/*
* The MIT License
*
* Copyright (c) 2013 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package htsjdk.samtools;
import htsjdk.samtools.util.PeekableIterator;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import htsjdk.samtools.SamPairUtil.SetMateInfoIterator;
public class SamPairUtilTest {
@Test(dataProvider = "testGetPairOrientation")
public void testGetPairOrientation(final String testName,
final int read1Start, final int read1Length, final boolean read1Reverse,
final int read2Start, final int read2Length, final boolean read2Reverse,
final SamPairUtil.PairOrientation expectedOrientation) {
final SAMFileHeader header = new SAMFileHeader();
header.addSequence(new SAMSequenceRecord("chr1", 100000000));
final SAMRecord rec1 = makeSamRecord(header, read1Start, read1Length, read1Reverse, true);
final SAMRecord rec2 = makeSamRecord(header, read2Start, read2Length, read2Reverse, false);
SamPairUtil.setMateInfo(rec1, rec2, header, true);
Assert.assertEquals(SamPairUtil.getPairOrientation(rec1), expectedOrientation, testName + " first end");
Assert.assertEquals(SamPairUtil.getPairOrientation(rec2), expectedOrientation, testName + " second end");
}
@Test(dataProvider = "testSetMateInfoMateCigar")
public void testSetMateInfoMateCigar(final String testName,
final int read1Start, final boolean read1Reverse, final String read1Cigar,
final int read2Start, final boolean read2Reverse, final String read2Cigar) {
final SAMFileHeader header = new SAMFileHeader();
header.addSequence(new SAMSequenceRecord("chr1", 100000000));
final SAMRecord rec1 = makeSamRecord2(header, read1Start, read1Reverse, read1Cigar, true);
final SAMRecord rec2 = makeSamRecord2(header, read2Start, read2Reverse, read2Cigar, false);
SamPairUtil.setMateInfo(rec1, rec2, header, true);
Assert.assertEquals(SAMUtils.getMateCigarString(rec1), rec2.getCigarString(), testName + " first end");
Assert.assertEquals(SAMUtils.getMateCigarString(rec2), rec1.getCigarString(), testName + " second end");
}
private void testSetMateInfoMateCigarOnSupplementalsAddRecord(final List<SAMRecord> records, final List<String> mateCigarList, final SAMRecord record, final String mateCigar) {
records.add(record);
mateCigarList.add(mateCigar);
}
@Test(dataProvider = "testSetMateInfoMateCigarOnSupplementals")
public void testSetMateInfoMateCigarOnSupplementals(final String testName,
final int read1Start, final boolean read1Reverse, final String read1Cigar,
final int read1SupplementalStart, final boolean read1SupplementalReverse, final String read1SupplementalCigar,
final int read2Start, final boolean read2Reverse, final String read2Cigar,
final int read2SupplementalStart, final boolean read2SupplementalReverse, final String read2SupplementalCigar
) {
final SAMFileHeader header = new SAMFileHeader();
header.addSequence(new SAMSequenceRecord("chr1", 100000000));
final List<SAMRecord> records = new ArrayList<SAMRecord>();
final List<String> mateCigarList = new ArrayList<String>();
final SAMRecord rec;
int numIterations = 10;
boolean isPaired = (0 < read1Start && 0 < read2Start);
for (int i = 0; i < numIterations; i++) {
final String readName = "READ" + i;
testSetMateInfoMateCigarOnSupplementalsAddRecord(records, mateCigarList, makeSamRecord3(header, read1Start, read1Reverse, read1Cigar, true, readName, isPaired, false), read2Cigar);
