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VCF headers now can be set to a particular VCF version after creation, which converts the header lines to the appropriate encoding on output. Plus some clean-up of the code. 

Also commented out the Tribble index out-of-date tests, the timing seems to be troublesome from the farm.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3702 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-07-01 05:32:14 +00:00
parent 4995950d04
commit 43ca595d15
5 changed files with 126 additions and 22 deletions
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49
java/src/org/broad/tribble/vcf/VCFHeader.java
View File

@ -13,7 +13,7 @@ import java.util.*;
*/
public class VCFHeader {
// the manditory header fields
// the mandatory header fields
public enum HEADER_FIELDS {
CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO
}
@ -30,8 +30,8 @@ public class VCFHeader {
// the header string indicator
public static final String HEADER_INDICATOR = "#";
// our header versionVCF
private VCFHeaderVersion versionVCF;
// our header version
private VCFHeaderVersion version;
/** do we have genotying data? */
private boolean hasGenotypingData = false;
@ -43,7 +43,7 @@ public class VCFHeader {
*/
public VCFHeader(Set<VCFHeaderLine> metaData) {
mMetaData = new TreeSet<VCFHeaderLine>(metaData);
checkVCFVersion();
loadVCFVersion();
}
/**
@ -59,31 +59,22 @@ public class VCFHeader {
mGenotypeSampleNames.add(col);
}
if (genotypeSampleNames.size() > 0) hasGenotypingData = true;
checkVCFVersion();
loadVCFVersion();
}
/**
* check our metadata for a VCF versionVCF tag, and throw an exception if the versionVCF is out of date
* or the versionVCF is not present
* check our metadata for a VCF version tag, and throw an exception if the version is out of date
* or the version is not present
*/
// TODO: fix this function
public void checkVCFVersion() {
VCFHeaderVersion version;
public void loadVCFVersion() {
List<VCFHeaderLine> toRemove = new ArrayList<VCFHeaderLine>();
for ( VCFHeaderLine line : mMetaData )
if ( VCFHeaderVersion.isFormatString(line.getKey())) {
version = VCFHeaderVersion.toHeaderVersion(line.getValue(),line.getKey());
if (version == null)
{
toRemove.add(line);
}
/**throw new RuntimeException("VCF version " + line.getValue() +
" is not supported; only versionVCF " + VCFHeaderVersion.VCF3_2 + " and greater can be used");*/
else return;
toRemove.add(line);
}
// remove old header lines for now,
mMetaData.removeAll(toRemove);
mMetaData.add(new VCFHeaderLine(VCFHeaderVersion.VCF3_3.getFormatString(), VCFHeaderVersion.VCF3_3.getVersionString()));
}
@ -106,7 +97,13 @@ public class VCFHeader {
* @return a set of the meta data
*/
public Set<VCFHeaderLine> getMetaData() {
return mMetaData;
Set<VCFHeaderLine> lines = new LinkedHashSet<VCFHeaderLine>();
if (version == null)
lines.add(new VCFHeaderLine(VCFHeaderVersion.VCF3_3.getFormatString(), VCFHeaderVersion.VCF3_3.getVersionString()));
else
lines.add(new VCFHeaderLine(version.getFormatString(), version.getVersionString()));
lines.addAll(mMetaData);
return lines;
}
/**
@ -131,6 +128,20 @@ public class VCFHeader {
public int getColumnCount() {
return HEADER_FIELDS.values().length + ((hasGenotypingData) ? mGenotypeSampleNames.size() + 1 : 0);
}
/**
* convert the header to a new VCF version
* @param version the version to convert to
*/
public void setVersion(VCFHeaderVersion version) {
if (version.equals(this.version))
return; // we're all set, do nothing
// store the new version, and update each of the header lines
this.version = version;
for (VCFHeaderLine line : mMetaData)
line.setVersion(version);
}
}

9
java/src/org/broad/tribble/vcf/VCFHeaderLine.java
View File

@ -97,4 +97,13 @@ public class VCFHeaderLine implements Comparable {
public int compareTo(Object other) {
return toString().compareTo(other.toString());
}
/**
* set the version string, which resets the current stored string representation if the version changed
* @param version
*/
public void setVersion(VCFHeaderVersion version) {
if (!version.equals(this.mVersion)) this.stringRep = null;
this.mVersion = version;
}
}

2
java/src/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4Codec.java
View File

@ -103,7 +103,7 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
* @param line the single # line (column names)
* @return the count of header lines
*/
private int createHeader(List<String> headerStrings, String line) {
public int createHeader(List<String> headerStrings, String line) {
headerStrings.add(line);
header = VCFReaderUtils.createHeader(headerStrings, VCFHeaderVersion.VCF4_0);

4
java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderUnitTest.java
View File

