No one should be calling the createHeader method(s) directly, but instead should be going through the full readHeader method (because it first sets the version); therefore I made them package protected and merged them. Updated the various unit tests that were using createHeader and were dangerously assuming that the header version was defaulting to 4.0 (which it no longer does).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5934 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks
parent
32ac7be86a
commit
420d8feff6
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@ -1,5 +1,6 @@
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package org.broadinstitute.sting.gatk.walkers.variantutils;
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import org.broad.tribble.readers.AsciiLineReader;
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import org.broad.tribble.vcf.VCFCodec;
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import org.broad.tribble.vcf.VCFHeader;
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import org.broad.tribble.vcf.VCFHeaderLine;
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@ -9,6 +10,7 @@ import org.broadinstitute.sting.utils.vcf.VCFUtils;
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import org.testng.annotations.Test;
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import java.io.StringBufferInputStream;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Set;
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@ -19,54 +21,50 @@ import java.util.Set;
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public class CombineVariantsUnitTest {
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// this header is a small subset of the header in VCFHeaderUnitTest: VCF4headerStrings
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public static String[] VCF4headerStringsSmallSubset = {
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"##fileformat=VCFv4.0",
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"##filedate=2010-06-21",
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"##reference=NCBI36",
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"##INFO=<ID=GC, Number=0, Type=Flag, Description=\"Overlap with Gencode CCDS coding sequence\">",
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"##INFO=<ID=DP, Number=1, Type=Integer, Description=\"Total number of reads in haplotype window\">",
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"##INFO=<ID=AF, Number=1, Type=Float, Description=\"Dindel estimated population allele frequency\">",
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"##FILTER=<ID=NoQCALL, Description=\"Variant called by Dindel but not confirmed by QCALL\">",
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"##FORMAT=<ID=GT, Number=1, Type=String, Description=\"Genotype\">",
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"##FORMAT=<ID=HQ, Number=2, Type=Integer, Description=\"Haplotype quality\">",
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"##FORMAT=<ID=GQ, Number=1, Type=Integer, Description=\"Genotype quality\">",
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};
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public static String VCF4headerStringsSmallSubset =
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"##fileformat=VCFv4.0\n" +
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"##filedate=2010-06-21\n"+
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"##reference=NCBI36\n"+
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"##INFO=<ID=GC, Number=0, Type=Flag, Description=\"Overlap with Gencode CCDS coding sequence\">\n"+
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"##INFO=<ID=DP, Number=1, Type=Integer, Description=\"Total number of reads in haplotype window\">\n"+
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"##INFO=<ID=AF, Number=1, Type=Float, Description=\"Dindel estimated population allele frequency\">\n"+
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"##FILTER=<ID=NoQCALL, Description=\"Variant called by Dindel but not confirmed by QCALL\">\n"+
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"##FORMAT=<ID=GT, Number=1, Type=String, Description=\"Genotype\">\n"+
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"##FORMAT=<ID=HQ, Number=2, Type=Integer, Description=\"Haplotype quality\">\n"+
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"##FORMAT=<ID=GQ, Number=1, Type=Integer, Description=\"Genotype quality\">\n"+
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"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n";
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// altered info field
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public static String[] VCF4headerStringsBrokenInfo = {
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"##fileformat=VCFv4.0",
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"##filedate=2010-06-21",
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"##reference=NCBI36",
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"##INFO=<ID=GC, Number=0, Type=Flag, Description=\"Overlap with Gencode CCDS coding sequence\">",
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"##INFO=<ID=DP, Number=1, Type=Integer, Description=\"Total number of reads in haplotype window\">",
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"##INFO=<ID=AF, Number=1, Type=String, Description=\"Dindel estimated population allele frequency\">", // string to integer
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"##FILTER=<ID=NoQCALL, Description=\"Variant called by Dindel but not confirmed by QCALL\">",
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"##FORMAT=<ID=GT, Number=1, Type=String, Description=\"Genotype\">",
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"##FORMAT=<ID=HQ, Number=2, Type=Integer, Description=\"Haplotype quality\">",
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"##FORMAT=<ID=GQ, Number=1, Type=Integer, Description=\"Genotype quality\">",
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};
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public static String VCF4headerStringsBrokenInfo =
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"##fileformat=VCFv4.0\n"+
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"##filedate=2010-06-21\n"+
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"##reference=NCBI36\n"+
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"##INFO=<ID=GC, Number=0, Type=Flag, Description=\"Overlap with Gencode CCDS coding sequence\">\n"+
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"##INFO=<ID=DP, Number=1, Type=Integer, Description=\"Total number of reads in haplotype window\">\n"+
