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Merged
merged 2 commits into from
Sep 17, 2024
Merged

Qsv matefile #375

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2bd5457
fix(qsv): fix file naming of matefile tmp files
newellf Sep 17, 2024
d88d2e9
fix(qsv): adding forgotten test file
newellf Sep 17, 2024
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2 changes: 1 addition & 1 deletion qsv/src/org/qcmg/qsv/discordantpair/MatePairsReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -85,7 +85,7 @@ private void setUpFilesToRead() {
//contains ND or TD
if (s.contains(type)) {

String key = s.substring(0, s.indexOf("_"));
String key = s.substring(0, s.indexOf("_xxx_"));
String value = dirString + s;

File file = new File(value);
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2 changes: 1 addition & 1 deletion qsv/src/org/qcmg/qsv/discordantpair/MatePairsWriter.java
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Expand Up @@ -28,7 +28,7 @@ public MatePairsWriter(PairClassification zp, String matePairFilePath, String ty
this.zp = zp;
this.matePairs = new TreeMap<String, Map<String, MatePair>>();
this.dirToWrite = matePairFilePath + zp.getPairingClassification() + FILE_SEPARATOR;
this.fileName = "_" + type + "_" + zp.getPairingClassification();
this.fileName = "_xxx_" + type + "_" + zp.getPairingClassification();
this.pairType = pairType;
}

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24 changes: 12 additions & 12 deletions qsv/test/org/qcmg/qsv/discordantpair/FindDiscorantPairClustersMTTest.java
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Expand Up @@ -74,8 +74,8 @@ public void tearDown() {

@Test
public void testRunTumorWithGermline() throws InterruptedException, ExecutionException, IOException {
TestUtil.createTmpClusterFile(matePairDir.getAbsolutePath() + FILE_SEPARATOR, PairClassification.AAC, "chr7_test_TD_AAC");
TestUtil.createTmpClusterFile(matePairDir.getAbsolutePath() + FILE_SEPARATOR, PairClassification.AAC, "chr7_test_ND_AAC");
TestUtil.createTmpClusterFile(matePairDir.getAbsolutePath() + FILE_SEPARATOR, PairClassification.AAC, "chr7_xxx_test_TD_AAC");
TestUtil.createTmpClusterFile(matePairDir.getAbsolutePath() + FILE_SEPARATOR, PairClassification.AAC, "chr7_xxx_test_ND_AAC");
findReader = new MatePairsReader(PairGroup.valueOf("AAC"), matePairDir.getAbsolutePath() + FILE_SEPARATOR, "test", "TD");
compareReader = new MatePairsReader(PairGroup.valueOf("AAC"), matePairDir.getAbsolutePath() + FILE_SEPARATOR, "test", "ND");
//germline
Expand All @@ -92,7 +92,7 @@ public void testRunTumorWithGermline() throws InterruptedException, ExecutionExc

@Test
public void testRunTumorWithSomatic() throws InterruptedException, ExecutionException, IOException {
TestUtil.createTmpClusterFile(matePairDir.getAbsolutePath() + FILE_SEPARATOR, PairClassification.AAC, "chr7_test_TD_AAC");
TestUtil.createTmpClusterFile(matePairDir.getAbsolutePath() + FILE_SEPARATOR, PairClassification.AAC, "chr7_xxx_test_TD_AAC");
findReader = new MatePairsReader(PairGroup.valueOf("AAC"), matePairDir.getAbsolutePath() + FILE_SEPARATOR, "test", "TD");
compareReader = new MatePairsReader(PairGroup.valueOf("AAC"), matePairDir.getAbsolutePath() + FILE_SEPARATOR, "test", "ND");
//germline
Expand All @@ -108,7 +108,7 @@ public void testRunTumorWithSomatic() throws InterruptedException, ExecutionExce

@Test
public void testRunNormal() throws InterruptedException, ExecutionException, IOException {
TestUtil.createTmpClusterFile(matePairDir.getAbsolutePath() + FILE_SEPARATOR, PairClassification.AAC, "chr7_test_ND_AAC");
TestUtil.createTmpClusterFile(matePairDir.getAbsolutePath() + FILE_SEPARATOR, PairClassification.AAC, "chr7_xxx_test_ND_AAC");
findReader = new MatePairsReader(PairGroup.valueOf("AAC"), matePairDir.getAbsolutePath() + FILE_SEPARATOR, "test", "TD");
compareReader = new MatePairsReader(PairGroup.valueOf("AAC"), matePairDir.getAbsolutePath() + FILE_SEPARATOR, "test", "ND");
findClusters = new FindDiscordantPairClustersMT(PairGroup.AAC, countDownLatch, compareReader,
Expand All @@ -124,8 +124,8 @@ public void testRunNormal() throws InterruptedException, ExecutionException, IOE

