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Renaming GVCF -> GCF

This commit is contained in:
Mark DePristo 2011-09-07 17:10:56 -04:00
parent b220ed0d75
commit 01b6177ce1
4 changed files with 41 additions and 46 deletions
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47
public/java/src/org/broadinstitute/sting/utils/gvcf/GVCF.java → public/java/src/org/broadinstitute/sting/utils/gcf/GCF.java
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@ -22,12 +22,9 @@
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.gvcf;
package org.broadinstitute.sting.utils.gcf;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.codecs.vcf.StandardVCFWriter;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
@ -42,7 +39,7 @@ import java.util.*;
* @author Your Name
* @since Date created
*/
public class GVCF {
public class GCF {
private final static int RECORD_TERMINATOR = 123456789;
private int chromOffset;
private int start, stop;
@ -54,10 +51,10 @@ public class GVCF {
private String info;
private int filterOffset;
private List<GVCFGenotype> genotypes = Collections.emptyList();
private List<GCFGenotype> genotypes = Collections.emptyList();
public GVCF(final GVCFHeaderBuilder gvcfHeaderBuilder, final VariantContext vc, boolean skipGenotypes) {
chromOffset = gvcfHeaderBuilder.encodeString(vc.getChr());
public GCF(final GCFHeaderBuilder GCFHeaderBuilder, final VariantContext vc, boolean skipGenotypes) {
chromOffset = GCFHeaderBuilder.encodeString(vc.getChr());
start = vc.getStart();
stop = vc.getEnd();
refPad = vc.hasReferenceBaseForIndel() ? vc.getReferenceBaseForIndel() : 0;
@ -67,22 +64,22 @@ public class GVCF {
alleleMap = new ArrayList<Allele>(vc.getNAlleles());
alleleOffsets = new int[vc.getNAlleles()];
alleleMap.add(vc.getReference());
alleleOffsets[0] = gvcfHeaderBuilder.encodeAllele(vc.getReference());
alleleOffsets[0] = GCFHeaderBuilder.encodeAllele(vc.getReference());
for ( int i = 0; i < vc.getAlternateAlleles().size(); i++ ) {
alleleMap.add(vc.getAlternateAllele(i));
alleleOffsets[i+1] = gvcfHeaderBuilder.encodeAllele(vc.getAlternateAllele(i));
alleleOffsets[i+1] = GCFHeaderBuilder.encodeAllele(vc.getAlternateAllele(i));
}
qual = (float)vc.getNegLog10PError(); //qualToByte(vc.getPhredScaledQual());
info = infoFieldString(vc, gvcfHeaderBuilder);
filterOffset = gvcfHeaderBuilder.encodeString(StandardVCFWriter.getFilterString(vc));
info = infoFieldString(vc, GCFHeaderBuilder);
filterOffset = GCFHeaderBuilder.encodeString(StandardVCFWriter.getFilterString(vc));
if ( ! skipGenotypes ) {
genotypes = encodeGenotypes(gvcfHeaderBuilder, vc);
genotypes = encodeGenotypes(GCFHeaderBuilder, vc);
}
}
public GVCF(DataInputStream inputStream, boolean skipGenotypes) throws IOException {
public GCF(DataInputStream inputStream, boolean skipGenotypes) throws IOException {
chromOffset = inputStream.readInt();
start = inputStream.readInt();
stop = inputStream.readInt();
@ -99,9 +96,9 @@ public class GVCF {
genotypes = Collections.emptyList();
inputStream.skipBytes(sizeOfGenotypes);
} else {
genotypes = new ArrayList<GVCFGenotype>(nGenotypes);
genotypes = new ArrayList<GCFGenotype>(nGenotypes);
for ( int i = 0; i < nGenotypes; i++ )
genotypes.add(new GVCFGenotype(this, inputStream));
genotypes.add(new GCFGenotype(this, inputStream));
}
int recordDone = inputStream.readInt();
@ -109,7 +106,7 @@ public class GVCF {
throw new UserException.MalformedFile("Record not terminated by RECORD_TERMINATOR key");
}
public VariantContext decode(final String source, final GVCFHeader header) {
