From 6b769e91d8368221d08bff859d9e2831daea3d3c Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Fri, 4 May 2012 00:00:13 -0400
Subject: [PATCH] BCF2: third checkpoint

* writer mostly implemented
* walkers to convert BCF2 <-> VCF
* almost working for sites-only files; genotypes still need work
* initial performance tests this afternoon will be on sites-only files
---
 .../sting/utils/codecs/vcf/VCFFilterHeaderLine.java             | 2 +-
 .../sting/utils/codecs/vcf/VCFFormatHeaderLine.java             | 2 +-
 .../org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java    | 2 +-
 .../sting/utils/codecs/vcf/VCFInfoHeaderLine.java               | 2 +-
 .../sting/utils/codecs/vcf/VCFSimpleHeaderLine.java             | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java
index dd0a333f3..006913959 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java
@@ -24,7 +24,7 @@ public class VCFFilterHeaderLine extends VCFSimpleHeaderLine  {
      * @param line      the header line
      * @param version   the vcf header version
      */
-    protected VCFFilterHeaderLine(String line, VCFHeaderVersion version) {
+    public VCFFilterHeaderLine(String line, VCFHeaderVersion version) {
         super(line, version, "FILTER", Arrays.asList("ID", "Description"));
     }
 }
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java
index 474c8dd14..5fc3187c5 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java
@@ -20,7 +20,7 @@ public class VCFFormatHeaderLine extends VCFCompoundHeaderLine {
         super(name, count, type, description, SupportedHeaderLineType.FORMAT);
     }
 
-    protected VCFFormatHeaderLine(String line, VCFHeaderVersion version) {
+    public VCFFormatHeaderLine(String line, VCFHeaderVersion version) {
         super(line, version, SupportedHeaderLineType.FORMAT);
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java
index 50ff3a656..20f71b956 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java
@@ -112,7 +112,7 @@ public class VCFHeader {
      * @param genotypeSampleNamesInAppearenceOrder genotype sample names
      */
 
-    protected void buildVCFReaderMaps(List<String> genotypeSampleNamesInAppearenceOrder) {
+    public void buildVCFReaderMaps(List<String> genotypeSampleNamesInAppearenceOrder) {
         sampleNamesInOrder = new ArrayList<String>(genotypeSampleNamesInAppearenceOrder.size());
         sampleNameToOffset = new HashMap<String, Integer>(genotypeSampleNamesInAppearenceOrder.size());
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFInfoHeaderLine.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFInfoHeaderLine.java
index 9b20f38a1..9f249c531 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFInfoHeaderLine.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFInfoHeaderLine.java
@@ -17,7 +17,7 @@ public class VCFInfoHeaderLine extends VCFCompoundHeaderLine {
         super(name, count, type, description, SupportedHeaderLineType.INFO);
     }
 
-    protected VCFInfoHeaderLine(String line, VCFHeaderVersion version) {
+    public VCFInfoHeaderLine(String line, VCFHeaderVersion version) {
         super(line, version, SupportedHeaderLineType.INFO);
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFSimpleHeaderLine.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFSimpleHeaderLine.java
index 05d603073..e0a057eec 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFSimpleHeaderLine.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFSimpleHeaderLine.java
@@ -48,7 +48,7 @@ public class VCFSimpleHeaderLine extends VCFHeaderLine implements VCFIDHeaderLin
      * @param key            the key for this header line
      * @param expectedTagOrdering the tag ordering expected for this header line
      */
-    protected VCFSimpleHeaderLine(String line, VCFHeaderVersion version, String key, List<String> expectedTagOrdering) {
+    public VCFSimpleHeaderLine(String line, VCFHeaderVersion version, String key, List<String> expectedTagOrdering) {
         super(key, "");
         Map<String, String> mapping = VCFHeaderLineTranslator.parseLine(version, line, expectedTagOrdering);
         name = mapping.get("ID");