From 01b6177ce15c2d4270ac863da1a2e4e43e020411 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Wed, 7 Sep 2011 17:10:56 -0400 Subject: [PATCH] Renaming GVCF -> GCF --- .../utils/{gvcf/GVCF.java => gcf/GCF.java} | 47 +++++++++---------- .../GCFGenotype.java} | 20 ++++---- .../GVCFHeader.java => gcf/GCFHeader.java} | 12 ++--- .../GCFHeaderBuilder.java} | 8 ++-- 4 files changed, 41 insertions(+), 46 deletions(-) rename public/java/src/org/broadinstitute/sting/utils/{gvcf/GVCF.java => gcf/GCF.java} (83%) rename public/java/src/org/broadinstitute/sting/utils/{gvcf/GVCFGenotype.java => gcf/GCFGenotype.java} (86%) rename public/java/src/org/broadinstitute/sting/utils/{gvcf/GVCFHeader.java => gcf/GCFHeader.java} (92%) rename public/java/src/org/broadinstitute/sting/utils/{gvcf/GVCFHeaderBuilder.java => gcf/GCFHeaderBuilder.java} (93%) diff --git a/public/java/src/org/broadinstitute/sting/utils/gvcf/GVCF.java b/public/java/src/org/broadinstitute/sting/utils/gcf/GCF.java similarity index 83% rename from public/java/src/org/broadinstitute/sting/utils/gvcf/GVCF.java rename to public/java/src/org/broadinstitute/sting/utils/gcf/GCF.java index 8568c1aab..5ab241ebf 100644 --- a/public/java/src/org/broadinstitute/sting/utils/gvcf/GVCF.java +++ b/public/java/src/org/broadinstitute/sting/utils/gcf/GCF.java @@ -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 genotypes = Collections.emptyList(); + private List 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(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(nGenotypes); + genotypes = new ArrayList(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 decodeGenotypes(final GVCFHeader header) { + private Map decodeGenotypes(final GCFHeader header) { if ( genotypes.isEmpty() ) return VariantContext.NO_GENOTYPES; else { @@ -138,15 +135,15 @@ public class GVCF { } } - private List encodeGenotypes(final GVCFHeaderBuilder gvcfHeaderBuilder, final VariantContext vc) { + private List encodeGenotypes(final GCFHeaderBuilder GCFHeaderBuilder, final VariantContext vc) { int nGenotypes = vc.getNSamples(); if ( nGenotypes > 0 ) { - List genotypes = new ArrayList(nGenotypes); + List genotypes = new ArrayList(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(";"); diff --git a/public/java/src/org/broadinstitute/sting/utils/gvcf/GVCFGenotype.java b/public/java/src/org/broadinstitute/sting/utils/gcf/GCFGenotype.java similarity index 86% rename from public/java/src/org/broadinstitute/sting/utils/gvcf/GVCFGenotype.java rename to public/java/src/org/broadinstitute/sting/utils/gcf/GCFGenotype.java index 2ef6d9b3a..dd1fb091c 100644 --- a/public/java/src/org/broadinstitute/sting/utils/gvcf/GVCFGenotype.java +++ b/public/java/src/org/broadinstitute/sting/utils/gcf/GCFGenotype.java @@ -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 allAlleles, Genotype genotype) { - gq = GVCF.qualToByte(genotype.getPhredScaledQual()); + public GCFGenotype(final GCFHeaderBuilder GCFHeaderBuilder, final List 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 alleleIndex) { + public Genotype decode(final String sampleName, final GCFHeader header, GCF GCF, List alleleIndex) { final List alleles = decodeAlleles(gt, alleleIndex); final double negLog10PError = gq / 10.0; final Set 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; } } diff --git a/public/java/src/org/broadinstitute/sting/utils/gvcf/GVCFHeader.java b/public/java/src/org/broadinstitute/sting/utils/gcf/GCFHeader.java similarity index 92% rename from public/java/src/org/broadinstitute/sting/utils/gvcf/GVCFHeader.java rename to public/java/src/org/broadinstitute/sting/utils/gcf/GCFHeader.java index c52c975bd..d0c765cc4 100644 --- a/public/java/src/org/broadinstitute/sting/utils/gvcf/GVCFHeader.java +++ b/public/java/src/org/broadinstitute/sting/utils/gcf/GCFHeader.java @@ -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 alleles; @@ -73,14 +71,14 @@ public class GVCFHeader { final List samples; final List> filters; - public GVCFHeader(final Map allelesIn, final Map stringIn, final Map samplesIn) { + public GCFHeader(final Map allelesIn, final Map stringIn, final Map 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) ) { diff --git a/public/java/src/org/broadinstitute/sting/utils/gvcf/GVCFHeaderBuilder.java b/public/java/src/org/broadinstitute/sting/utils/gcf/GCFHeaderBuilder.java similarity index 93% rename from public/java/src/org/broadinstitute/sting/utils/gvcf/GVCFHeaderBuilder.java rename to public/java/src/org/broadinstitute/sting/utils/gcf/GCFHeaderBuilder.java index 2d045b8ea..40e01ec72 100644 --- a/public/java/src/org/broadinstitute/sting/utils/gvcf/GVCFHeaderBuilder.java +++ b/public/java/src/org/broadinstitute/sting/utils/gcf/GCFHeaderBuilder.java @@ -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 alleles = new HashMap(); Map strings = new HashMap(); Map samples = new HashMap(); - 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); }