From 1e6794c53985f02b27d0f7418c0d1784b28ad754 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Mon, 17 Oct 2011 15:56:02 -0400 Subject: [PATCH 2/5] fixing typo in VariantsToTable docs --- .../sting/gatk/walkers/variantutils/VariantsToTable.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java index 7b0b81d2a..bf16b2dfb 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java @@ -134,7 +134,7 @@ public class VariantsToTable extends RodWalker { /** * By default, this tool throws a UserException when it encounters a field without a value in some record. This - * is generally useful when you mistype -F CHROM, so that you get a friendly warning about CHRMO not being + * is generally useful when you mistype -F CHROM, so that you get a friendly warning about CHROM not being * found before the tool runs through 40M 1000G records. However, in some cases you genuinely want to allow such * fields (e.g., AC not being calculated for filtered records, if included). When provided, this argument * will cause VariantsToTable to write out NA values for missing fields instead of throwing an error. From 1a92ee3593417941a31b32e60cb34796d9bd5d95 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Tue, 18 Oct 2011 10:57:02 -0400 Subject: [PATCH 4/5] No longer adds a binding of ID -> . when the ID field is dot in the VCF -- Really we should make ID a primary key in VariantContext. Putting it into the attributes is just annoying now --- .../sting/utils/codecs/vcf/AbstractVCFCodec.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java index c86b91b79..6b101ca74 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java @@ -381,7 +381,8 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec, } } - attributes.put(VariantContext.ID_KEY, id); + if ( ! id.equals(VCFConstants.EMPTY_ID_FIELD) ) + attributes.put(VariantContext.ID_KEY, id); return attributes; } From f77f2eeb7d1abf58766f430974f0c7c395740f0e Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Tue, 18 Oct 2011 13:04:43 -0400 Subject: [PATCH 5/5] Fix for new ID structure --- .../sting/gatk/walkers/variantutils/VariantsToTable.java | 1 + 1 file changed, 1 insertion(+) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java index bf16b2dfb..5dbd3f5fd 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java @@ -313,6 +313,7 @@ public class VariantsToTable extends RodWalker { getters.put("FILTER", new Getter() { public String get(VariantContext vc) { return vc.isNotFiltered() ? "PASS" : Utils.join(",", vc.getFilters()); } }); + getters.put("ID", new Getter() { public String get(VariantContext vc) { return vc.hasID() ? vc.getID() : "."; } }); getters.put("HET", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHetCount()); } }); getters.put("HOM-REF", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHomRefCount()); } }); getters.put("HOM-VAR", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHomVarCount()); } });