From 86890c63574eba41bbbce6c52e2614f6c81b6f27 Mon Sep 17 00:00:00 2001
From: Christopher Hartl <chartl@broadinstitute.org>
Date: Mon, 11 Jul 2011 16:16:15 -0400
Subject: [PATCH 2/2] N and K (in binomial probability) got switched in RFA
 Walker with the last commit. No longer will NaNs be produced.

Added: TableToVCF. Kind of a longer-term project, but there are lots of variant calls available in a weird tabular format. I used this to convert Ju Et Al small indels to VCF. I'll check against the 1000G ASN superpopulation calls to see if we see a good amount of recapitulation, and if so, i'll put them in unvalidated comparisons. Minor chances to the TableCodec and TableFeatures to allow for this (the codec can sometimes drop a column, and the feature now allows you to grab on to its header).
---
 .../sting/gatk/refdata/features/table/TableCodec.java       | 0
 .../sting/gatk/refdata/features/table/TableFeature.java     | 6 +++++-
 .../broadinstitute/sting/utils/variantcontext/Allele.java   | 2 +-
 3 files changed, 6 insertions(+), 2 deletions(-)
 mode change 100644 => 100755 public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java
 mode change 100644 => 100755 public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java

diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java
old mode 100644
new mode 100755
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java
old mode 100644
new mode 100755
index 6ff0384a0..4b4ebe450
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java
@@ -55,10 +55,14 @@ public class TableFeature implements Feature {
     }
 
     public List<String> getAllValues() {
-        return getValuesTo(values.size()-1);
+        return getValuesTo(values.size());
     }
 
     public List<String> getValuesTo(int columnPosition) {
         return values.subList(0,columnPosition);
     }
+
+    public List<String> getHeader() {
+        return keys;
+    }
 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java
index a9ba46159..901de6fae 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java
@@ -108,7 +108,7 @@ public class Allele implements Comparable<Allele> {
         this.bases = bases;
 
         if ( ! acceptableAlleleBases(bases) )
-            throw new IllegalArgumentException("Unexpected base in allele bases " + new String(bases));
+            throw new IllegalArgumentException("Unexpected base in allele bases \'" + new String(bases)+"\'");
     }
 
     private Allele(String bases, boolean isRef) {