public VariantContext decode(final String source, final GCFHeader header) {
final String contig = header.getString(chromOffset);
alleleMap = header.getAlleles(alleleOffsets);
double negLog10PError = qual; // QualityUtils.qualToErrorProb(qual);
@ -122,7 +119,7 @@ public class GVCF {
return new VariantContext(source, contig, start, stop, alleleMap, genotypes, negLog10PError, filters, attributes, refPadByte);
}
private Map<String, Genotype> decodeGenotypes(final GVCFHeader header) {
private Map<String, Genotype> decodeGenotypes(final GCFHeader header) {
if ( genotypes.isEmpty() )
return VariantContext.NO_GENOTYPES;
else {
@ -138,15 +135,15 @@ public class GVCF {
}
}
private List<GVCFGenotype> encodeGenotypes(final GVCFHeaderBuilder gvcfHeaderBuilder, final VariantContext vc) {
private List<GCFGenotype> encodeGenotypes(final GCFHeaderBuilder GCFHeaderBuilder, final VariantContext vc) {
int nGenotypes = vc.getNSamples();
if ( nGenotypes > 0 ) {
List<GVCFGenotype> genotypes = new ArrayList<GVCFGenotype>(nGenotypes);
List<GCFGenotype> genotypes = new ArrayList<GCFGenotype>(nGenotypes);
for ( int i = 0; i < nGenotypes; i++ ) genotypes.add(null);
for ( Genotype g : vc.getGenotypes().values() ) {
int i = gvcfHeaderBuilder.encodeSample(g.getSampleName());
genotypes.set(i, new GVCFGenotype(gvcfHeaderBuilder, alleleMap, g));
int i = GCFHeaderBuilder.encodeSample(g.getSampleName());
genotypes.set(i, new GCFGenotype(GCFHeaderBuilder, alleleMap, g));
}
return genotypes;
@ -174,7 +171,7 @@ public class GVCF {
outputStream.writeInt(nGenotypes);
outputStream.writeInt(expectedSizeOfGenotypes);
int obsSizeOfGenotypes = 0;
for ( GVCFGenotype g : genotypes )
for ( GCFGenotype g : genotypes )
obsSizeOfGenotypes += g.write(outputStream);
if ( obsSizeOfGenotypes != expectedSizeOfGenotypes )
throw new RuntimeException("Expect and observed genotype sizes disagree! expect = " + expectedSizeOfGenotypes + " obs =" + obsSizeOfGenotypes);
@ -183,7 +180,7 @@ public class GVCF {
return outputStream.size() - startSize;
}
private final String infoFieldString(VariantContext vc, final GVCFHeaderBuilder gvcfHeaderBuilder) {
private final String infoFieldString(VariantContext vc, final GCFHeaderBuilder GCFHeaderBuilder) {
StringBuilder s = new StringBuilder();
boolean first = true;
@ -191,7 +188,7 @@ public class GVCF {
String key = field.getKey();
if ( key.equals(VariantContext.ID_KEY) || key.equals(VariantContext.UNPARSED_GENOTYPE_MAP_KEY) || key.equals(VariantContext.UNPARSED_GENOTYPE_PARSER_KEY) )
continue;
int stringIndex = gvcfHeaderBuilder.encodeString(key);
int stringIndex = GCFHeaderBuilder.encodeString(key);
String outputValue = StandardVCFWriter.formatVCFField(field.getValue());
if ( outputValue != null ) {
if ( ! first ) s.append(";");

20
public/java/src/org/broadinstitute/sting/utils/gvcf/GVCFGenotype.java → public/java/src/org/broadinstitute/sting/utils/gcf/GCFGenotype.java
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@ -22,7 +22,7 @@
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.gvcf;
package org.broadinstitute.sting.utils.gcf;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
@ -38,7 +38,7 @@ import java.util.*;
* @author Your Name
* @since Date created
*/
public class GVCFGenotype {
public class GCFGenotype {
private byte gq;
private int gt;
private int dp;
@ -48,8 +48,8 @@ public class GVCFGenotype {
// todo -- what to do about phasing? Perhaps we shouldn't support it
// todo -- is the FL field generic or just a flag? Should we even support per sample filtering?
