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Moved GlobalEdgeGreedySWPairwiseAlignment to the archive

This commit is contained in:
Valentin Ruano-Rubio 2014-05-21 10:17:55 -04:00
parent 7c8a1ae892
commit 979ab0453e
2 changed files with 3 additions and 262 deletions
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6
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -162,7 +162,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
}
final Set<Pair<GenomeLoc, HaplotypeCallerGenotypingEngine.Event>> VCsAsSet = new HashSet<>(VCs);
return VCsAsSet.size() != VCs.size(); // The set will remove duplicate Events.
return VCsAsSet.size() != VCs.size(); // The se will remove duplicate Events.
}
@ -309,7 +309,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
executeTest("testLackSensitivityDueToBadHaplotypeSelectionFix", spec);
}
@Test(priority= -3)
@Test
public void testMissingKeyAlternativeHaplotypesBugFix() {
final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s --no_cmdline_in_header ",
b37KGReferenceWithDecoy, privateTestDir + "lost-alt-key-hap.bam", privateTestDir + "lost-alt-key-hap.interval_list");
@ -328,7 +328,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
executeTest("testBadLikelihoodsDueToBadHaplotypeSelectionFix", spec);
}
@Test(priority = -100)
@Test
public void testDifferentIndelLocationsDueToSWExactDoubleComparisonsFix() {
final String SHORT_INTERVAL = "12:7342264-7342464";
final String LONG_INTERVAL = "12:7342270-7342824";

259
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignmentUnitTest.java
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@ -1,259 +0,0 @@
/*
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package org.broadinstitute.sting.utils.smithwaterman;
import htsjdk.samtools.TextCigarCodec;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
public class GlobalEdgeGreedySWPairwiseAlignmentUnitTest extends BaseTest {
private final static boolean DEBUG = false;
@Test(enabled = !DEBUG)
public void testReadAlignedToRefComplexAlignment() {
final String reference = "AAAGGACTGACTG";
final String read = "ACTGACTGACTG";
final GlobalEdgeGreedySWPairwiseAlignment sw = new GlobalEdgeGreedySWPairwiseAlignment(reference.getBytes(), read.getBytes());
Assert.assertEquals(sw.getCigar().toString(), "1M1D11M");
}
@Test(enabled = !DEBUG)
public void testIndelsAtStartAndEnd() {
final String match = "CCCCC";
final String reference = "AAA" + match;
final String read = match + "GGG";
final int expectedStart = 0;
final String expectedCigar = "3D5M3I";
final GlobalEdgeGreedySWPairwiseAlignment sw = new GlobalEdgeGreedySWPairwiseAlignment(reference.getBytes(), read.getBytes());
Assert.assertEquals(sw.getAlignmentStart2wrt1(), expectedStart);
Assert.assertEquals(sw.getCigar().toString(), expectedCigar);
}
@Test(enabled = !DEBUG)
public void testDegenerateAlignmentWithIndelsAtBothEnds() {
logger.warn("testDegenerateAlignmentWithIndelsAtBothEnds");
final String ref = "TGTGTGTGTGTGTGACAGAGAGAGAGAGAGAGAGAGAGAGAGAGA";
final String alt = "ACAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA";
final int expectedStart = 0;
final String expectedCigar = "6I45M";
final GlobalEdgeGreedySWPairwiseAlignment sw = new GlobalEdgeGreedySWPairwiseAlignment(ref.getBytes(), alt.getBytes(), SWParameterSet.STANDARD_NGS);
Assert.assertEquals(sw.getAlignmentStart2wrt1(), expectedStart);
Assert.assertEquals(sw.getCigar().toString(), expectedCigar);
}
@Test(enabled = !DEBUG)
public void testAlignReallyLongDeletion() {