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"##INFO=<ID=AF, Number=1, Type=String, Description=\"Dindel estimated population allele frequency\">\n"+ // string to integer
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"##FILTER=<ID=NoQCALL, Description=\"Variant called by Dindel but not confirmed by QCALL\">\n"+
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"##FORMAT=<ID=GT, Number=1, Type=String, Description=\"Genotype\">\n"+
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"##FORMAT=<ID=HQ, Number=2, Type=Integer, Description=\"Haplotype quality\">\n"+
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"##FORMAT=<ID=GQ, Number=1, Type=Integer, Description=\"Genotype quality\">\n"+
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"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n";
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// altered format field
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public static String[] VCF4headerStringsBrokenFormat = {
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"##fileformat=VCFv4.0",
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"##filedate=2010-06-21",
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"##reference=NCBI36",
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"##INFO=<ID=GC, Number=0, Type=Flag, Description=\"Overlap with Gencode CCDS coding sequence\">",
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"##INFO=<ID=DP, Number=1, Type=Integer, Description=\"Total number of reads in haplotype window\">",
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"##INFO=<ID=AF, Number=1, Type=Float, Description=\"Dindel estimated population allele frequency\">",
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"##FILTER=<ID=NoQCALL, Description=\"Variant called by Dindel but not confirmed by QCALL\">",
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"##FORMAT=<ID=GT, Number=6, Type=String, Description=\"Genotype\">", // changed 1 to 6 here
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"##FORMAT=<ID=HQ, Number=2, Type=Integer, Description=\"Haplotype quality\">",
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"##FORMAT=<ID=GQ, Number=1, Type=Integer, Description=\"Genotype quality\">",
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};
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public static String VCF4headerStringsBrokenFormat =
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"##fileformat=VCFv4.0\n"+
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"##filedate=2010-06-21\n"+
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"##reference=NCBI36\n"+
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"##INFO=<ID=GC, Number=0, Type=Flag, Description=\"Overlap with Gencode CCDS coding sequence\">\n"+
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"##INFO=<ID=DP, Number=1, Type=Integer, Description=\"Total number of reads in haplotype window\">\n"+
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"##INFO=<ID=AF, Number=1, Type=Float, Description=\"Dindel estimated population allele frequency\">\n"+
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"##FILTER=<ID=NoQCALL, Description=\"Variant called by Dindel but not confirmed by QCALL\">\n"+
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"##FORMAT=<ID=GT, Number=6, Type=String, Description=\"Genotype\">\n"+ // changed 1 to 6 here
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"##FORMAT=<ID=HQ, Number=2, Type=Integer, Description=\"Haplotype quality\">\n"+
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"##FORMAT=<ID=GQ, Number=1, Type=Integer, Description=\"Genotype quality\">\n"+
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"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n";
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private VCFHeader createHeader(String[] headerStr) {
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private VCFHeader createHeader(String headerStr) {
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VCFCodec codec = new VCFCodec();
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List<String> headerFields = new ArrayList<String>();
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for (String str : headerStr)
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headerFields.add(str);
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VCFHeader head = (VCFHeader)codec.createHeader(headerFields,"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO");
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Assert.assertEquals(head.getMetaData().size(), headerStr.length /* for the # line */);
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VCFHeader head = (VCFHeader)codec.readHeader(new AsciiLineReader(new StringBufferInputStream(headerStr)));
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return head;
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}
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@ -78,7 +76,7 @@ public class CombineVariantsUnitTest {
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headers.add(one);
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headers.add(two);
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Set<VCFHeaderLine> lines = VCFUtils.smartMergeHeaders(headers, null);
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Assert.assertEquals(lines.size(), VCFHeaderUnitTest.VCF4headerStrings.length);
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Assert.assertEquals(lines.size(), VCFHeaderUnitTest.VCF4headerStringCount);
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}
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@Test(expectedExceptions=IllegalStateException.class)
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@ -89,7 +87,7 @@ public class CombineVariantsUnitTest {
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headers.add(one);
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headers.add(two);
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Set<VCFHeaderLine> lines = VCFUtils.smartMergeHeaders(headers, null);
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Assert.assertEquals(lines.size(), VCFHeaderUnitTest.VCF4headerStrings.length);
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Assert.assertEquals(lines.size(), VCFHeaderUnitTest.VCF4headerStringCount);
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}
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@Test
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@ -100,6 +98,6 @@ public class CombineVariantsUnitTest {
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headers.add(one);
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headers.add(two);
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Set<VCFHeaderLine> lines = VCFUtils.smartMergeHeaders(headers, null);
