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Error message fixes for the following issues: 

nvjpM4yOwQAu3fNGxi4oXLuVpKn6aAlf,1GL0OuXK2xKQfvbu34tWYgbojSVSLo0l,
ehEGBJOfgc4V7qj8W0Homf5ICuVK5Sm3,cZsreLm1CbY3aYKZhV7DOSvQNwur41zp,
GlrlyGEyP9kJDIRCQNFQp7BGJBXSzdDJ,hyz1uiHXr39ANmdZu9K1epOSX8EL3mDw,
q0n4EucZESCI4LZhQik306zD4VAuH2cb.  

Messages:
camrhG5tHzlY9WUSEVpVZGkU1tyJqKb5,s0OX2g7nYRctJxyFoQCa6clac9IsjHyi,
THIAtjllvYNlnTmiMnJEIHd2Ju4gqQIO,jwVk3JYZJNHloW7HO4LeGxFexknqro0v,
BFNRGOGmGGJNNPZqgeF1ikTNFfskbyLc,...

Were fixed in 4392.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4428 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-10-05 03:37:13 +00:00
parent e340be34d8
commit 250c18e679
3 changed files with 10 additions and 9 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java
View File

@ -212,7 +212,7 @@ public class FastaSequenceIndexBuilder {
return sequenceIndex;
}
catch (IOException e) {
throw new UserException.CouldNotReadInputFile(fastaFile, String.format("Could not read fasta file"), e);
throw new UserException.CouldNotReadInputFile(fastaFile, "Could not read fasta file", e);
}
catch (Exception e) {
throw new ReviewedStingException(e.getMessage(), e);

3
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
View File

@ -240,7 +240,8 @@ public class GenomeAnalysisEngine extends AbstractGenomeAnalysisEngine {
found = true;
}
if (!found)
throw new ArgumentException(String.format("Unable to find reference metadata (%s,%s)", required.name(), required.type()));
throw new ArgumentException(String.format("Walker requires reference metadata to be supplied named '%s' of type '%s', but this metadata was not provided. " +
"Please supply the specified metadata file.", required.name(), required.type().getSimpleName()));
}
// Check to see that no forbidden rods are present.

14
java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceDataSource.java
View File

@ -30,6 +30,7 @@ import net.sf.picard.reference.FastaSequenceIndexBuilder;
import net.sf.picard.sam.CreateSequenceDictionary;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.picard.reference.FastaSequenceIndex;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.file.FSLockWithShared;
import org.broadinstitute.sting.utils.file.FileSystemInabilityToLockException;
@ -53,13 +54,8 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener
public ReferenceDataSource(File fastaFile) {
// does the fasta file exist? check that first...
if (!fastaFile.exists()) {
if (!fastaFile.getParentFile().exists())
throw new UserException("The fasta file path you provided is invalid. The directory " +
fastaFile.getParentFile().getAbsolutePath() + " does not exist." );
else
throw new UserException("The fasta file you provided does not exist.");
}
if (!fastaFile.exists())
throw new UserException("The fasta file you specified (" + fastaFile.getAbsolutePath() + ") does not exist.");
File indexFile = new File(fastaFile.getAbsolutePath() + ".fai");
File dictFile;
@ -89,6 +85,10 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener
logger.info("Unable to create write lock: " + ex.getMessage());
logger.info("Skipping index creation.");
}
catch(UserException e) {
// Rethrow all user exceptions as-is; there should be more details in the UserException itself.
throw e;
}
catch (Exception e) {
// If lock creation succeeded, the failure must have been generating the index.
// If lock creation failed, just skip over index creation entirely.