.getStart() + 1, startingLoc.getStop() + 1);
;
}
@Override
@ -131,8 +132,8 @@ class FakePeekingRODIterator implements LocationAwareSeekableRODIterator {
@Override
public RODRecordList next() {
System.err.println("Next -> " + location);
curROD = new ReadMetaDataTrackerTest.FakeRODatum(location,name);
location = GenomeLocParser.createGenomeLoc(location.getContigIndex(),location.getStart()+1,location.getStop()+1);
curROD = new ReadMetaDataTrackerTest.FakeRODatum(location, name);
location = GenomeLocParser.createGenomeLoc(location.getContigIndex(), location.getStart() + 1, location.getStop() + 1);
FakeRODRecordList list = new FakeRODRecordList();
list.add(curROD);
return list;

29
java/test/org/broadinstitute/sting/gatk/refdata/ReadMetaDataTrackerTest.java
View File

@ -75,9 +75,9 @@ public class ReadMetaDataTrackerTest extends BaseTest {
// count the positions
int count = 0;
for (Long x : tracker.getPositionMapping().keySet()) {
for (Long x : tracker.getReadOffsetMapping().keySet()) {
count++;
Assert.assertEquals(2, tracker.getPositionMapping().get(x).size());
Assert.assertEquals(2, tracker.getReadOffsetMapping().get(x).size());
}
Assert.assertEquals(10, count);
}
@ -89,9 +89,9 @@ public class ReadMetaDataTrackerTest extends BaseTest {
// count the positions
int count = 0;
for (Long x : tracker.getPositionMapping().keySet()) {
for (Long x : tracker.getReadOffsetMapping().keySet()) {
count++;
Assert.assertEquals(1, tracker.getPositionMapping().get(x).size());
Assert.assertEquals(1, tracker.getReadOffsetMapping().get(x).size());
}
Assert.assertEquals(10, count);
}
@ -103,7 +103,7 @@ public class ReadMetaDataTrackerTest extends BaseTest {
// count the positions
int count = 0;
Map<Long, Collection<ReferenceOrderedDatum>> map = tracker.getPositionMapping("default");
Map<Long, Collection<ReferenceOrderedDatum>> map = tracker.getReadOffsetMapping("default");
for (Long x : map.keySet()) {
count++;
Assert.assertEquals(1, map.get(x).size());
@ -117,7 +117,7 @@ public class ReadMetaDataTrackerTest extends BaseTest {
ReadMetaDataTracker tracker = getRMDT(1, nameSet, false); // create both RODs of the same type
// count the positions
int count = 0;
Map<Long, Collection<ReferenceOrderedDatum>> map = tracker.getPositionMapping(FakeRODatum.class);
Map<Long, Collection<ReferenceOrderedDatum>> map = tracker.getReadOffsetMapping(FakeRODatum.class);
for (Long x : map.keySet()) {
count++;
Assert.assertEquals(2, map.get(x).size());
@ -126,6 +126,7 @@ public class ReadMetaDataTrackerTest extends BaseTest {
}
// @Test this test can be uncommented to determine the speed impacts of any changes to the RODs for reads system
public void filterByMassiveDupType() {
for (int y = 0; y < 20; y++) {
@ -135,7 +136,7 @@ public class ReadMetaDataTrackerTest extends BaseTest {
ReadMetaDataTracker tracker = getRMDT(1, nameSet, false); // create both RODs of the same type
// count the positions
int count = 0;
Map<Long, Collection<ReferenceOrderedDatum>> map = tracker.getPositionMapping(FakeRODatum.class);
Map<Long, Collection<ReferenceOrderedDatum>> map = tracker.getReadOffsetMapping(FakeRODatum.class);
for (Long x : map.keySet()) {
count++;
Assert.assertEquals(y + 2, map.get(x).size());
@ -154,7 +155,7 @@ public class ReadMetaDataTrackerTest extends BaseTest {
// count the positions
int count = 0;
Map<Long, Collection<ReferenceOrderedDatum>> map = tracker.getPositionMapping(Fake2RODatum.class);
Map<Long, Collection<ReferenceOrderedDatum>> map = tracker.getReadOffsetMapping(Fake2RODatum.class);
for (long x : map.keySet()) {
count++;
Assert.assertEquals(1, map.get(x).size());
@ -168,9 +169,9 @@ public class ReadMetaDataTrackerTest extends BaseTest {
// count the positions
int count = 0;
for (Long x : tracker.getPositionMapping().keySet()) {
for (Long x : tracker.getReadOffsetMapping().keySet()) {
count++;
Assert.assertEquals(1, tracker.getPositionMapping().get(x).size());
Assert.assertEquals(1, tracker.getReadOffsetMapping().get(x).size());
}
Assert.assertEquals(2, count);
}
@ -181,9 +182,9 @@ public class ReadMetaDataTrackerTest extends BaseTest {
// count the positions
int count = 0;
for (Long x : tracker.getGenomeLocMapping().keySet()) {
for (Long x : tracker.getContigOffsetMapping().keySet()) {
count++;
Assert.assertEquals(1, tracker.getGenomeLocMapping().get(x).size());
Assert.assertEquals(1, tracker.getContigOffsetMapping().get(x).size());
}
Assert.assertEquals(10, count);
}
@ -219,9 +220,7 @@ public class ReadMetaDataTrackerTest extends BaseTest {
}
/**
* for testing, we want a fake rod with a different classname, for the get-by-class-name functions
*/
/** for testing, we want a fake rod with a different classname, for the get-by-class-name functions */
static public class Fake2RODatum extends FakeRODatum {
public Fake2RODatum(GenomeLoc location, String name) {