VCFHeaderLine headerLine = header.getOtherHeaderLine(VCFHeader.REFERENCE_KEY);
if (headerLine == null)
{
- Cache.log.error("VCF reference header not found");
+ Cache.error("VCF reference header not found");
return null;
}
String ref = headerLine.getValue();
}
else
{
- Cache.log.error("VCF reference not found: " + ref);
+ Cache.error("VCF reference not found: " + ref);
}
return seq;
{
if (reference == null)
{
- Cache.log.error("No VCF ##reference found, defaulting to "
+ Cache.error("No VCF ##reference found, defaulting to "
+ DEFAULT_REFERENCE + ":" + DEFAULT_SPECIES);
reference = DEFAULT_REFERENCE; // default to GRCh37 if not specified
}
GeneLociI seqCoords = seq.getGeneLoci();
if (seqCoords == null)
{
- Cache.log.warn(String.format(
+ Cache.warn(String.format(
"Can't query VCF for %s as chromosome coordinates not known",
seq.getName()));
return null;
// returned with the Ensembl sequence; todo: support aliases?
if (!vcfSpecies.equalsIgnoreCase(species))
{
- Cache.log.warn("No VCF loaded to " + seq.getName()
+ Cache.warn("No VCF loaded to " + seq.getName()
+ " as species not matched");
return null;
}
vcfAssembly);
if (newRange == null)
{
- Cache.log.error(
+ Cache.error(
String.format("Failed to map %s:%s:%s:%d:%d to %s", species,
chromosome, seqRef, range[0], range[1],
vcfAssembly));
*/
String msg = String.format("Error reading VCF for %s:%d-%d: %s ",
map.chromosome, vcfStart, vcfEnd,e.getLocalizedMessage());
- Cache.log.error(msg);
+ Cache.error(msg);
}
}
VCFInfoHeaderLine infoHeader = header.getInfoHeaderLine(infoId);
if (infoHeader == null)
{
- Cache.log.error("Field " + infoId + " has no INFO header");
+ Cache.error("Field " + infoId + " has no INFO header");
return false;
}
VCFHeaderLineType infoType = infoHeader.getType();
if (!badData.contains(token))
{
badData.add(token);
- Cache.log.error(String.format("Invalid VCF data at %s:%d %s=%s",
+ Cache.error(String.format("Invalid VCF data at %s:%d %s=%s",
variant.getContig(), variant.getStart(), infoId, value));
}
}