org.broadinstitute.hellbender.testutils.ReadClipperTestUtils Maven / Gradle / Ivy
package org.broadinstitute.hellbender.testutils;
import com.google.common.collect.Lists;
import htsjdk.samtools.*;
import org.broadinstitute.hellbender.utils.read.ArtificialReadUtils;
import org.broadinstitute.hellbender.utils.read.CigarBuilder;
import org.broadinstitute.hellbender.utils.read.CigarUtils;
import org.broadinstitute.hellbender.utils.read.GATKRead;
import java.util.*;
import java.util.stream.Collectors;
public final class ReadClipperTestUtils {
//Should contain all the utils needed for tests to mass produce
//reads, cigars, and other needed classes
static final byte[] BASES = {'A', 'C', 'T', 'G'};
static final byte[] QUALS = {2, 15, 25, 30};
static final List> LEADING_CLIPS = Arrays.asList(
Collections.emptyList(),
Collections.singletonList(new CigarElement(1, CigarOperator.HARD_CLIP)),
Collections.singletonList(new CigarElement(1, CigarOperator.SOFT_CLIP)),
Arrays.asList(new CigarElement(1, CigarOperator.HARD_CLIP), new CigarElement(1, CigarOperator.SOFT_CLIP)));
static final List> TRAILING_CLIPS = LEADING_CLIPS.stream().map(Lists::reverse).collect(Collectors.toList());
static final CigarElement[] CORE_CIGAR_ELEMENTS = {
new CigarElement(1, CigarOperator.INSERTION),
new CigarElement(1, CigarOperator.DELETION),
new CigarElement(1, CigarOperator.MATCH_OR_MISMATCH)};
static final CigarElement[] CORE_CIGAR_ELEMENTS_INCLUDING_SKIPS = {
new CigarElement(1, CigarOperator.INSERTION),
new CigarElement(1, CigarOperator.DELETION),
new CigarElement(1, CigarOperator.MATCH_OR_MISMATCH),
new CigarElement(1, CigarOperator.SKIPPED_REGION)};
/**
* Make a read from the CIGAR string
*
* @param cigarString string used to create a CIGAR
* @return artificial read
*/
public static GATKRead makeReadFromCigar(String cigarString) {
return makeReadFromCigar(TextCigarCodec.decode(cigarString));
}
/**
* Make a read from the CIGAR.
*
* @param cigar
* @return artificial read
*/
public static GATKRead makeReadFromCigar(Cigar cigar) {
return makeReadFromCigar(cigar, 0);
}
private static GATKRead makeReadFromCigar(Cigar cigar, int lengthChange) {
int readLength = cigar.getReadLength();
if (readLength >= -lengthChange) {
readLength += lengthChange;
}
return ArtificialReadUtils.createArtificialRead(arrayFromArrayWithLength(BASES, readLength), arrayFromArrayWithLength(QUALS, readLength), cigar.toString());
}
private static byte [] arrayFromArrayWithLength(final byte[] array, final int length) {
final byte [] output = new byte[length];
for (int j = 0; j < length; j++) {
output[j] = array[(j % array.length)];
}
return output;
}
/**
* Make a read from the CIGAR
*
* @param cigarString string used to create a CIGAR
* @param lengthChange change in read length relative the CIGAR length
* @return artificial read
*/
public static GATKRead makeReadFromCigar(String cigarString, int lengthChange) {
return makeReadFromCigar(TextCigarCodec.decode(cigarString), lengthChange);
}
/**
* This function generates every valid permutation of cigar strings (with a given set of cigarElement) with a given length.
*
* A valid cigar object obeys the following rules:
* - No Hard/Soft clips in the middle of the read
* - No deletions in the beginning / end of the read
* - No repeated adjacent element (e.g. 1M2M, this should be 3M)
* - No consecutive I/D elements
*
* @param maximumCigarElements the maximum number of elements in the cigar
* @return a list with all valid Cigar objects
*/
public static List generateCigarList(int maximumCigarElements, final boolean includeSkips) {
final CigarElement[] coreElements = includeSkips ? CORE_CIGAR_ELEMENTS_INCLUDING_SKIPS : CORE_CIGAR_ELEMENTS;
List cigarList = new ArrayList<>();
for (final List leadingClipElements : LEADING_CLIPS) {
for (final List trailingClipElements : TRAILING_CLIPS) {
final int maximumCoreElements = maximumCigarElements - leadingClipElements.size() - trailingClipElements.size();
if (maximumCoreElements < 1) {
continue;
}
int numCoreElements = coreElements.length;
int[] cigarCombination = new int[maximumCoreElements];
Arrays.fill(cigarCombination, 0);
int currentIndex = 0;
while (true) {
try {
final Cigar coreCigar = createCigarFromCombination(cigarCombination, coreElements); // create the cigar
if (CigarUtils.isGood(coreCigar)) {// check if it's valid
final CigarBuilder builder = new CigarBuilder();
builder.addAll(leadingClipElements);
builder.addAll(coreCigar.getCigarElements());
builder.addAll(trailingClipElements);
cigarList.add(builder.make()); // add it
}
} catch (final Exception ex) {
} // we are creating random cigars, many of which are invalid.
boolean currentIndexChanged = false;
while (currentIndex < maximumCoreElements && cigarCombination[currentIndex] == numCoreElements - 1) {
currentIndex++; // find the next index to increment
currentIndexChanged = true; // keep track of the fact that we have changed indices!
}
if (currentIndex == maximumCoreElements) // if we hit the end of the array, we're done.
break;
cigarCombination[currentIndex]++; // otherwise advance the current index
if (currentIndexChanged) { // if we have changed index, then...
for (int i = 0; i < currentIndex; i++)
cigarCombination[i] = 0; // reset everything from 0->currentIndex
currentIndex = 0; // go back to the first index
}
}
}
}
return cigarList;
}
private static Cigar createCigarFromCombination(int[] cigarCombination, CigarElement[] cigarElements) {
return new Cigar(Arrays.stream(cigarCombination).mapToObj(n -> cigarElements[n]).collect(Collectors.toList()));
}
}