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/*
* Copyright (C) 2014-2021 Brian L. Browning
*
* This file is part of Beagle
*
* Beagle is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Beagle is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package vcf;
import blbutil.Const;
import java.io.PrintWriter;
/**
* <p>Class {@code VcfRecBuilder} contains methods for constructing
* and printing a VCF record in VCF 4.2 format. The FORMAT field data
* for each sample is added sequentially to the record via the
* {@code addSampleData()} method.
*
* </p>
* <p>Instances of class {@code VcfRecBuilder} are not thread-safe.
* </p>
*
* @author Brian L. Browning {@code <browning@uw.edu>}
*/
public final class VcfRecBuilder {
/**
* The default initial size for the string buffer, which is 50
* characters.
*/
public static final int DEFAULT_INIT_SIZE = 50;
private final StringBuilder sb;
private final Marker marker;
private final int nAlleles;
/**
* Constructs a new {@code VcfRecBuilder} instance with an initial
* capacity for the specified number of samples.
*
* @param marker the marker
* @param nSamples the number of samples
* @throws IllegalArgumentException if {@code nSamples < 0}
*/
public VcfRecBuilder(Marker marker, int nSamples) {
if (nSamples < 0) {
throw new IllegalArgumentException(String.valueOf(nSamples));
}
StringBuilder buffer = new StringBuilder(100 + 4*nSamples);
writeFixedFields(marker, buffer);
this.marker = marker;
this.nAlleles = marker.nAlleles();
this.sb = buffer;
}
/**
* Returns the current marker. Returns {@code null} if
* {@code this.reset()} has not been previously invoked.
* @return the current marker.
*/
public Marker marker() {
return marker;
}
/**
* Adds the specified diploid phased genotype to the VCF record for
* the current marker.
* @param a1 the first allele
* @param a2 the second allele
* @throws IllegalStateException if {@code this.marker() == null}
* @throws IndexOutOfBoundsException if
* {@code a1 < 0 || a1 >= this.marker().nAlleles()}
* @throws IndexOutOfBoundsException if
* {@code a2 < 0 || a2 >= this.marker().nAlleles()}
*/
public void addSampleData(int a1, int a2) {
if (a1 < 0 || a1 >= nAlleles) {
throw new IndexOutOfBoundsException(String.valueOf(a1));
}
if (a2 < 0 || a2 >= nAlleles) {
throw new IndexOutOfBoundsException(String.valueOf(a2));
}
sb.append(Const.tab);
sb.append(a1);
sb.append(Const.phasedSep);
sb.append(a2);
}
/**
* Adds the specified haploid phased genotype to the VCF record for
* the current marker.
* @param allele the allele
* @throws IllegalStateException if {@code this.marker() == null}
* @throws IndexOutOfBoundsException if
* {@code allele < 0 || allele >= this.marker().nAlleles()}
*/
public void addSampleData(int allele) {
if (allele < 0 || allele >= nAlleles) {
throw new IndexOutOfBoundsException(String.valueOf(allele));
}
sb.append(Const.tab);
sb.append(allele);
}
/**
* Prints the current VCF record for the current marker to the specified
* {@code PrintWriter}.
* @param out the {@code PrintWriter} to which the VCF record will be
* printed
* @throws NullPointerException if {@code out == null}
*/
public void writeRec(PrintWriter out) {
out.println(sb);
}
private static void writeFixedFields(Marker marker, StringBuilder sb) {
appendMarker(marker, sb);
sb.append(Const.tab);
sb.append(Const.MISSING_DATA_CHAR); // QUAL
sb.append(Const.tab);
sb.append("PASS"); // FILTER
sb.append(Const.tab);
if (marker.end()==-1) {
sb.append(Const.MISSING_DATA_CHAR); // INFO
}
else {
sb.append("END=");
sb.append(marker.end());
}
sb.append(Const.tab);
sb.append("GT"); // FORMAT
}
private static void appendMarker(Marker marker, StringBuilder sb) {
sb.append(marker.chrom());
sb.append(Const.tab);
sb.append(marker.pos());
int nIds = marker.nIds();
if (nIds==0) {
sb.append(Const.tab);
sb.append(Const.MISSING_DATA_CHAR);
}
else {
for (int j=0; j<nIds; ++j) {
sb.append(j==0 ? Const.tab : Const.semicolon);
sb.append(marker.id(j));
}
}
int nAlleles = marker.nAlleles();
if (nAlleles==1) {
sb.append(Const.tab);
sb.append(marker.allele(0));
sb.append(Const.tab);
sb.append(Const.MISSING_DATA_CHAR);
}
else {
for (int j=0; j<nAlleles; ++j) {
sb.append(j<2 ? Const.tab : Const.comma);
sb.append(marker.allele(j));
}
}
}
}
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