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Assert.assertEquals(lines.size(), VCFHeaderUnitTest.VCF4headerStrings.length);
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Assert.assertEquals(lines.size(), VCFHeaderUnitTest.VCF4headerStringCount);
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}
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}
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@ -1,5 +1,6 @@
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package org.broadinstitute.sting.utils.genotype.vcf;
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import org.broad.tribble.readers.AsciiLineReader;
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import org.broad.tribble.vcf.*;
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import org.testng.Assert;
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import org.broadinstitute.sting.BaseTest;
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@ -9,6 +10,7 @@ import org.testng.annotations.Test;
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import java.io.File;
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import java.io.IOException;
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import java.io.PrintWriter;
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import java.io.StringBufferInputStream;
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import java.util.ArrayList;
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import java.util.List;
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@ -21,13 +23,10 @@ import java.util.List;
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*/
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public class VCFHeaderUnitTest extends BaseTest {
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private VCFHeader createHeader(String[] headerStr) {
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private VCFHeader createHeader(String headerStr) {
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VCFCodec codec = new VCFCodec();
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List<String> headerFields = new ArrayList<String>();
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for (String str : headerStr)
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headerFields.add(str);
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VCFHeader header = (VCFHeader)codec.createHeader(headerFields,"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO");
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Assert.assertEquals(header.getMetaData().size(), headerStr.length /* for the # line */);
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VCFHeader header = (VCFHeader)codec.readHeader(new AsciiLineReader(new StringBufferInputStream(headerStr)));
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Assert.assertEquals(header.getMetaData().size(), VCF4headerStringCount);
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return header;
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}
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@ -39,7 +38,7 @@ public class VCFHeaderUnitTest extends BaseTest {
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@Test
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public void testVCF4ToVCF4_alternate() {
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VCFHeader header = createHeader(VCF4headerStrings_with_negitiveOne);
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VCFHeader header = createHeader(VCF4headerStrings_with_negativeOne);
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checkMD5ofHeaderFile(header, "ad8c4cf85e868b0261ab49ee2c613088");
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}
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@ -59,41 +58,45 @@ public class VCFHeaderUnitTest extends BaseTest {
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Assert.assertTrue(md5sum.equals(md5SumFile(myTempFile)));
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}
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public static String[] VCF4headerStrings = {
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"##fileformat=VCFv4.0",
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"##filedate=2010-06-21",
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"##reference=NCBI36",
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"##INFO=<ID=GC, Number=0, Type=Flag, Description=\"Overlap with Gencode CCDS coding sequence\">",
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"##INFO=<ID=DP, Number=1, Type=Integer, Description=\"Total number of reads in haplotype window\">",
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"##INFO=<ID=AF, Number=1, Type=Float, Description=\"Dindel estimated population allele frequency\">",
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"##INFO=<ID=CA, Number=1, Type=String, Description=\"Pilot 1 callability mask\">",
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"##INFO=<ID=HP, Number=1, Type=Integer, Description=\"Reference homopolymer tract length\">",
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"##INFO=<ID=NS, Number=1, Type=Integer, Description=\"Number of samples with data\">",
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"##INFO=<ID=DB, Number=0, Type=Flag, Description=\"dbSNP membership build 129 - type match and indel sequence length match within 25 bp\">",
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"##INFO=<ID=NR, Number=1, Type=Integer, Description=\"Number of reads covering non-ref variant on reverse strand\">",
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"##INFO=<ID=NF, Number=1, Type=Integer, Description=\"Number of reads covering non-ref variant on forward strand\">",
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"##FILTER=<ID=NoQCALL, Description=\"Variant called by Dindel but not confirmed by QCALL\">",
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"##FORMAT=<ID=GT, Number=1, Type=String, Description=\"Genotype\">",
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"##FORMAT=<ID=HQ, Number=2, Type=Integer, Description=\"Haplotype quality\">",
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"##FORMAT=<ID=GQ, Number=1, Type=Integer, Description=\"Genotype quality\">",
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};
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public static int VCF4headerStringCount = 16;
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public static String VCF4headerStrings =
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"##fileformat=VCFv4.0\n"+
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"##filedate=2010-06-21\n"+
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"##reference=NCBI36\n"+
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"##INFO=<ID=GC, Number=0, Type=Flag, Description=\"Overlap with Gencode CCDS coding sequence\">\n"+
