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Added KEEP_UNCONDTIONAL option which permits even sites with only filtered records to be included as unfiltered sites in the output

This commit is contained in:
Menachem Fromer 2012-01-19 18:19:58 -05:00
parent ced6775de3
commit 066da80a3d
1 changed files with 6 additions and 2 deletions
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8
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
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@ -464,7 +464,11 @@ public class VariantContextUtils {
/**
* Requires all records present at site to be unfiltered. VCF files that don't contain the record don't influence this.
*/
KEEP_IF_ALL_UNFILTERED
KEEP_IF_ALL_UNFILTERED,
/**
* If any record is present at this site (regardless of possibly being filtered), then all such records are kept and the filters are reset.
*/
KEEP_UNCONDITIONAL
}
/**
@ -635,7 +639,7 @@ public class VariantContextUtils {
}
// if at least one record was unfiltered and we want a union, clear all of the filters
if ( filteredRecordMergeType == FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED && nFiltered != VCs.size() )
if ( (filteredRecordMergeType == FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED && nFiltered != VCs.size()) || filteredRecordMergeType == FilteredRecordMergeType.KEEP_UNCONDITIONAL )
filters.clear();