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Updating variant jar. 

The update contains:
1. documentation changes for VariantContext and Allele (which used to discuss the now obsolete null allele)
2. better error messages for VCFs containing complex rearrangements with breakends
3. instead of failing badly on format field lists with '.'s, just ignore them
Also, there is a trivial change to use a more efficient method to remove a bunch of attributes from a VC.

Delivers PT#s 59675378, 59496612, and 60524016.
This commit is contained in:
Eric Banks 2013-12-31 13:23:11 -05:00
parent 5a1564d1f2
commit f82a7c3f4c
3 changed files with 6 additions and 6 deletions
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10
public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
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@ -1152,11 +1152,11 @@ public class GATKVariantContextUtils {
* @param builder the VC builder
*/
private static void removeStaleAttributesAfterMerge(final VariantContextBuilder builder) {
builder.rmAttribute(VCFConstants.ALLELE_COUNT_KEY);
builder.rmAttribute(VCFConstants.ALLELE_FREQUENCY_KEY);
builder.rmAttribute(VCFConstants.ALLELE_NUMBER_KEY);
builder.rmAttribute(VCFConstants.MLE_ALLELE_COUNT_KEY);
builder.rmAttribute(VCFConstants.MLE_ALLELE_FREQUENCY_KEY);
builder.rmAttributes(Arrays.asList(VCFConstants.ALLELE_COUNT_KEY,
VCFConstants.ALLELE_FREQUENCY_KEY,
VCFConstants.ALLELE_NUMBER_KEY,
VCFConstants.MLE_ALLELE_COUNT_KEY,
VCFConstants.MLE_ALLELE_FREQUENCY_KEY));
}
/**

BIN
settings/repository/org.broadinstitute/variant-1.104.1634.jar → settings/repository/org.broadinstitute/variant-1.105.1640.jar
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2
settings/repository/org.broadinstitute/variant-1.104.1634.xml → settings/repository/org.broadinstitute/variant-1.105.1640.xml
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@ -1,3 +1,3 @@
<ivy-module version="1.0">
<info organisation="org.broadinstitute" module="variant" revision="1.104.1634" status="integration" />
<info organisation="org.broadinstitute" module="variant" revision="1.105.1640" status="integration" />
</ivy-module>