if (0 < read1SupplementalStart) {
testSetMateInfoMateCigarOnSupplementalsAddRecord(records, mateCigarList, makeSamRecord3(header, read1SupplementalStart, read1SupplementalReverse, read1SupplementalCigar, true, readName, isPaired, true), read2Cigar);
}
if (0 < read2Start) {
testSetMateInfoMateCigarOnSupplementalsAddRecord(records, mateCigarList, makeSamRecord3(header, read2Start, read2Reverse, read2Cigar, false, readName, isPaired, false), read1Cigar);
}
if (0 < read2SupplementalStart) {
testSetMateInfoMateCigarOnSupplementalsAddRecord(records, mateCigarList, makeSamRecord3(header, read2SupplementalStart, read2SupplementalReverse, read2SupplementalCigar, false, readName, isPaired, true), read1Cigar);
}
}
// Count the number of mate cigars we expect to add
int expectedNumberOfMateCigarsAdded = 0;
for (final String mateCigar : mateCigarList) {
if (null != mateCigar) expectedNumberOfMateCigarsAdded++;
}
int i = 0;
SetMateInfoIterator iterator = new SetMateInfoIterator(records.iterator(), true);
while (iterator.hasNext()) {
final SAMRecord record = iterator.next();
final Cigar mateCigar = SAMUtils.getMateCigar(record);
final String mateCigarString = (null == mateCigar) ? null : mateCigar.toString();
Assert.assertEquals(mateCigarString, mateCigarList.get(i), testName);
i++;
}
Assert.assertEquals(expectedNumberOfMateCigarsAdded, iterator.getNumMateCigarsAdded(), testName);
iterator.close();
}
private SAMRecord makeSamRecord(final SAMFileHeader header, final int alignmentStart, final int readLength,
final boolean reverse, final boolean firstOfPair) {
final SAMRecord rec = new SAMRecord(header);
rec.setReferenceIndex(0);
final StringBuilder sb = new StringBuilder();
final byte[] quals = new byte[readLength];
for (int i = 0; i < readLength; ++i) {
sb.append("A");
quals[i] = 20;
}
rec.setReadString(sb.toString());
rec.setBaseQualities(quals);
rec.setAlignmentStart(alignmentStart);
rec.setCigarString(readLength + "M");
rec.setReadPairedFlag(true);
rec.setReadNegativeStrandFlag(reverse);
if (firstOfPair) rec.setFirstOfPairFlag(true);
else rec.setSecondOfPairFlag(true);
return rec;
}
private SAMRecord makeSamRecord2(final SAMFileHeader header, final int alignmentStart, boolean reverse,
String cigarString, final boolean firstOfPair) {
return makeSamRecord3(header, alignmentStart, reverse, cigarString, firstOfPair, null, true, false);
}
private SAMRecord makeSamRecord3(final SAMFileHeader header, final int alignmentStart, boolean reverse,
String cigarString, final boolean firstOfPair, final String name, final boolean isPaired, final boolean isSupplemental) {
final SAMRecord rec = new SAMRecord(header);
final StringBuilder sb = new StringBuilder();
final Cigar cigar = TextCigarCodec.getSingleton().decode(cigarString);
final int readLength = cigar.getReadLength();
rec.setReferenceIndex(0);
final byte[] quals = new byte[readLength];
for (int i = 0; i < readLength; ++i) {
sb.append("A");
quals[i] = 20;
}
rec.setReadString(sb.toString());
rec.setBaseQualities(quals);
rec.setAlignmentStart(alignmentStart);
rec.setCigar(cigar);
rec.setReadNegativeStrandFlag(reverse);
if (isPaired) {
rec.setReadPairedFlag(true);
if (firstOfPair) rec.setFirstOfPairFlag(true);
else rec.setSecondOfPairFlag(true);
}
if (null != name) rec.setReadName(name);
rec.setSupplementaryAlignmentFlag(isSupplemental);
return rec;
}
