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Better error message to the BAMScheduler 

In the case where the BAM file was aligned using a reference but analysis is being attempted with a different reference.
This commit is contained in:
Mauricio Carneiro 2012-05-02 16:10:00 -04:00
parent a5d17e02c7
commit f51a1d0d61
1 changed files with 5 additions and 3 deletions
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8
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java
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@ -27,13 +27,12 @@ package org.broadinstitute.sting.gatk.datasources.reads;
import net.sf.picard.util.PeekableIterator; import net.sf.picard.util.PeekableIterator;
import net.sf.samtools.GATKBAMFileSpan; import net.sf.samtools.GATKBAMFileSpan;
import net.sf.samtools.GATKChunk; import net.sf.samtools.GATKChunk;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileSpan;
import net.sf.samtools.SAMSequenceDictionary; import net.sf.samtools.SAMSequenceDictionary;
import net.sf.samtools.SAMSequenceRecord; import net.sf.samtools.SAMSequenceRecord;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.GenomeLocSortedSet; import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.sam.ReadUtils;
@ -265,7 +264,10 @@ public class BAMScheduler implements Iterator<FilePointer> {
// Naive algorithm: find all elements in current contig for proper schedule creation. // Naive algorithm: find all elements in current contig for proper schedule creation.
List<GenomeLoc> lociInContig = new LinkedList<GenomeLoc>(); List<GenomeLoc> lociInContig = new LinkedList<GenomeLoc>();
for(GenomeLoc locus: loci) { for(GenomeLoc locus: loci) {
if(!GenomeLoc.isUnmapped(locus) && dataSource.getHeader().getSequence(locus.getContig()).getSequenceIndex() == lastReferenceSequenceLoaded) if (!GenomeLoc.isUnmapped(locus) && dataSource.getHeader().getSequence(locus.getContig()) == null)
throw new ReviewedStingException("BAM file(s) do not have the contig: " + locus.getContig() + ". You are probably using a different reference than the one this file was aligned with");
if (!GenomeLoc.isUnmapped(locus) && dataSource.getHeader().getSequence(locus.getContig()).getSequenceIndex() == lastReferenceSequenceLoaded)
lociInContig.add(locus); lociInContig.add(locus);
} }