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convert Runtime exceptions in the CRAM code into CRAMExceptions (also… #1557

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convert Runtime exceptions in the CRAM code into CRAMExceptions (also… #1557

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5 changes: 3 additions & 2 deletions src/main/java/htsjdk/samtools/cram/build/CRAMReferenceRegion.java
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMSequenceRecord;
import htsjdk.samtools.cram.CRAMException;
import htsjdk.samtools.cram.ref.CRAMReferenceSource;
import htsjdk.samtools.cram.ref.ReferenceContext;

Expand All @@ -47,7 +48,7 @@ public class CRAMReferenceRegion {
*/
public CRAMReferenceRegion(final CRAMReferenceSource cramReferenceSource, final SAMFileHeader samFileHeader) {
if (cramReferenceSource == null) {
throw new IllegalArgumentException("A valid reference must be supplied to retrieve records from the CRAM stream.");
throw new CRAMException("A valid reference must be supplied to retrieve records from the CRAM stream.");
}
this.referenceSource = cramReferenceSource;
this.samFileHeader = samFileHeader;
Expand All @@ -73,7 +74,7 @@ public byte[] getReferenceBases(final int referenceIndex) {
final SAMSequenceRecord sequence = samFileHeader.getSequence(referenceIndex);
referenceBases = referenceSource.getReferenceBases(sequence, true);
if (referenceBases == null) {
throw new IllegalArgumentException(
throw new CRAMException(
String.format(
"A reference must be supplied (reference sequence %s not found).",
sequence));
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