@Test
public void testFindCxxClusters() throws Exception {
TestUtil.createTmpClusterFile(matePairDir.getAbsolutePath() + FILE_SEPARATOR, PairClassification.Cxx, "chr4-chr15_test_TD_AAC");
TestUtil.createTmpClusterFile(matePairDir.getAbsolutePath() + FILE_SEPARATOR, PairClassification.Cxx, "chr4-chr15_test_ND_AAC");
TestUtil.createTmpClusterFile(matePairDir.getAbsolutePath() + FILE_SEPARATOR, PairClassification.Cxx, "chr4-chr15_xxx_test_TD_AAC");
TestUtil.createTmpClusterFile(matePairDir.getAbsolutePath() + FILE_SEPARATOR, PairClassification.Cxx, "chr4-chr15_xxx_test_ND_AAC");

findReader = new MatePairsReader(PairGroup.valueOf("Cxx"), matePairDir.getAbsolutePath() + FILE_SEPARATOR, "test", "TD");
compareReader = new MatePairsReader(PairGroup.valueOf("Cxx"), matePairDir.getAbsolutePath() + FILE_SEPARATOR, "test", "ND");
Expand All @@ -143,10 +143,10 @@ public void testFindCxxClusters() throws Exception {

@Test
public void testFindClusters() throws Exception {
TestUtil.createTmpClusterFile(matePairDir.getAbsolutePath() + FILE_SEPARATOR, PairClassification.AAC, "chr7_test_TD_AAC");
TestUtil.createTmpClusterFile(matePairDir.getAbsolutePath() + FILE_SEPARATOR, PairClassification.AAC, "chr7_xxx_test_TD_AAC");
findClusters = new FindDiscordantPairClustersMT(PairGroup.AAC, countDownLatch, findReader, compareReader, tumor, normal, countReport, "", true);
findReader = new MatePairsReader(PairGroup.valueOf("AAC"), matePairDir.getAbsolutePath() + FILE_SEPARATOR, "test", "TD");
List<MatePair> pairs = TestUtil.readInMatePairs(new File(matePairDir.getAbsolutePath() + FILE_SEPARATOR + "AAC" + FILE_SEPARATOR + "chr7_test_TD_AAC"));
List<MatePair> pairs = TestUtil.readInMatePairs(new File(matePairDir.getAbsolutePath() + FILE_SEPARATOR + "AAC" + FILE_SEPARATOR + "chr7_xxx_test_TD_AAC"));

assertEquals(6, pairs.size());
List<DiscordantPairCluster> list = findClusters.findClusters(pairs);
Expand All @@ -157,17 +157,17 @@ public void testFindClusters() throws Exception {

@Test
public void testClassifyGermlineCluster() throws IOException, Exception {
TestUtil.createTmpClusterFile(matePairDir.getAbsolutePath() + FILE_SEPARATOR, PairClassification.AAC, "chr7_test_ND_AAC");
TestUtil.createTmpClusterFile(matePairDir.getAbsolutePath() + FILE_SEPARATOR, PairClassification.AAC, "chr7_xxx_test_ND_AAC");
findClusters = new FindDiscordantPairClustersMT(PairGroup.AAC, countDownLatch, findReader, compareReader, tumor, normal, countReport, "", true);
List<MatePair> pairs = TestUtil.readInMatePairs(new File(matePairDir.getAbsolutePath() + FILE_SEPARATOR + "AAC" + FILE_SEPARATOR + "chr7_test_ND_AAC"));
List<MatePair> pairs = TestUtil.readInMatePairs(new File(matePairDir.getAbsolutePath() + FILE_SEPARATOR + "AAC" + FILE_SEPARATOR + "chr7_xxx_test_ND_AAC"));
findClusters.classifyClusters(Arrays.asList(TestUtil.setupSolidCluster(PairGroup.AAC, "somatic", testFolder.getRoot(), "chr7", "chr7")), pairs);

