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At some time in the recent past, we lost our ability to process the '-L all' 

argument.  Brought it back, and added an integrationtest to make sure it
stays around.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4390 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-09-30 15:58:43 +00:00
parent f34b4c6b82
commit 78343be52c
2 changed files with 94 additions and 23 deletions
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54
java/src/org/broadinstitute/sting/gatk/AbstractGenomeAnalysisEngine.java
View File

@ -156,36 +156,44 @@ public abstract class AbstractGenomeAnalysisEngine {
*/
protected void initializeIntervals() {
// return null if no interval arguments at all
// return if no interval arguments at all
if ((argCollection.intervals == null) && (argCollection.excludeIntervals == null) && (argCollection.RODToInterval == null))
return;
else {
// if include argument isn't given, create new set of all possible intervals
GenomeLocSortedSet includeSortedSet = (argCollection.intervals == null && argCollection.RODToInterval == null ?
GenomeLocSortedSet.createSetFromSequenceDictionary(this.referenceDataSource.getReference().getSequenceDictionary()) :
loadIntervals(argCollection.intervals,
argCollection.intervalMerging,
GenomeLocParser.mergeIntervalLocations(checkRODToIntervalArgument(),argCollection.intervalMerging)));
// if '-L all' was specified, verify that it was the only -L specified and return if so.
for(String interval: argCollection.intervals) {
if(interval.trim().equals("all")) {
if(argCollection.intervals.size() > 1)
throw new UserException("'-L all' was specified along with other intervals or interval lists; the GATK cannot combine '-L all' with other intervals.");
// if no exclude arguments, can return parseIntervalArguments directly
if (argCollection.excludeIntervals == null)
intervals = includeSortedSet;
// '-L all' was specified and seems valid. Return.
return;
}
}
// if include argument isn't given, create new set of all possible intervals
GenomeLocSortedSet includeSortedSet = (argCollection.intervals == null && argCollection.RODToInterval == null ?
GenomeLocSortedSet.createSetFromSequenceDictionary(this.referenceDataSource.getReference().getSequenceDictionary()) :
loadIntervals(argCollection.intervals,
argCollection.intervalMerging,
GenomeLocParser.mergeIntervalLocations(checkRODToIntervalArgument(),argCollection.intervalMerging)));
// if no exclude arguments, can return parseIntervalArguments directly
if (argCollection.excludeIntervals == null)
intervals = includeSortedSet;
// otherwise there are exclude arguments => must merge include and exclude GenomeLocSortedSets
else {
GenomeLocSortedSet excludeSortedSet = loadIntervals(argCollection.excludeIntervals, argCollection.intervalMerging, null);
intervals = includeSortedSet.subtractRegions(excludeSortedSet);
// logging messages only printed when exclude (-XL) arguments are given
long toPruneSize = includeSortedSet.coveredSize();
long toExcludeSize = excludeSortedSet.coveredSize();
long intervalSize = intervals.coveredSize();
logger.info(String.format("Initial include intervals span %d loci; exclude intervals span %d loci", toPruneSize, toExcludeSize));
logger.info(String.format("Excluding %d loci from original intervals (%.2f%% reduction)",
toPruneSize - intervalSize, (toPruneSize - intervalSize) / (0.01 * toPruneSize)));
}
else {
GenomeLocSortedSet excludeSortedSet = loadIntervals(argCollection.excludeIntervals, argCollection.intervalMerging, null);
intervals = includeSortedSet.subtractRegions(excludeSortedSet);
// logging messages only printed when exclude (-XL) arguments are given
long toPruneSize = includeSortedSet.coveredSize();
long toExcludeSize = excludeSortedSet.coveredSize();
long intervalSize = intervals.coveredSize();
logger.info(String.format("Initial include intervals span %d loci; exclude intervals span %d loci", toPruneSize, toExcludeSize));
logger.info(String.format("Excluding %d loci from original intervals (%.2f%% reduction)",
toPruneSize - intervalSize, (toPruneSize - intervalSize) / (0.01 * toPruneSize)));
}
}

63
java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java 100644
View File

@ -0,0 +1,63 @@
/*
* Copyright (c) 2010, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.interval;
import org.broadinstitute.sting.WalkerTest;
import org.junit.Test;
import java.util.Arrays;
import java.util.Collections;
/**
* Test the GATK core interval parsing mechanism.
*/
public class IntervalIntegrationTest extends WalkerTest {
@Test
public void testAllImplicitIntervalParsing() {
String md5 = "7821db9e14d4f8e07029ff1959cd5a99";
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T CountLoci" +
" -I " + validationDataLocation + "OV-0930.normal.chunk.bam" +
" -R " + hg18Reference +
" -o %s",
1, // just one output file
Arrays.asList(md5));
executeTest("testAllIntervalsImplicit",spec);
}
@Test
public void testAllExplicitIntervalParsing() {
String md5 = "7821db9e14d4f8e07029ff1959cd5a99";
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T CountLoci" +
" -I " + validationDataLocation + "OV-0930.normal.chunk.bam" +
" -R " + hg18Reference +
" -L all" +
" -o %s",
1, // just one output file
Arrays.asList(md5));
executeTest("testAllIntervalsExplicit",spec);
}
}