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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
This commit is contained in:
David Roazen 2012-05-04 00:00:13 -04:00
parent fa84d50a2b
commit 6b769e91d8
5 changed files with 5 additions and 5 deletions
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2
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java
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@ -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"));
}
}

2
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java
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@ -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);
}

2
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java
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@ -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());

2
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFInfoHeaderLine.java
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@ -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);
}

2
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFSimpleHeaderLine.java
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@ -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");