assertEquals(1, findClusters.getClustersMap().get("germline").size());
}

@Test
public void testClassifySomaticCluster() throws IOException, Exception {
TestUtil.createTmpClusterFile(matePairDir.getAbsolutePath() + FILE_SEPARATOR, PairClassification.AAC, "chr7_test_ND_AAC");
TestUtil.createTmpClusterFile(matePairDir.getAbsolutePath() + FILE_SEPARATOR, PairClassification.AAC, "chr7_xxx_test_ND_AAC");
findClusters = new FindDiscordantPairClustersMT(PairGroup.AAC, countDownLatch, findReader, compareReader, tumor, normal, countReport, query, true);

findClusters.classifyClusters(Arrays.asList(TestUtil.setupSolidCluster(PairGroup.AAC, "somatic", testFolder.getRoot(), "chr7", "chr7")), Arrays.asList(new MatePair("722_126_792:20110412030837875,chr4,100,200,Cxx,129,false,722_126_792:20110412030837875,chr15,300,400,Cxx,65,false,F2F1\n")));
Expand All @@ -176,7 +176,7 @@ public void testClassifySomaticCluster() throws IOException, Exception {

@Test
public void testClassifyNormalGermlineCluster() throws IOException, Exception {
TestUtil.createTmpClusterFile(matePairDir.getAbsolutePath() + FILE_SEPARATOR, PairClassification.AAC, "chr7_test_ND_AAC");
TestUtil.createTmpClusterFile(matePairDir.getAbsolutePath() + FILE_SEPARATOR, PairClassification.AAC, "chr7_xxx_test_ND_AAC");
findClusters = new FindDiscordantPairClustersMT(PairGroup.AAC, countDownLatch, compareReader, findReader, normal, tumor, countReport, query, true);

findClusters.classifyClusters(Arrays.asList(TestUtil.setupSolidCluster(PairGroup.AAC, "somatic", testFolder.getRoot(), "chr7", "chr7")), Collections.emptyList());
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2 changes: 1 addition & 1 deletion qsv/test/org/qcmg/qsv/discordantpair/FindMatePairsMTTest.java
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Expand Up @@ -63,7 +63,7 @@ public void testSetUpPairClassificationWriters() throws Exception {

assertEquals(testFolder.getRoot().toString() + FILE_SEPARATOR + "matepair" + FILE_SEPARATOR + "AAC"
+ FILE_SEPARATOR, findMatePairs.getMatePairWritersMap().get(PairClassification.AAC).getDirToWrite());
assertEquals("_test_AAC", findMatePairs.getMatePairWritersMap().get(PairClassification.AAC).getFileName());
assertEquals("_xxx_test_AAC", findMatePairs.getMatePairWritersMap().get(PairClassification.AAC).getFileName());
}

@Test
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18 changes: 17 additions & 1 deletion qsv/test/org/qcmg/qsv/discordantpair/MatePairsReaderTest.java
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Expand Up @@ -21,7 +21,8 @@ public class MatePairsReaderTest {
private MatePairsReader reader;
private File matePairDir;
private static final String FILE_SEPERATOR = System.getProperty("file.separator");
private String fileName = "chr7_test_TD_AAC";
private String fileName = "chr7_xxx_test_TD_AAC";
private String fileNameChrUn = "chrUn_KI270438v1_xxx_test_TD_AAC";

@Rule
public TemporaryFolder testFolder = new TemporaryFolder();
Expand All @@ -30,11 +31,16 @@ public class MatePairsReaderTest {
public void setUp() throws IOException, QSVException {
matePairDir = testFolder.newFolder("matepair");
TestUtil.createTmpClusterFile(matePairDir.getAbsolutePath() + FILE_SEPERATOR, PairClassification.AAC, fileName);
TestUtil.createTmpClusterChrUnFile(matePairDir.getAbsolutePath() + FILE_SEPERATOR, PairClassification.AAC, fileNameChrUn);

reader = new MatePairsReader(PairGroup.AAC, matePairDir.getAbsolutePath() + FILE_SEPERATOR, fileName, "TD");
assertNotNull(reader.getFilesToRead());
assertNotNull(reader.getFilesToRead().get("chr7"));
assertEquals(1, reader.getFilesToRead().get("chr7").size());
assertEquals(fileName, reader.getFilesToRead().get("chr7").getFirst().getName());
assertNotNull(reader.getFilesToRead().get("chrUn_KI270438v1"));
assertEquals(1, reader.getFilesToRead().get("chrUn_KI270438v1").size());
assertEquals(fileNameChrUn, reader.getFilesToRead().get("chrUn_KI270438v1").getFirst().getName());
}