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"##INFO=<ID=DP, Number=1, Type=Integer, Description=\"Total number of reads in haplotype window\">\n"+
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"##INFO=<ID=AF, Number=1, Type=Float, Description=\"Dindel estimated population allele frequency\">\n"+
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"##INFO=<ID=CA, Number=1, Type=String, Description=\"Pilot 1 callability mask\">\n"+
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"##INFO=<ID=HP, Number=1, Type=Integer, Description=\"Reference homopolymer tract length\">\n"+
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"##INFO=<ID=NS, Number=1, Type=Integer, Description=\"Number of samples with data\">\n"+
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"##INFO=<ID=DB, Number=0, Type=Flag, Description=\"dbSNP membership build 129 - type match and indel sequence length match within 25 bp\">\n"+
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"##INFO=<ID=NR, Number=1, Type=Integer, Description=\"Number of reads covering non-ref variant on reverse strand\">\n"+
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"##INFO=<ID=NF, Number=1, Type=Integer, Description=\"Number of reads covering non-ref variant on forward strand\">\n"+
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"##FILTER=<ID=NoQCALL, Description=\"Variant called by Dindel but not confirmed by QCALL\">\n"+
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"##FORMAT=<ID=GT, Number=1, Type=String, Description=\"Genotype\">\n"+
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"##FORMAT=<ID=HQ, Number=2, Type=Integer, Description=\"Haplotype quality\">\n"+
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"##FORMAT=<ID=GQ, Number=1, Type=Integer, Description=\"Genotype quality\">\n"+
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"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n";
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public static String VCF4headerStrings_with_negativeOne =
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"##fileformat=VCFv4.0\n"+
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"##filedate=2010-06-21\n"+
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"##reference=NCBI36\n"+
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"##INFO=<ID=GC, Number=0, Type=Flag, Description=\"Overlap with Gencode CCDS coding sequence\">\n"+
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"##INFO=<ID=YY, Number=., Type=Integer, Description=\"Some weird value that has lots of parameters\">\n"+
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"##INFO=<ID=AF, Number=1, Type=Float, Description=\"Dindel estimated population allele frequency\">\n"+
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"##INFO=<ID=CA, Number=1, Type=String, Description=\"Pilot 1 callability mask\">\n"+
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"##INFO=<ID=HP, Number=1, Type=Integer, Description=\"Reference homopolymer tract length\">\n"+
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"##INFO=<ID=NS, Number=1, Type=Integer, Description=\"Number of samples with data\">\n"+
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"##INFO=<ID=DB, Number=0, Type=Flag, Description=\"dbSNP membership build 129 - type match and indel sequence length match within 25 bp\">\n"+
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"##INFO=<ID=NR, Number=1, Type=Integer, Description=\"Number of reads covering non-ref variant on reverse strand\">\n"+
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"##INFO=<ID=NF, Number=1, Type=Integer, Description=\"Number of reads covering non-ref variant on forward strand\">\n"+
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"##FILTER=<ID=NoQCALL, Description=\"Variant called by Dindel but not confirmed by QCALL\">\n"+
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"##FORMAT=<ID=GT, Number=1, Type=String, Description=\"Genotype\">\n"+
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"##FORMAT=<ID=HQ, Number=2, Type=Integer, Description=\"Haplotype quality\">\n"+
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"##FORMAT=<ID=TT, Number=., Type=Integer, Description=\"Lots of TTs\">\n"+
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"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n";
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public static String[] VCF4headerStrings_with_negitiveOne = {
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"##fileformat=VCFv4.0",
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"##filedate=2010-06-21",
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"##reference=NCBI36",
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"##INFO=<ID=GC, Number=0, Type=Flag, Description=\"Overlap with Gencode CCDS coding sequence\">",
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"##INFO=<ID=YY, Number=., Type=Integer, Description=\"Some weird value that has lots of parameters\">",
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"##INFO=<ID=AF, Number=1, Type=Float, Description=\"Dindel estimated population allele frequency\">",
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"##INFO=<ID=CA, Number=1, Type=String, Description=\"Pilot 1 callability mask\">",
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"##INFO=<ID=HP, Number=1, Type=Integer, Description=\"Reference homopolymer tract length\">",
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"##INFO=<ID=NS, Number=1, Type=Integer, Description=\"Number of samples with data\">",
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"##INFO=<ID=DB, Number=0, Type=Flag, Description=\"dbSNP membership build 129 - type match and indel sequence length match within 25 bp\">",
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"##INFO=<ID=NR, Number=1, Type=Integer, Description=\"Number of reads covering non-ref variant on reverse strand\">",
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"##INFO=<ID=NF, Number=1, Type=Integer, Description=\"Number of reads covering non-ref variant on forward strand\">",
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"##FILTER=<ID=NoQCALL, Description=\"Variant called by Dindel but not confirmed by QCALL\">",
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"##FORMAT=<ID=GT, Number=1, Type=String, Description=\"Genotype\">",
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"##FORMAT=<ID=HQ, Number=2, Type=Integer, Description=\"Haplotype quality\">",
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"##FORMAT=<ID=TT, Number=., Type=Integer, Description=\"Lots of TTs\">",
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};
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}
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