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Refactored the VCF codec classes to minimize code duplication (which happened during the VCF3/4 split). Now, both codecs extend the AbstractVCFCodec class and all shared functionality exists there. Only methods that differ between the various codecs (e.g. because FILTER strings are encoded differently) are defined in the actual codecs. While I was in there, I put in checks for invalid empty inputs in the ID, FILTER, and INFO fields. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5917 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-06-01 19:40:47 +00:00
parent 81d9808eea
commit c7fe062cb7
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
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@ -31,9 +31,9 @@ import net.sf.samtools.util.StringUtil;
import org.apache.commons.jexl2.*;
import org.broad.tribble.util.popgen.HardyWeinbergCalculation;
import org.broad.tribble.util.variantcontext.*;
import org.broad.tribble.vcf.AbstractVCFCodec;
import org.broadinstitute.sting.gatk.walkers.phasing.ReadBackedPhasingWalker;
import org.broadinstitute.sting.utils.*;
import org.broad.tribble.vcf.VCFCodecUtils;
import org.broad.tribble.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
@ -566,7 +566,7 @@ public class VariantContextUtils {
VariantContext merged = new VariantContext(name, loc.getContig(), loc.getStart(), loc.getStop(), alleles, genotypes, negLog10PError, filters, (mergeInfoWithMaxAC ? maxACAttributes : attributes) );
// Trim the padded bases of all alleles if necessary
merged = VCFCodecUtils.createVariantContextWithTrimmedAlleles(merged);
merged = AbstractVCFCodec.createVariantContextWithTrimmedAlleles(merged);
if ( printMessages && remapped ) System.out.printf("Remapped => %s%n", merged);
return merged;