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fixing the test I broke 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3454 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-05-28 02:06:20 +00:00
parent 6485e8383d
commit a4d834cc01
1 changed files with 13 additions and 12 deletions
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25
java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java
View File

@ -1,5 +1,6 @@
package org.broadinstitute.sting.gatk.datasources.providers;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.picard.reference.ReferenceSequence;
import net.sf.picard.reference.ReferenceSequenceFile;
import net.sf.samtools.*;
@ -47,7 +48,7 @@ public abstract class LocusViewTemplate extends BaseTest {
GenomeLoc shardBounds = GenomeLocParser.createGenomeLoc("chr1", 1, 5);
Shard shard = new LocusShard(Collections.singletonList(shardBounds));
WindowMaker windowMaker = new WindowMaker(iterator,shard.getGenomeLocs());
WindowMaker windowMaker = new WindowMaker(iterator,shard.getGenomeLocs(),new ArrayList<SamRecordFilter>());
WindowMaker.WindowMakerIterator window = windowMaker.next();
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, null, window.getLocus(), window, null, null);
@ -63,7 +64,7 @@ public abstract class LocusViewTemplate extends BaseTest {
GenomeLoc shardBounds = GenomeLocParser.createGenomeLoc("chr1", 1, 5);
Shard shard = new LocusShard(Collections.singletonList(shardBounds));
WindowMaker windowMaker = new WindowMaker(iterator,shard.getGenomeLocs());
WindowMaker windowMaker = new WindowMaker(iterator,shard.getGenomeLocs(),new ArrayList<SamRecordFilter>());
WindowMaker.WindowMakerIterator window = windowMaker.next();
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), window.getLocus(), window, null, null);
@ -78,7 +79,7 @@ public abstract class LocusViewTemplate extends BaseTest {
SAMRecordIterator iterator = new SAMRecordIterator(read);
Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc("chr1", 1, 10)));
WindowMaker windowMaker = new WindowMaker(iterator,shard.getGenomeLocs());
WindowMaker windowMaker = new WindowMaker(iterator,shard.getGenomeLocs(),new ArrayList<SamRecordFilter>());
WindowMaker.WindowMakerIterator window = windowMaker.next();
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), window.getLocus(), window, null, null);
LocusView view = createView(dataProvider);
@ -92,7 +93,7 @@ public abstract class LocusViewTemplate extends BaseTest {
SAMRecordIterator iterator = new SAMRecordIterator(read);
Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc("chr1", 1, 10)));
WindowMaker windowMaker = new WindowMaker(iterator,shard.getGenomeLocs());
WindowMaker windowMaker = new WindowMaker(iterator,shard.getGenomeLocs(),new ArrayList<SamRecordFilter>());
WindowMaker.WindowMakerIterator window = windowMaker.next();
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), window.getLocus(), window, null, null);
LocusView view = createView(dataProvider);
@ -106,7 +107,7 @@ public abstract class LocusViewTemplate extends BaseTest {
SAMRecordIterator iterator = new SAMRecordIterator(read);
Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc("chr1", 1, 10)));
WindowMaker windowMaker = new WindowMaker(iterator,shard.getGenomeLocs());
WindowMaker windowMaker = new WindowMaker(iterator,shard.getGenomeLocs(),new ArrayList<SamRecordFilter>());
WindowMaker.WindowMakerIterator window = windowMaker.next();
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), window.getLocus(), window, null, null);
LocusView view = createView(dataProvider);
@ -120,7 +121,7 @@ public abstract class LocusViewTemplate extends BaseTest {
SAMRecordIterator iterator = new SAMRecordIterator(read);
Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc("chr1", 6, 15)));
WindowMaker windowMaker = new WindowMaker(iterator,shard.getGenomeLocs());
WindowMaker windowMaker = new WindowMaker(iterator,shard.getGenomeLocs(),new ArrayList<SamRecordFilter>());
WindowMaker.WindowMakerIterator window = windowMaker.next();
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), window.getLocus(), window, null, null);
LocusView view = createView(dataProvider);
@ -134,7 +135,7 @@ public abstract class LocusViewTemplate extends BaseTest {
SAMRecordIterator iterator = new SAMRecordIterator(read);
Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc("chr1", 1, 10)));
WindowMaker windowMaker = new WindowMaker(iterator,shard.getGenomeLocs());
WindowMaker windowMaker = new WindowMaker(iterator,shard.getGenomeLocs(),new ArrayList<SamRecordFilter>());
WindowMaker.WindowMakerIterator window = windowMaker.next();
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), window.getLocus(), window, null, null);
LocusView view = createView(dataProvider);
@ -149,7 +150,7 @@ public abstract class LocusViewTemplate extends BaseTest {
SAMRecordIterator iterator = new SAMRecordIterator(read1, read2);
Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc("chr1", 1, 10)));
WindowMaker windowMaker = new WindowMaker(iterator,shard.getGenomeLocs());
WindowMaker windowMaker = new WindowMaker(iterator,shard.getGenomeLocs(),new ArrayList<SamRecordFilter>());
WindowMaker.WindowMakerIterator window = windowMaker.next();
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), window.getLocus(), window, null, null);
LocusView view = createView(dataProvider);
@ -168,7 +169,7 @@ public abstract class LocusViewTemplate extends BaseTest {
SAMRecordIterator iterator = new SAMRecordIterator(read1, read2, read3, read4);
Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc("chr1", 1, 10)));
WindowMaker windowMaker = new WindowMaker(iterator,shard.getGenomeLocs());
WindowMaker windowMaker = new WindowMaker(iterator,shard.getGenomeLocs(),new ArrayList<SamRecordFilter>());
WindowMaker.WindowMakerIterator window = windowMaker.next();
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), window.getLocus(), window, null, null);
LocusView view = createView(dataProvider);
@ -187,7 +188,7 @@ public abstract class LocusViewTemplate extends BaseTest {
SAMRecordIterator iterator = new SAMRecordIterator(read1, read2, read3, read4);
Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc("chr1", 1, 10)));
WindowMaker windowMaker = new WindowMaker(iterator,shard.getGenomeLocs());
WindowMaker windowMaker = new WindowMaker(iterator,shard.getGenomeLocs(),new ArrayList<SamRecordFilter>());
WindowMaker.WindowMakerIterator window = windowMaker.next();
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), window.getLocus(), window, null, null);
LocusView view = createView(dataProvider);
@ -208,7 +209,7 @@ public abstract class LocusViewTemplate extends BaseTest {
SAMRecordIterator iterator = new SAMRecordIterator(read1, read2, read3, read4, read5, read6);
Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc("chr1", 1, 10)));
WindowMaker windowMaker = new WindowMaker(iterator,shard.getGenomeLocs());
WindowMaker windowMaker = new WindowMaker(iterator,shard.getGenomeLocs(),new ArrayList<SamRecordFilter>());
WindowMaker.WindowMakerIterator window = windowMaker.next();
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), window.getLocus(), window, null, null);
LocusView view = createView(dataProvider);
@ -236,7 +237,7 @@ public abstract class LocusViewTemplate extends BaseTest {
read07, read08, read09, read10, read11, read12);
Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc("chr1", 6, 15)));
WindowMaker windowMaker = new WindowMaker(iterator,shard.getGenomeLocs());
WindowMaker windowMaker = new WindowMaker(iterator,shard.getGenomeLocs(),new ArrayList<SamRecordFilter>());
WindowMaker.WindowMakerIterator window = windowMaker.next();
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), window.getLocus(), window, null, null);
LocusView view = createView(dataProvider);