@DataProvider(name = "testGetPairOrientation")
public Object[][] testGetPairOrientationDataProvider() {
/**
* @param testName
* @param read1Start
* @param read1Length
* @param read1Reverse
* @param read2Start
* @param read2Length
* @param read2Reverse
* @param expectedOrientation
*/
return new Object[][] {
{"normal innie", 1, 100, false, 500, 100, true, SamPairUtil.PairOrientation.FR},
{"overlapping innie", 1, 100, false, 50, 100, true, SamPairUtil.PairOrientation.FR},
{"second end enclosed innie", 1, 100, false, 50, 50, true, SamPairUtil.PairOrientation.FR},
{"first end enclosed innie", 1, 50, false, 1, 100, true, SamPairUtil.PairOrientation.FR},
{"completely overlapping innie", 1, 100, false, 1, 100, true, SamPairUtil.PairOrientation.FR},
{"normal outie", 1, 100, true, 500, 100, false, SamPairUtil.PairOrientation.RF},
{"nojump outie", 1, 100, true, 101, 100, false, SamPairUtil.PairOrientation.RF},
{"forward tandem", 1, 100, true, 500, 100, true, SamPairUtil.PairOrientation.TANDEM},
{"reverse tandem", 1, 100, false, 500, 100, false, SamPairUtil.PairOrientation.TANDEM},
{"overlapping forward tandem", 1, 100, true, 50, 100, true, SamPairUtil.PairOrientation.TANDEM},
{"overlapping reverse tandem", 1, 100, false, 50, 100, false, SamPairUtil.PairOrientation.TANDEM},
{"second end enclosed forward tandem", 1, 100, true, 50, 50, true, SamPairUtil.PairOrientation.TANDEM},
{"second end enclosed reverse tandem", 1, 100, false, 50, 50, false, SamPairUtil.PairOrientation.TANDEM},
{"first end enclosed forward tandem", 1, 50, true, 1, 100, true, SamPairUtil.PairOrientation.TANDEM},
{"first end enclosed reverse tandem", 1, 50, false, 1, 100, false, SamPairUtil.PairOrientation.TANDEM},
};
}
@DataProvider(name = "testSetMateInfoMateCigar")
public Object[][] testSetMateInfoMateCigarDataProvider() {
/**
* @param testName
* @param read1Start
* @param read1Reverse
* @param read1Cigar
* @param read2Start
* @param read2Reverse
* @param read2Cigar
*/
return new Object[][] {
{"50M/50M", 1, false, "50M", 500, true, "50M"},
{"50M/25M5I20M", 1, false, "50M", 500, true, "25M5I20M"},
{"25M5I20M/50M", 1, false, "25M5I20M", 500, true, "50M"},
{"50M/25M5D20M", 1, false, "50M", 500, true, "25M5D20M"},
{"25M5D20M/50M", 1, false, "25M5D20M", 500, true, "50M"},
};
}
@DataProvider(name = "testSetMateInfoMateCigarOnSupplementals")
public Object[][] testSetMateInfoMateCigarOnSupplementalsDataProvider() {
/**
* @param testName
* @param read1Start
* @param read1Reverse
* @param read1Cigar
* @param read1SupplementalStart
* @param read1SupplementalReverse
* @param read1SupplementalCigar
* @param read2Start
* @param read2Reverse
* @param read2Cigar
* @param read2SupplementalStart
* @param read2SupplementalReverse
* @param read2SupplementalCigar
* */
return new Object[][] {
{"fragment", 1, false, "50M", -1, false, null, -1, false, null, -1, false, null},
{"fragment with supplemental", 1, false, "50M", 10, false, "50M", -1, false, null, -1, false, null},
{"pair", 1, false, "50M", -1, false, null, 1, false, "20M", -1, false, null},
{"pair first supplemental", 1, false, "50M", 10, false, "50M", 1, false, "20M", -1, false, null},
{"pair second supplemental", 1, false, "50M", -1, false, null, 1, false, "20M", 10, false, "50M"},
{"pair both supplemental", 1, false, "50M", 10, false, "50M", 1, false, "20M", 10, false, "50M"}
};
}
}