@ -77,7 +77,7 @@ public class TribbleRMDTrackBuilderUnitTest extends BaseTest {
// test to make sure we delete the index and regenerate if it's out of date
@Test
//@Test
public void testBuilderIndexOutOfDate() {
Logger logger = Logger.getLogger(TribbleRMDTrackBuilder.class);
File vcfFile = createOutofDateIndexFile(new File(validationDataLocation + "/ROD_validation/newerTribbleTrack.vcf"));
@ -95,7 +95,7 @@ public class TribbleRMDTrackBuilderUnitTest extends BaseTest {
}
// test to make sure we delete the index and regenerate if it's out of date
@Test
//@Test
public void testBuilderIndexGoodDate() {
Logger logger = Logger.getLogger(TribbleRMDTrackBuilder.class);
File vcfFile = createCorrectDateIndexFile(new File(validationDataLocation + "/ROD_validation/newerTribbleTrack.vcf"));

84
java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFHeaderUnitTest.java 100644
View File

@ -0,0 +1,84 @@
package org.broadinstitute.sting.utils.genotype.vcf;
import org.broad.tribble.vcf.VCFHeader;
import org.broad.tribble.vcf.VCFHeaderLine;
import org.broad.tribble.vcf.VCFHeaderVersion;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.refdata.features.vcf4.VCF4Codec;
import org.junit.Assert;
import org.junit.Test;
import java.io.File;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.List;
/**
* Created by IntelliJ IDEA.
* User: aaron
* Date: Jun 30, 2010
* Time: 3:32:08 PM
* To change this template use File | Settings | File Templates.
*/
public class VCFHeaderUnitTest extends BaseTest {
@Test
public void testVCF4ToVCF3() {
VCF4Codec codec = new VCF4Codec();
List<String> headerFields = new ArrayList<String>();
for (String str : VCF3_3headerStrings)
headerFields.add(str);
Assert.assertEquals(17,codec.createHeader(headerFields,"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"));
codec.getHeader(VCFHeader.class).setVersion(VCFHeaderVersion.VCF3_3);
checkMD5ofHeaderFile(codec, "5873e029bd50d6836b86438bccd15456");
}
@Test
public void testVCF4ToVCF4() {
VCF4Codec codec = new VCF4Codec();
List<String> headerFields = new ArrayList<String>();
for (String str : VCF3_3headerStrings)
headerFields.add(str);
Assert.assertEquals(17, codec.createHeader(headerFields, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"));
checkMD5ofHeaderFile(codec, "4648aa1169257e0a8a9d30131adb5f35");
}
private void checkMD5ofHeaderFile(VCF4Codec codec, String md5sum) {
File myTempFile = null;
PrintWriter pw = null;
try {
myTempFile = File.createTempFile("VCFHeader","vcf");
myTempFile.deleteOnExit();
pw = new PrintWriter(myTempFile);
} catch (IOException e) {
Assert.fail("Unable to make a temp file!");
}
for (VCFHeaderLine line : codec.getHeader(VCFHeader.class).getMetaData())
pw.println(line);
pw.close();
Assert.assertTrue(md5sum.equals(md5SumFile(myTempFile)));
}
public String[] VCF3_3headerStrings = {
"##fileformat=VCFv4.0",
"##filedate=2010-06-21",
"##reference=NCBI36",
"##INFO=<ID=GC, Number=0, Type=Flag, Description=\"Overlap with Gencode CCDS coding sequence\">",
"##INFO=<ID=DP, Number=1, Type=Integer, Description=\"Total number of reads in haplotype window\">",
"##INFO=<ID=AF, Number=1, Type=Float, Description=\"Dindel estimated population allele frequency\">",
"##INFO=<ID=CA, Number=1, Type=String, Description=\"Pilot 1 callability mask\">",
"##INFO=<ID=HP, Number=1, Type=Integer, Description=\"Reference homopolymer tract length\">",
"##INFO=<ID=NS, Number=1, Type=Integer, Description=\"Number of samples with data\">",
"##INFO=<ID=DB, Number=0, Type=Flag, Description=\"dbSNP membership build 129 - type match and indel sequence length match within 25 bp\">",
"##INFO=<ID=NR, Number=1, Type=Integer, Description=\"Number of reads covering non-ref variant on reverse strand\">",
"##INFO=<ID=NF, Number=1, Type=Integer, Description=\"Number of reads covering non-ref variant on forward strand\">",
"##FILTER=<ID=NoQCALL, Description=\"Variant called by Dindel but not confirmed by QCALL\">",
"##FORMAT=<ID=GT, Number=1, Type=String, Description=\"Genotype\">",
"##FORMAT=<ID=HQ, Number=2, Type=Integer, Description=\"Haplotype quality\">",
"##FORMAT=<ID=GQ, Number=1, Type=Integer, Description=\"Genotype quality\">",
};
}