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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.Filter;
import blbutil.Utilities;
import java.io.File;
import java.util.Collection;
import java.util.HashSet;
import java.util.Set;
/**
* Class {@code FilterUtil} contains static methods for constructing
* marker filters.
*
* @author Brian L. Browning {@code <browning@uw.edu>}
*/
public final class FilterUtil {
private FilterUtil() {
// private constructor to prevent instantiation
}
/**
* Returns a filter that excludes markers that have an identifier
* or genome coordinates that matches a line of the specified file,
* or returns {@code null} if the {@code excludeMarkersFile} parameter is
* {@code null}. Genome coordinates must be in "CHROM:POS" format.
* @param excludeMarkersFile a file that contains an identifier
* or genome coordinate of one excluded marker on each line
* @return a filter that excludes markers that have an identifier
* or genome coordinates that matches a line of the specified file,
* or {@code null} if the {@code excludeMarkersFile} parameter is
* {@code null}
*
* @throws IllegalArgumentException if the specified file does not exist
* @throws IllegalArgumentException if the specified file is a directory
* @throws IllegalArgumentException if any line of the specified
* file contains two non-white-space characters separated by one or
* more white-space characters
*/
public static Filter<Marker> markerFilter(File excludeMarkersFile) {
Set<String> excludeIds;
if (excludeMarkersFile==null) {
return Filter.acceptAllFilter();
}
else {
excludeIds = Utilities.idSet(excludeMarkersFile);
return idFilter(excludeIds);
}
}
/**
* Returns a filter that excludes samples that have an identifier
* that matches a line of the specified file, or returns {@code null} if
* the {@code excludeSamplesFile} parameter is {@code null}
* @param excludeSamplesFile a file which contains an identifier
* of one excluded sample on each line
* @return a filter that excludes samples that have an identifier
* that matches a line of the specified file, or {@code null} if
* the {@code excludeSamplesFile} parameter is {@code null}
*
* @throws IllegalArgumentException if the specified file does not exist
* @throws IllegalArgumentException if the specified file is a directory
* @throws IllegalArgumentException if any line of the specified
* file contains two non-white-space characters separated by one or
* more white-space characters
*/
public static Filter<String> sampleFilter(File excludeSamplesFile) {
if (excludeSamplesFile==null) {
return Filter.acceptAllFilter();
}
else {
Set<String> exclude = Utilities.idSet(excludeSamplesFile);
return Filter.excludeFilter(exclude);
}
}
/**
* Returns {@code true} if the specified marker has an identifier
* is in the specified set, or if ("marker.chrom()" + ":" + "marker.pos()")
* is in the specified set, and returns {@code false} otherwise.
* @param marker a marker
* @param set a set of marker identifiers and chromosome positions in
* "CHROM:POS" format
* @return {@code true} if the specified marker has an identifier
* is in the specified set or if ("marker.chrom()" + ":" + "marker.pos()")
* is in the specified set
* @throws NullPointerException if {@code marker == null || set == null}
*/
public static boolean markerIsInSet(Marker marker, Set<String> set) {
for (int j=0, n=marker.nIds(); j<n; ++j) {
if (set.contains(marker.id(j))) {
return true;
}
}
String posId = marker.chrom() + ':' + marker.pos();
return set.contains(posId);
}
/**
* Returns a filter that accepts all markers which do not have an
* identifier or chromomsome position present in the specified
* collection.
* A marker is excluded if {@code exclude.contains(marker.id(j)) == true}
* for any {@code 0 <= j < marker.nIds()} or if
* {@code exclude.contains(marker.chrom() + ":" + marker.pos()) == true}.
* @param exclude a collection of marker identifiers and chromosome
* positions in "CHROM:POS" format
* @return a filter that accepts all markers which do not have an
* identifier or chromomsome position present in the specified
* collection
* @throws NullPointerException if {@code exclude == null}
*/
public static Filter<Marker> idFilter(Collection<String> exclude) {
final Set<String> excludeSet = new HashSet<>(exclude);
if (excludeSet.isEmpty()) {
return Marker -> true;
}
else {
return (Marker marker) -> !markerIsInSet(marker, excludeSet);
}
}
}
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