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Fix #3838 Tabix based annotator fails if chromosome is not present in the tabix resource #3853

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merged 1 commit into from
Oct 7, 2015
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Fix #3838 Tabix based annotator fails if chromosome is not present in the tabix resource #3853

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23 changes: 20 additions & 3 deletions ...s-data-annotators/src/main/java/org/molgenis/data/annotator/tabix/TabixVcfRepository.java
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Original file line number Diff line number Diff line change
Expand Up @@ -89,9 +89,26 @@ public Iterable<Entity> findAll(Query q)
public synchronized List<Entity> query(String chrom, long posFrom, long posTo)
{
String queryString = String.format("%s:%s-%s", checkNotNull(chrom), checkNotNull(posFrom), checkNotNull(posTo));
Collection<String> lines = getLines(tabixReader.query(queryString));
return lines.stream().map(line -> line.split("\t")).map(vcfToEntitySupplier.get()::toEntity)
.filter(entity -> positionMatches(entity, posFrom, posTo)).collect(Collectors.toList());
try
{
Collection<String> lines = getLines(tabixReader.query(queryString));
return lines.stream().map(line -> line.split("\t")).map(vcfToEntitySupplier.get()::toEntity)
.filter(entity -> positionMatches(entity, posFrom, posTo)).collect(Collectors.toList());
}
catch (NullPointerException e)
{
LOG.warn("Unable to read from tabix resource for query: " + queryString
+ " (Position not present in resource file?)");
LOG.debug("", e);
}
catch (ArrayIndexOutOfBoundsException e)
{
LOG.warn("Unable to read from tabix resource for query: " + queryString
+ " (Chromosome not present in resource file?)");
LOG.debug("", e);
}

return Collections.emptyList();
}

/**
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