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Adding error in LiftoverVcf if reference dictionary does not exist (Issue #1157) #1189

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merged 5 commits into from
Jul 6, 2018
Merged

Adding error in LiftoverVcf if reference dictionary does not exist (Issue #1157) #1189

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ff698ab
handling lack of sequence dictionary exception
kachulis Jun 21, 2018
c13a20b
some clean up of LiftoverVcf PR
kachulis Jul 5, 2018
a4d3c8f
LiftoverVcfTest changes
kachulis Jul 5, 2018
3e4a680
more cleanup
kachulis Jul 5, 2018
702e383
some more cleanup
kachulis Jul 5, 2018
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5 changes: 5 additions & 0 deletions src/main/java/picard/vcf/LiftoverVcf.java
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Original file line number Diff line number Diff line change
Expand Up @@ -284,6 +284,11 @@ protected int doWork() {
log.info("Loading up the target reference genome.");
final ReferenceSequenceFileWalker walker = new ReferenceSequenceFileWalker(REFERENCE_SEQUENCE);
final Map<String, ReferenceSequence> refSeqs = new HashMap<>();
// check if sequence dictionary exists
if (walker.getSequenceDictionary() == null) {
log.error("Reference " + REFERENCE_SEQUENCE.getAbsolutePath() + " must have an associated Dictionary .dict file in the same directory.");
return 1;
}
for (final SAMSequenceRecord rec : walker.getSequenceDictionary().getSequences()) {
refSeqs.put(rec.getSequenceName(), walker.get(rec.getSequenceIndex()));
}
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55 changes: 54 additions & 1 deletion src/test/java/picard/util/LiftoverVcfTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,12 @@
import htsjdk.samtools.util.Interval;
import htsjdk.variant.variantcontext.*;
import htsjdk.variant.vcf.VCFFileReader;
import htsjdk.samtools.SAMException;
import org.testng.Assert;
import org.testng.annotations.AfterClass;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import picard.PicardException;
import picard.cmdline.CommandLineProgramTest;
import picard.vcf.LiftoverVcf;
import picard.vcf.VcfTestUtils;
Expand All @@ -21,7 +23,9 @@
import java.io.File;
import java.io.IOException;
import java.util.*;

import java.nio.file.Path;
import java.nio.file.Files;
import java.nio.file.StandardCopyOption;
/**
* Test class for LiftoverVcf.
* <p>
Expand Down Expand Up @@ -1169,4 +1173,53 @@ public void testLiftOverNoCallAndSymbolic(final LiftOver liftOver, final Variant
Assert.assertEquals(resultAlleles, result.getAttributeAsStringList(LiftoverVcf.ORIGINAL_ALLELES, null));
}
}

@Test()
public void testNoDictionary() throws IOException {
final Path liftOutput = Files.createTempFile("tmpouput", ".vcf");
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with all these deleteOnExit, I wonder if it's cleaner to have a
try{
....
} finally {
TestUtil.recursiveDelete(...);
}

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maybe not....nevermind.

liftOutput.toFile().deleteOnExit();
final Path rejectOutput = Files.createTempFile("tmpreject", ".vcf");
rejectOutput.toFile().deleteOnExit();
final Path input = TEST_DATA_PATH.toPath().resolve("testLiftoverBiallelicIndels.vcf");
final Path tmpCopyDir = Files.createTempDirectory("copy");
tmpCopyDir.toFile().deleteOnExit();
final Path referenceCopy = tmpCopyDir.resolve("refCopy.fasta");
referenceCopy.toFile().deleteOnExit();
Files.copy(REFERENCE_FILE.toPath(), referenceCopy);
final String[] args = new String[]{
"INPUT=" + input,
"OUTPUT=" + liftOutput,
"REJECT=" + rejectOutput,
"CHAIN=" + CHAIN_FILE,
"REFERENCE_SEQUENCE=" + referenceCopy,
};
Assert.assertEquals(runPicardCommandLine(args), 1);
}

@Test(expectedExceptions = SAMException.class, expectedExceptionsMessageRegExp = "File exists but is not readable:.*")
public void testUnreadableDictionary() throws IOException {
final Path liftOutput = Files.createTempFile("tmpouput", ".vcf");
liftOutput.toFile().deleteOnExit();
final Path rejectOutput = Files.createTempFile("tmpreject", ".vcf");
rejectOutput.toFile().deleteOnExit();
final Path input = TEST_DATA_PATH.toPath().resolve("testLiftoverBiallelicIndels.vcf");
final Path tmpCopyDir = Files.createTempDirectory("copy");
tmpCopyDir.toFile().deleteOnExit();
final Path referenceCopy = tmpCopyDir.resolve("refCopy.fasta");
referenceCopy.toFile().deleteOnExit();
Files.copy(REFERENCE_FILE.toPath(), referenceCopy);
final Path dictCopy = referenceCopy.resolveSibling(referenceCopy.toFile().getName().replaceAll("fasta$", "dict"));
dictCopy.toFile().deleteOnExit();
final Path dictionary = REFERENCE_FILE.toPath().resolveSibling(REFERENCE_FILE.getName().replaceAll("fasta$", "dict"));
Files.copy(dictionary, dictCopy);
dictCopy.toFile().setReadable(false);
final String[] args = new String[]{
"INPUT=" + input,
"OUTPUT=" + liftOutput,
"REJECT=" + rejectOutput,
"CHAIN=" + CHAIN_FILE,
"REFERENCE_SEQUENCE=" + referenceCopy,
};
runPicardCommandLine(args);
}
}