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More informative error messages when dictionaries don't match #1870
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Original file line number | Diff line number | Diff line change |
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@@ -223,9 +223,13 @@ private void checkDictionaryGoodForFingerprinting(final SAMSequenceDictionary se | |
final SAMSequenceDictionary activeDictionary = getActiveDictionary(haplotypes); | ||
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if (sequenceDictionaryToCheck.getSequences().size() < activeDictionary.size()) { | ||
throw new IllegalArgumentException("Dictionary on fingerprinted file smaller than that on Haplotype Database!"); | ||
throw new SequenceUtil.SequenceListsDifferException("Dictionary on fingerprinted file smaller than that on Haplotype Database!"); | ||
} | ||
try { | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. and also this? |
||
SequenceUtil.assertSequenceDictionariesEqual(activeDictionary, sequenceDictionaryToCheck, true); | ||
} catch (final SequenceUtil.SequenceListsDifferException e) { | ||
throw new PicardException("Dictionary on fingerprinted file does not match dictionary in Haplotype Database.", e); | ||
} | ||
SequenceUtil.assertSequenceDictionariesEqual(activeDictionary, sequenceDictionaryToCheck, true); | ||
} | ||
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private static SAMSequenceDictionary getActiveDictionary(final HaplotypeMap haplotypes) { | ||
|
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48 changes: 48 additions & 0 deletions
48
src/test/java/picard/util/SequenceDictionaryUtilsTest.java
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,48 @@ | ||
package picard.util; | ||
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import htsjdk.samtools.SAMSequenceDictionary; | ||
import htsjdk.samtools.SAMSequenceRecord; | ||
import org.testng.annotations.DataProvider; | ||
import org.testng.annotations.Test; | ||
import picard.PicardException; | ||
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import java.util.List; | ||
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public class SequenceDictionaryUtilsTest { | ||
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@Test | ||
public void testSequenceDictionaryPositive() { | ||
final SAMSequenceDictionary s1 = new SAMSequenceDictionary( | ||
List.of( | ||
new SAMSequenceRecord("chr1", 10), | ||
new SAMSequenceRecord("chr2", 15), | ||
new SAMSequenceRecord("chr3", 20) | ||
) | ||
); | ||
SequenceDictionaryUtils.assertSequenceDictionariesEqual( | ||
s1, | ||
"s1", | ||
new SAMSequenceDictionary(s1.getSequences()), | ||
"s2"); | ||
} | ||
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@DataProvider | ||
public Object[][] sequenceDictionaryNegativeProvider() { | ||
return new Object[][]{ | ||
{ | ||
new SAMSequenceDictionary(List.of(new SAMSequenceRecord("chr1", 100))), | ||
new SAMSequenceDictionary(List.of(new SAMSequenceRecord("chr1", 200))) | ||
}, | ||
{ | ||
new SAMSequenceDictionary(List.of(new SAMSequenceRecord("chr1", 10))), | ||
new SAMSequenceDictionary(List.of(new SAMSequenceRecord("chr2", 10))) | ||
}, | ||
}; | ||
} | ||
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@Test(dataProvider = "sequenceDictionaryNegativeProvider", expectedExceptions = PicardException.class) | ||
public void testSequenceDictionaryNegative(final SAMSequenceDictionary s1, final SAMSequenceDictionary s2 ) { | ||
SequenceDictionaryUtils.assertSequenceDictionariesEqual(s1, "s1", s2, "s2"); | ||
} | ||
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} |
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this should be able to switch to
SequenceDictionaryUtils.assertSequenceDictionariesEqual
as well, right?There was a problem hiding this comment.
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I didn't change these because they use the extra
checkPrefixOnly
argument, which the others don't. So rather than create another overload in Picard, I left these as direct calls to htsjdk. If you think its worth it though I could add a second method for those cases though.There was a problem hiding this comment.
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ahh, I see. No I think that's fine in that case.