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Fix for GATK run report ids: 

mOVsxGfDiiSMxVs2PPTVjzYTVbizlD6e
  f9kUHUADFsZ0LiTGxRL5zPmq9kZcA4cQ
  8eGHWJFAlBVmgxwPi3sMd1RmiN2PwHOf
  iLhvHWveypKb2F8vKS5irHylc3pYvlOb
  HDttXKUMEVoPrvVeWrH7E0htxYyNydMx
plus a bit of cleanup of custom exceptions in the sharding system.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4330 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-09-22 19:49:25 +00:00
parent 20b38b38f3
commit 8f75d88519
5 changed files with 10 additions and 94 deletions
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3
java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
View File

@ -113,7 +113,8 @@ public class SAMDataSource implements SimpleDataSource {
readerIDs = reads.getSAMReaderIDs();
for (SAMReaderID readerID : reads.getSAMReaderIDs()) {
if (!readerID.samFile.canRead())
throw new SimpleDataSourceLoadException("SAMDataSource: Unable to load file: " + readerID.samFile.getName());
throw new UserException.CouldNotReadInputFile(readerID.samFile,"file is not present or user does not have appropriate permissions. " +
"Please check that the file is present and readable and try again.");
}
resourcePool = new SAMResourcePool(Integer.MAX_VALUE);

2
java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSource.java
View File

@ -32,6 +32,6 @@ public interface SimpleDataSource extends Serializable {
* @param shard the region
* @return an iterator of the appropriate type, that is limited by the region
*/
public Iterator seek(Shard shard) throws SimpleDataSourceLoadException;
public Iterator seek(Shard shard);
}

39
java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceLoadException.java
View File

@ -1,39 +0,0 @@
package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
/**
*
* User: aaron
* Date: Apr 6, 2009
* Time: 4:21:58 PM
*
* The Broad Institute
* SOFTWARE COPYRIGHT NOTICE AGREEMENT
* This software and its documentation are copyright 2009 by the
* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. Neither
* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
*
*/
/**
* @author aaron
* @version 1.0
* @date Apr 6, 2009
* <p/>
* Class SimpleDataSourceLoadException
* <p/>
* Generate this on a simple data source load exception
*/
public class SimpleDataSourceLoadException extends ReviewedStingException {
public SimpleDataSourceLoadException(String msg) {
super(msg);
}
public SimpleDataSourceLoadException(String msg,Throwable throwable) {
super(msg,throwable);
}
}

47
java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceSplitException.java
View File

@ -1,47 +0,0 @@
package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
/*
* Copyright (c) 2009 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.
*/
/**
* @author aaron
* @version 1.0
* @date Apr 1, 2009
* <p/>
* Class SimpleDataSourceSplitFailure
* <p/>
* an exception that get's thrown if we can't split up a data source appropriately
*/
public class SimpleDataSourceSplitException extends ReviewedStingException {
public SimpleDataSourceSplitException(String msg) {
super(msg);
}
}

13
java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMBAMDataSourceUnitTest.java
View File

@ -11,6 +11,7 @@ import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
@ -116,9 +117,9 @@ public class SAMBAMDataSourceUnitTest extends BaseTest {
}
}
}
catch (SimpleDataSourceLoadException e) {
catch (UserException.CouldNotReadInputFile e) {
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
fail("testLinearBreakIterateAll: We Should get a SimpleDataSourceLoadException");
fail("testLinearBreakIterateAll: We Should get a UserException.CouldNotReadInputFile exception");
}
}
@ -162,9 +163,9 @@ public class SAMBAMDataSourceUnitTest extends BaseTest {
datum.close();
}
}
catch (SimpleDataSourceLoadException e) {
catch (UserException.CouldNotReadInputFile e) {
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
fail("testLinearBreakIterateAll: We Should get a SimpleDataSourceLoadException");
fail("testLinearBreakIterateAll: We Should get a UserException.CouldNotReadInputFile exception");
}
@ -201,9 +202,9 @@ public class SAMBAMDataSourceUnitTest extends BaseTest {
datum.close();
}
}
catch (SimpleDataSourceLoadException e) {
catch (UserException.CouldNotReadInputFile e) {
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
fail("testLinearBreakIterateAll: We Should get a SimpleDataSourceLoadException");
fail("testLinearBreakIterateAll: We Should get a UserException.CouldNotReadInputFile exception");
}
/*int pos = 0;