@After
Expand All @@ -55,4 +61,14 @@ public void testReadInPairs() throws Exception {
assertEquals("1789_1456_806:20110221052813657", list.get(0).getReadName());
}

@Test
public void testReadInChrUnPairs() throws Exception {
List<File> files = new ArrayList<File>();
files.add(new File(matePairDir.getAbsolutePath() + FILE_SEPERATOR + "AAC" + FILE_SEPERATOR + fileNameChrUn));
List<MatePair> list = reader.getMatePairsListByFiles(files, true);

assertEquals(4, list.size());
assertEquals("H3HHCALXX:2:1105:3188332:0:07262735-323a-489b-bd6d-10dcdc6726d0", list.get(0).getReadName());
}

}
2 changes: 1 addition & 1 deletion qsv/test/org/qcmg/qsv/discordantpair/MatePairsWriterTest.java
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Expand Up @@ -49,7 +49,7 @@ public void testAddNewMatePair() {
public void testWriteMatePairsToFile() throws IOException {
writer.addNewMatePair(matePairs.getFirst());
writer.writeMatePairsToFile();
File file = new File(mateDir, "chr7-1_TD_AAC");
File file = new File(mateDir, "chr7-1_xxx_TD_AAC");
assertTrue(file.exists());
assertTrue(file.length() > 100);
}
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28 changes: 26 additions & 2 deletions qsv/test/org/qcmg/qsv/util/TestUtil.java
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Expand Up @@ -643,9 +643,33 @@ public static String createTmpClusterFile(String dirName, PairClassification pc,

return outFile;
}

public static String createTmpClusterChrUnFile(String dirName, PairClassification pc, String fileName) throws IOException {

File testDir = new File(dirName + pc.getPairingClassification());
testDir.mkdir();
String outFile = testDir + FILE_SEPARATOR + fileName;

try (BufferedWriter writer = new BufferedWriter(new FileWriter(new File(outFile)))) {

if (pc.equals(PairClassification.AAC)) {
writeChrUnAACPairs(writer);
}
}

return outFile;
}

public static void writeAACPairs(BufferedWriter writer) throws IOException {

public static void writeChrUnAACPairs(BufferedWriter writer) throws IOException {
writer.write("H3HHCALXX:2:1105:3188332:0:07262735-323a-489b-bd6d-10dcdc6726d0,chrUn_KI270438v1,88809,88954,AAC,97,false,H3HHCALXX:2:1105:3188332:0:07262735-323a-489b-bd6d-10dcdc6726d0,chrUn_KI270438v1,92960,93119,AAC,145,true,F1R2" + NEWLINE);
writer.write("H3HHCALXX:2:1105:4467207:0:07262735-323a-489b-bd6d-10dcdc6726d0,chrUn_KI270438v1,88917,89066,AAC,97,false,H3HHCALXX:2:1105:4467207:0:07262735-323a-489b-bd6d-10dcdc6726d0,chrUn_KI270438v1,93030,93161,AAC,145,true,F1R2" + NEWLINE);
writer.write("H3HHCALXX:2:1108:478183:0:07262735-323a-489b-bd6d-10dcdc6726d0,chrUn_KI270438v1,102130,102212,AAC,161,false,H3HHCALXX:2:1108:478183:0:07262735-323a-489b-bd6d-10dcdc6726d0,chrUn_KI270438v1,108627,108768,AAC,81,true,F2R1" + NEWLINE);
writer.write("H3HHCALXX:2:1213:3573424:0:07262735-323a-489b-bd6d-10dcdc6726d0,chrUn_KI270438v1,100014,100163,AAC,161,false,H3HHCALXX:2:1213:3573424:0:07262735-323a-489b-bd6d-10dcdc6726d0,chrUn_KI270438v1,102786,102935,AAC,81,true,F2R1" + NEWLINE);

}

public static void writeAACPairs(BufferedWriter writer) throws IOException {

writer.write("254_166_1407:20110221052813657,chr7,140188379,140188428,AAC,129,false,254_166_1407:20110221052813657,chr7,140191044,140191093,AAC,65,false,F2F1," + NEWLINE);
writer.write("1789_1456_806:20110221052813657,chr7,140188227,140188276,AAC,129,false,1789_1456_806:20110221052813657,chr7,140191179,140191228,AAC,65,false,F2F1," + NEWLINE);
writer.write("515_451_1845:20110221052813657,chr7,140188449,140188498,AAC,129,false,515_451_1845:20110221052813657,chr7,140191238,140191287,AAC,65,false,F2F1" + NEWLINE);
Expand Down