final String ref = "CGGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTGGCCAGGCTGGTCTTGAACTCCTGACCTCAGGTGATCCACTCGCCTCGGTCTCCCAAAGTGTTGGGATTACAGGCATGAACCACTGCACCTGGCCTAGTGTTTGGGAAAACTATACTAGGAAAAGAATAGTTGCTTTAAGTCATTCTTTGATTATTCTGAGAATTGGCATATAGCTGCCATTATAACCTACTTTTGCTAAATATAATAATAATAATCATTATTTTTATTTTTTGAGACAGGGTCTTGTTTTGTCACCCCGGCTGGAGTGAAGTGGCGCAATCTCGGCTCACTGCAACCTCCACCTCCGGGTGCAAGCAATTCTCCTGCCTCAGCCTCTTGAGTAGCTAGGATTACAGGCACAAGCCATCATGCCCAGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTGGTCAGGCTGGTCTTGAACTCCTGACCTCAGGT";
final String alt = "CGGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTGGTCAGGCTGGTCTTGAACTCCTGACCTCAGGT";
final GlobalEdgeGreedySWPairwiseAlignment sw = new GlobalEdgeGreedySWPairwiseAlignment(ref.getBytes(), alt.getBytes(), SWParameterSet.STANDARD_NGS);
Assert.assertEquals(sw.getAlignmentStart2wrt1(), 0);
Assert.assertEquals(sw.getCigar().toString(), "47M419D31M");
}
public static final Parameters params = new Parameters(20.0, -10.0, -26.0, -1.1,0.00001);
@DataProvider(name = "SWData")
public Object[][] makeSWData() {
List<Object[]> tests = new ArrayList<Object[]>();
// simple cases
tests.add(new Object[]{"A", "C", "1M"});
tests.add(new Object[]{"AAA", "AAA", "3M"});
tests.add(new Object[]{"AAA", "AGA", "3M"});
tests.add(new Object[]{"AAA", "GAA", "3M"});
tests.add(new Object[]{"AAA", "AAG", "3M"});
// small single indels
tests.add(new Object[]{"ACACACAC", "ACACAC", "6M2D"});
tests.add(new Object[]{"ACACAC", "ACACACAC", "6M2I"});
tests.add(new Object[]{"XXACACACXX", "XXACACACACXX", "8M2I2M"});
tests.add(new Object[]{"XXACACACXX", "XXACACXX", "6M2D2M"});
tests.add(new Object[]{"ACGT", "AACGT", "1I4M"});
tests.add(new Object[]{"ACGT", "ACCGT", "2M1I2M"});
tests.add(new Object[]{"ACGT", "ACGGT", "3M1I1M"});
tests.add(new Object[]{"ACGT", "ACGTT", "4M1I"});
tests.add(new Object[]{"ACGT", "CGT", "1D3M"});
tests.add(new Object[]{"ACGT", "AGT", "1M1D2M"});
tests.add(new Object[]{"ACGT", "ACT", "2M1D1M"});
tests.add(new Object[]{"ACGT", "ACG", "3M1D"});
// mismatches through out the sequences
final String ref = "ACGTAACCGGTT";
for ( int diff = 0; diff < ref.length(); diff++ ) {
final byte[] altBases = ref.getBytes();
altBases[diff] = 'N';
tests.add(new Object[]{ref, new String(altBases), ref.length() + "M"});
}
for ( int diff1 = 0; diff1 < ref.length(); diff1++ ) {
for ( int diff2 = 0; diff2 < ref.length(); diff2++ ) {
final byte[] altBases = ref.getBytes();
altBases[diff1] = 'N';
altBases[diff2] = 'N';
tests.add(new Object[]{ref, new String(altBases), ref.length() + "M"});
}
}
// prefixes and suffixes matching
final String totalPrefix = "ACG";
final String totalSuffix = "GCT";
for ( int prefixSize = 0; prefixSize < totalPrefix.length(); prefixSize++) {
for ( int suffixSize = 0; suffixSize < totalPrefix.length(); suffixSize++) {
if ( prefixSize + suffixSize == 0 )
continue;
for ( int indelSize = 1; indelSize < 50; indelSize++ ) {
final String prefix = totalPrefix.substring(0, prefixSize);
final String suffix = totalSuffix.substring(0, suffixSize);
final String insert = Utils.dupString("N", indelSize);
tests.add(new Object[]{prefix + suffix, prefix + insert + suffix, prefix.length() + "M" + indelSize + "I" + suffix.length() + "M"});
tests.add(new Object[]{prefix + insert + suffix, prefix + suffix, prefix.length() + "M" + indelSize + "D" + suffix.length() + "M"});
}
}
}
// larger indels with prefixes/suffixes
tests.add(new Object[]{"ACTGTTTTGAACATCAGTTATTTTAAACTTTTAAGTTGTTAGCACAGCAAAAGCAACAAAATTCTAAGTGCAGTAATCACTTTACTGCGTGGTCATATGAAATCAAGGCAATGTTATGAGTATTACTGGAAAGCTGGACAGAGTAACGGGAAAAGTGACTAAAACTATGC", "CCTGTTTTGAACATCAGTTATTTTAAACTTTTAAGTTGTTAGCACAGCAAAAGCAACAAAATTCTAAGTGCAGTAATCACTTTACTGCGTGGTCATATGAAATCAAGGCAATGTTATGAGTATTACTGGAAAGCTGGACAGAGTAACGGGAAAAGTGACT", "160M10D"});
