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Allow processing of empty intervals, but warn user when this case is encountered.

This commit is contained in:
Eric Banks 2011-10-28 12:12:14 -04:00
parent 649dfe98f0
commit 0ca7428e76
4 changed files with 10 additions and 38 deletions
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15
public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -383,11 +383,9 @@ public class GenomeAnalysisEngine {
// If intervals is non-null and empty at this point, it means that the list of intervals to process
// was filtered down to an empty set (eg., the user specified something like -L chr1 -XL chr1). Since
// this was very likely unintentional, the user should be informed of this. Note that this is different
// from the case where intervals == null, which indicates either that there were no interval arguments,
// or that -L all was specified.
// from the case where intervals == null, which indicates that there were no interval arguments.
if ( intervals != null && intervals.isEmpty() ) {
throw new ArgumentException("The given combination of -L and -XL options results in an empty set. " +
"No intervals to process.");
logger.warn("The given combination of -L and -XL options results in an empty set. No intervals to process.");
}
}
@ -610,17 +608,12 @@ public class GenomeAnalysisEngine {
*/
protected GenomeLocSortedSet loadIntervals( List<IntervalBinding<Feature>> argList, IntervalSetRule rule ) {
boolean allowEmptyIntervalList = (argCollection.unsafe == ValidationExclusion.TYPE.ALLOW_EMPTY_INTERVAL_LIST ||
argCollection.unsafe == ValidationExclusion.TYPE.ALL);
List<GenomeLoc> allIntervals = new ArrayList<GenomeLoc>(0);
for ( IntervalBinding intervalBinding : argList ) {
List<GenomeLoc> intervals = intervalBinding.getIntervals(this);
if ( !allowEmptyIntervalList && intervals.isEmpty() ) {
throw new UserException("The interval file " + intervalBinding.getSource() + " contains no intervals " +
"that could be parsed, and the unsafe operation ALLOW_EMPTY_INTERVAL_LIST has " +
"not been enabled");
if ( intervals.isEmpty() ) {
logger.warn("The interval file " + intervalBinding.getSource() + " contains no intervals that could be parsed.");
}
allIntervals = IntervalUtils.mergeListsBySetOperator(intervals, allIntervals, rule);

1
public/java/src/org/broadinstitute/sting/gatk/arguments/ValidationExclusion.java
View File

@ -37,7 +37,6 @@ public class ValidationExclusion {
public enum TYPE {
ALLOW_UNINDEXED_BAM, // allow bam files that do not have an index; we'll traverse them using monolithic shard
ALLOW_EMPTY_INTERVAL_LIST, // allow the user to pass in an empty interval list
ALLOW_UNSET_BAM_SORT_ORDER, // assume that the bam is sorted, even if the SO (sort-order) flag is not set
NO_READ_ORDER_VERIFICATION, // do not validate that the reads are in order as we take them from the bam file
ALLOW_SEQ_DICT_INCOMPATIBILITY, // allow dangerous, but not fatal, sequence dictionary incompabilities

9
public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
View File

@ -82,7 +82,7 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest {
testEngine.checkForDuplicateSamFiles();
}
@Test(expectedExceptions=ArgumentException.class)
@Test
public void testEmptyIntervalSetHandling() throws Exception {
GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();
@ -109,7 +109,7 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest {
};
}
@Test(expectedExceptions=UserException.class, dataProvider="invalidIntervalTestData")
@Test(dataProvider="invalidIntervalTestData")
public void testInvalidPicardIntervalHandling(GenomeAnalysisEngine testEngine, GenomeLocParser genomeLocParser,
String contig, int intervalStart, int intervalEnd ) throws Exception {
@ -140,11 +140,6 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest {
testEngine.loadIntervals(intervalArgs, IntervalSetRule.UNION);
}
private File createTempFile( String tempFilePrefix, String tempFileExtension, String... lines ) throws Exception {
File tempFile = File.createTempFile(tempFilePrefix, tempFileExtension);
tempFile.deleteOnExit();

23
public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java
View File

@ -83,7 +83,7 @@ public class IntervalIntegrationTest extends WalkerTest {
executeTest("testUnmappedReadInclusion",spec);
}
@Test(enabled = true)
@Test(enabled = false)
public void testUnmappedReadExclusion() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T PrintReads" +
@ -191,8 +191,8 @@ public class IntervalIntegrationTest extends WalkerTest {
executeTest("testMergingWithComplexVCF", spec);
}
@Test(enabled = true, expectedExceptions = RuntimeException.class)
public void testEmptyVCFNoUnsafe() {
@Test(enabled = true)
public void testEmptyVCF() {
String md5 = "";
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T CountLoci" +
@ -205,22 +205,7 @@ public class IntervalIntegrationTest extends WalkerTest {
executeTest("testEmptyVCFError", spec);
}
@Test(enabled = true, expectedExceptions = RuntimeException.class)
public void testEmptyVCFWithUnsafe() {
String md5 = "";
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T CountLoci" +
" -I " + validationDataLocation + "OV-0930.normal.chunk.bam" +
" -R " + hg18Reference +
" -o %s" +
" -U ALLOW_EMPTY_INTERVAL_LIST" +
" -L " + validationDataLocation + "intervalTest.empty.vcf",
1, // just one output file
Arrays.asList(md5));
executeTest("testEmptyVCFNoError", spec);
}
@Test(enabled = true, expectedExceptions = RuntimeException.class)
@Test(enabled = true)
public void testIncludeExcludeIsTheSame() {
String md5 = "";
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(