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The system now requires a dictionary file for a fasta file, or it throws an error. You can't just operate without a sequence dictionary any longer. We will transition to a GenomeLoc system that assumes a dictionary is available. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@319 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-04-07 22:19:54 +00:00
parent 9c4fc633aa
commit 00722e19bc
2 changed files with 10 additions and 10 deletions
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9
java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
View File

@ -399,11 +399,10 @@ public abstract class TraversalEngine {
//this.refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(refFileName);
this.refFile = new FastaSequenceFile2(refFileName); // todo: replace when FastaSequenceFile2 is in picard
this.refIter = new ReferenceIterator(this.refFile);
// if (!GenomeLoc.setupRefContigOrdering(this.refFile)) {
// // We couldn't process the reference contig ordering, fail since we need it
// logger.fatal(String.format("We couldn't load the contig dictionary associated with %s. At the current time we require this dictionary file to efficiently access the FASTA file. In the near future this program will automatically construct the dictionary for you and save it down.", refFileName));
// throw new RuntimeException("We couldn't load the contig dictionary associated with " + refFileName + ". At the current time we require this dictionary file to efficiently access the FASTA file. In the near future this program will automatically construct the dictionary for you and save it down.");
// }
if (!GenomeLoc.setupRefContigOrdering(this.refFile)) {
// We couldn't process the reference contig ordering, fail since we need it
Utils.scareUser(String.format("We couldn't load the contig dictionary associated with %s. At the current time we require this dictionary file to efficiently access the FASTA file. Please use /seq/software/picard/current/bin/CreateSequenceDictionary.jar to create a sequence dictionary for your file", refFileName));
}
}
}

11
java/src/org/broadinstitute/sting/utils/Utils.java
View File

@ -35,11 +35,12 @@ public class Utils {
}
public static void scareUser(final String msg) {
logger.fatal(String.format("********************************************************************************"));
logger.fatal(String.format("* ERROR:"));
logger.fatal(String.format("*"));
logger.fatal(String.format("* %s", msg));
logger.fatal(String.format("********************************************************************************"));
System.out.printf("********************************************************************************%n");
System.out.printf("* ERROR:%n");
System.out.printf("*%n");
System.out.printf("* %s%n", msg);
System.out.printf("********************************************************************************%n");
logger.fatal(msg);
throw new RuntimeException(msg);
}