tests.add(new Object[]{"LLLLLTATTAAGTAGTGCTCTATGTTGTCAACTAATTTATTTCCCATTTCAAACATTAGTTGACATGTTTTCATTTCTCTTTTGGAAGGAAACAACTAAATATGTTATCAATCCATCATTTACTTGTACAATAAATAAAGTTCTAAATCACTGCACAGTGTAAAATGGCAAATAGACTTCCCCATAACACAAAGCCATCCTGAAAAGTTTTGTTCATTTTAGAAGRRRRR", "LLLLLARRRRR", "5M219D6M"});
tests.add(new Object[]{"LLLLLTATTTTTTRRRRR", "LLLLLARRRRR", "5M7D6M"});
// systematic testing
for ( final int forwardMatches : Arrays.asList(0, 1, 5, 10)) {
for ( final int forwardMismatches : Arrays.asList(0, 1, 2)) {
for ( final int middleMatches : Arrays.asList(0, 1, 5, 10)) {
for ( final int delSize : Arrays.asList(0, 1, 2, 3 )) {
for ( final int insSize : Arrays.asList(0, 1, 2, 3 )) {
for ( final int reverseMismatches : Arrays.asList(0, 1, 2)) {
for ( final int reverseMatches : Arrays.asList(0, 1, 5, 10)) {
// if there is an insertion and deletion, they should cancel each other out (at least partially)
final int overlap = Math.min(delSize, insSize);
final int myDelSize = delSize - overlap;
final int myInsSize = insSize - overlap;
// this case is too difficult to create a CIGAR for because SW will (legitimately) prefer to switch the indel and mismatches
final int totalMismatches = forwardMismatches + reverseMismatches;
if ( (myDelSize > 0 || myInsSize > 0 ) && (totalMismatches >= myDelSize || totalMismatches >= myInsSize) )
continue;
final StringBuilder refBuilder = new StringBuilder();
final StringBuilder altBuilder = new StringBuilder();
final StringBuilder cigarBuilder = new StringBuilder();
refBuilder.append(Utils.dupString('A', forwardMatches + forwardMismatches + middleMatches));
altBuilder.append(Utils.dupString('A', forwardMatches));
altBuilder.append(Utils.dupString('C', forwardMismatches));
altBuilder.append(Utils.dupString('A', middleMatches));
cigarBuilder.append(forwardMatches + forwardMismatches + middleMatches);
cigarBuilder.append("M");
if ( myDelSize > 0 ) {
refBuilder.append(Utils.dupString('G', myDelSize));
cigarBuilder.append(myDelSize);
cigarBuilder.append("D");
}
if ( myInsSize > 0 ) {
altBuilder.append(Utils.dupString('T', myInsSize));
cigarBuilder.append(myInsSize);
cigarBuilder.append("I");
}
if ( overlap > 0 ) {
refBuilder.append(Utils.dupString('G', overlap));
altBuilder.append(Utils.dupString('T', overlap));
cigarBuilder.append(overlap);
cigarBuilder.append("M");
}
if ( delSize > 0 || insSize > 0 ) {
refBuilder.append(Utils.dupString('A', middleMatches));
altBuilder.append(Utils.dupString('A', middleMatches));
cigarBuilder.append(middleMatches);
cigarBuilder.append("M");
}
refBuilder.append(Utils.dupString('A', reverseMismatches + reverseMatches));
altBuilder.append(Utils.dupString('C', reverseMismatches));
altBuilder.append(Utils.dupString('A', reverseMatches));
cigarBuilder.append(reverseMismatches + reverseMatches);
cigarBuilder.append("M");
if ( refBuilder.length() > 0 && altBuilder.length() > 0 )
tests.add(new Object[]{refBuilder.toString(), altBuilder.toString(), cigarBuilder.toString()});
}
}
}
}
}
}
}
return tests.toArray(new Object[][]{});
}
@Test(dataProvider = "SWData", enabled = !DEBUG)
public void testSW(final String seq1, final String seq2, final String expectedCigar) {
final GlobalEdgeGreedySWPairwiseAlignment alignment = new GlobalEdgeGreedySWPairwiseAlignment(seq1.getBytes(), seq2.getBytes(), new Parameters(5.0, -5.0, -25.0, -1.0, 0.00001));
Assert.assertEquals(alignment.getCigar(), AlignmentUtils.consolidateCigar(TextCigarCodec.getSingleton().decode(expectedCigar)));
}
/**
* For debugging purposes only
*/
@Test(enabled = DEBUG)
public void testDebugging() {
final String ref = "A";
final String alt = "C";
final GlobalEdgeGreedySWPairwiseAlignment sw = new GlobalEdgeGreedySWPairwiseAlignment(ref.getBytes(), alt.getBytes(), new Parameters(5.0, -5.0, -25.0, -1.0, 0.00001));
Assert.assertEquals(sw.getCigar().toString(), "1M");
}
}