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fixed sam by reads test for the new filtering code 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1180 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-07-07 05:45:50 +00:00
parent 2a86f2f833
commit 033bafe7a1
2 changed files with 49 additions and 83 deletions
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6
java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java
View File

@ -153,6 +153,9 @@ public class ArtificialSAMUtils {
elements.add(new CigarElement(length, CigarOperator.characterToEnum('M')));
record.setCigar(new Cigar(elements));
record.setProperPairFlag(false);
if (refIndex == -1) {
record.setReadUmappedFlag(true);
}
return record;
}
@ -175,6 +178,9 @@ public class ArtificialSAMUtils {
SAMRecord rec = createArtificialRead(header, name, refIndex, alignmentStart, bases.length);
rec.setReadBases(bases);
rec.setBaseQualities(qual);
if (refIndex == -1) {
rec.setReadUmappedFlag(true);
}
return rec;
}

126
java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMByReadsTest.java
View File

@ -63,16 +63,16 @@ public class SAMByReadsTest extends BaseTest {
// setup the test files
fl.add(new File("/humgen/gsa-scr1/GATK_Data/Validation_Data/index_test.bam"));
reads = new Reads(fl);
}
/** Test out that we can shard the file and iterate over every read */
/**
* Test out that we can shard the file and iterate over every read
*/
@Test
public void testToUnmappedReads() {
ArtificialResourcePool gen = new ArtificialResourcePool(createArtificialSamHeader(1,10,100,1000),
ArtificialSAMUtils.mappedAndUnmappedReadIterator(1, 100, 10, 1000) );
ArtificialResourcePool gen = new ArtificialResourcePool(createArtificialSamHeader(1, 1, 1, 50),
ArtificialSAMUtils.mappedAndUnmappedReadIterator(1, 1, 1, 10));
GenomeLocParser.setupRefContigOrdering(gen.getHeader().getSequenceDictionary());
try {
@ -81,94 +81,69 @@ public class SAMByReadsTest extends BaseTest {
SAMDataSource data = new SAMDataSource(reads);
data.setResourcePool(gen);
for (int x = 0; x < 10; x++) {
++iterations;
StingSAMIterator ret = data.toUnmappedReads(100);
// count the reads we've gotten back
if (ret == null) {
fail("On iteration " + iterations + " we were returned a null pointer, after seeing " + unmappedReadsSeen + " reads out of a 1000");
}
while (ret.hasNext()) {
ret.next();
unmappedReadsSeen++;
}
++iterations;
StingSAMIterator ret = data.toUnmappedReads(100);
// count the reads we've gotten back
if (ret == null) {
fail("On iteration " + iterations + " we were returned a null pointer, after seeing " + unmappedReadsSeen + " reads out of a 1000");
}
assertEquals(1000,unmappedReadsSeen);
}
catch (SimpleDataSourceLoadException e) {
while (ret.hasNext()) {
ret.next();
unmappedReadsSeen++;
}
assertEquals(10, unmappedReadsSeen);
} catch (SimpleDataSourceLoadException e) {
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
fail("testLinearBreakIterateAll: We Should not get a SimpleDataSourceLoadException");
}
}
/** Test out that we can shard the file and iterate over every read */
/**
* Test out that we can shard the file and iterate over every read
*/
@Test
public void testShardingOfReadsSize14() {
ArtificialResourcePool gen = new ArtificialResourcePool(createArtificialSamHeader(1,10,100,1000),
ArtificialSAMUtils.queryReadIterator(1,10,100,1000) );
GenomeLocParser.setupRefContigOrdering(gen.getHeader().getSequenceDictionary());
targetReadCount = 14;
public void testShardingOfReadsEvenSplit() {
try {
Thread.sleep(5000);
} catch (InterruptedException e) {
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
}
ArtificialResourcePool gen = new ArtificialResourcePool(createArtificialSamHeader(1, 1, 10, 50),
ArtificialSAMUtils.mappedAndUnmappedReadIterator(1, 1, 10, 10));
GenomeLocParser.setupRefContigOrdering(gen.getHeader().getSequenceDictionary());
targetReadCount = 5;
try {
int iterations = 0;
int readCount = 0;
SAMDataSource data = new SAMDataSource(reads);
ArrayList<Integer> readsPerShard = new ArrayList<Integer>();
data.setResourcePool(gen);
shardStrategy = ShardStrategyFactory.shatter(ShardStrategyFactory.SHATTER_STRATEGY.READS, gen.getHeader().getSequenceDictionary(), targetReadCount);
while (shardStrategy.hasNext()) {
int initialReadCount = readCount;
StingSAMIterator ret = data.seek(shardStrategy.next());
assertTrue(ret != null);
while (ret.hasNext()) {
ret.next();
readCount++;
}
readsPerShard.add(readCount-initialReadCount);
ret.close();
iterations++;
}
// assert that we saw 2000 reads
assertEquals(2000,readCount);
/**
* this next assertion is based on the following logic:
* 14 reads per shard = 8 shards per each 100 read chromosome
* 10 chromosomes = 8 * 10 = 80
* 1000 unmapped reads / 14 = 72
* 1 iteration at the end to know we're done
* 80 + 72 + 1 = 153
*/
assertEquals(153,iterations);
}
catch (SimpleDataSourceLoadException e) {
assertEquals(20, readCount);
} catch (SimpleDataSourceLoadException e) {
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
fail("testLinearBreakIterateAll: We Should not get a SimpleDataSourceLoadException");
}
}
/** Test out that we can shard the file and iterate over every read */
/**
* Test out that we can shard the file and iterate over every read
*/
@Test
public void testShardingOfReadsSize25() {
ArtificialResourcePool gen = new ArtificialResourcePool(createArtificialSamHeader(1,10,100,1000),
ArtificialSAMUtils.queryReadIterator(1,10,100,1000) );
public void testShardingOfReadsOddRemainder() {
ArtificialResourcePool gen = new ArtificialResourcePool(createArtificialSamHeader(1, 1, 10, 100),
ArtificialSAMUtils.mappedAndUnmappedReadIterator(1, 1, 10, 10));
GenomeLocParser.setupRefContigOrdering(gen.getHeader().getSequenceDictionary());
targetReadCount = 25;
targetReadCount = 3;
try {
int iterations = 0;
int readCount = 0;
SAMDataSource data = new SAMDataSource(reads);
@ -185,36 +160,21 @@ public class SAMByReadsTest extends BaseTest {
readCount++;
}
ret.close();
iterations++;
}
// assert that we saw 2000 reads
assertEquals(2000,readCount);
assertEquals(20, readCount);
/**
* this next assertion is based on the following logic:
* 25 reads per shard = 5 shards (1 on the end to realize we're done)
* 10 chromosomes = 5 * 10 = 50
* 1000 unmapped reads / 25 = 40
* 1 iteration at the end to know we're done
* 50 + 40 + 1 = 91
*/
assertEquals(91,iterations);
}
catch (SimpleDataSourceLoadException e) {
} catch (SimpleDataSourceLoadException e) {
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
fail("testLinearBreakIterateAll: We Should not get a SimpleDataSourceLoadException");
}
}
private SAMFileHeader createArtificialSamHeader(int startingChr, int endingChr, int readCount, int readSize) {
return ArtificialSAMUtils.createArtificialSamHeader( ( endingChr - startingChr ) + 1,
startingChr,
readCount + readSize );
return ArtificialSAMUtils.createArtificialSamHeader((endingChr - startingChr) + 1,
startingChr,
readCount + readSize);
}
}