public GVCFGenotype(final GVCFHeaderBuilder gvcfHeaderBuilder, final List<Allele> allAlleles, Genotype genotype) {
gq = GVCF.qualToByte(genotype.getPhredScaledQual());
public GCFGenotype(final GCFHeaderBuilder GCFHeaderBuilder, final List<Allele> allAlleles, Genotype genotype) {
gq = GCF.qualToByte(genotype.getPhredScaledQual());
gt = encodeAlleles(genotype.getAlleles(), allAlleles);
dp = genotype.getAttributeAsInt("DP", 0);
@ -65,13 +65,13 @@ public class GVCFGenotype {
return nAlleles*(nAlleles+1) / 2;
}
public GVCFGenotype(GVCF gvcf, DataInputStream inputStream) throws IOException {
public GCFGenotype(GCF GCF, DataInputStream inputStream) throws IOException {
int gqInt = inputStream.readUnsignedByte();
gq = (byte)gqInt;
gt = inputStream.readInt();
dp = inputStream.readInt();
ad = GVCF.readIntArray(inputStream, gvcf.getNAlleles());
pl = GVCF.readByteArray(inputStream, nAllelesToNPls(gvcf.getNAlleles()));
ad = GCF.readIntArray(inputStream, GCF.getNAlleles());
pl = GCF.readByteArray(inputStream, nAllelesToNPls(GCF.getNAlleles()));
}
// 2 alleles => 1 + 8 + 8 + 3 => 20
@ -82,7 +82,7 @@ public class GVCFGenotype {
+ 1 * pl.length; // pl
}
public Genotype decode(final String sampleName, final GVCFHeader header, GVCF gvcf, List<Allele> alleleIndex) {
public Genotype decode(final String sampleName, final GCFHeader header, GCF GCF, List<Allele> alleleIndex) {
final List<Allele> alleles = decodeAlleles(gt, alleleIndex);
final double negLog10PError = gq / 10.0;
final Set<String> filters = Collections.emptySet();
@ -140,8 +140,8 @@ public class GVCFGenotype {
outputStream.writeByte(gq);
outputStream.writeInt(gt);
outputStream.writeInt(dp);
GVCF.writeIntArray(ad, outputStream, false);
GVCF.writeByteArray(pl, outputStream, false);
GCF.writeIntArray(ad, outputStream, false);
GCF.writeByteArray(pl, outputStream, false);
return outputStream.size() - startSize;
}
}

12
public/java/src/org/broadinstitute/sting/utils/gvcf/GVCFHeader.java → public/java/src/org/broadinstitute/sting/utils/gcf/GCFHeader.java
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@ -22,11 +22,9 @@
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.gvcf;
package org.broadinstitute.sting.utils.gcf;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.codecs.vcf.AbstractVCFCodec;
import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.UserException;
@ -64,8 +62,8 @@ import java.util.*;
* @author Your Name
* @since Date created
*/
public class GVCFHeader {
final protected static Logger logger = Logger.getLogger(GVCFHeader.class);
public class GCFHeader {
final protected static Logger logger = Logger.getLogger(GCFHeader.class);
private static byte[] MAGIC_HEADER = "GVCF0.1\1".getBytes();
final List<Allele> alleles;
@ -73,14 +71,14 @@ public class GVCFHeader {
final List<String> samples;
final List<Set<String>> filters;
public GVCFHeader(final Map<Allele, Integer> allelesIn, final Map<String, Integer> stringIn, final Map<String, Integer> samplesIn) {
public GCFHeader(final Map<Allele, Integer> allelesIn, final Map<String, Integer> stringIn, final Map<String, Integer> samplesIn) {
this.alleles = linearize(allelesIn);
this.strings = linearize(stringIn);
this.samples = linearize(samplesIn);
this.filters = null; // not used with this constructor
}
public GVCFHeader(DataInputStream inputStream) throws IOException {
public GCFHeader(DataInputStream inputStream) throws IOException {
byte[] headerTest = new byte[MAGIC_HEADER.length];
inputStream.read(headerTest);
if ( ! Arrays.equals(headerTest, MAGIC_HEADER) ) {

8
public/java/src/org/broadinstitute/sting/utils/gvcf/GVCFHeaderBuilder.java → public/java/src/org/broadinstitute/sting/utils/gcf/GCFHeaderBuilder.java
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@ -22,7 +22,7 @@
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.gvcf;
package org.broadinstitute.sting.utils.gcf;
import org.broadinstitute.sting.utils.variantcontext.Allele;
@ -56,13 +56,13 @@ import java.util.Map;
* @author Your Name
* @since Date created
*/
public class GVCFHeaderBuilder {
public class GCFHeaderBuilder {
Map<Allele, Integer> alleles = new HashMap<Allele, Integer>();
Map<String, Integer> strings = new HashMap<String, Integer>();
Map<String, Integer> samples = new HashMap<String, Integer>();
public GVCFHeader createHeader() {
return new GVCFHeader(alleles, strings, samples);
public GCFHeader createHeader() {
return new GCFHeader(alleles, strings, samples);
}
public int encodeString(final String chr) { return encode(strings, chr); }