From 0604ce55d1b4d418b30d3ece80b740fbb6a9e57d Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Mon, 3 Oct 2011 09:19:58 -0700
Subject: [PATCH] PedReader support for ; separated lines, not only newline

---
 .../sting/gatk/samples/PedReader.java              | 10 ++++++----
 .../sting/gatk/samples/PedReaderUnitTest.java      | 14 ++++++++++----
 2 files changed, 16 insertions(+), 8 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/samples/PedReader.java b/public/java/src/org/broadinstitute/sting/gatk/samples/PedReader.java
index 27b9181de..72c5ec12c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/samples/PedReader.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/samples/PedReader.java
@@ -30,10 +30,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
 
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.Reader;
+import java.io.*;
 import java.util.*;
 
 /**
@@ -146,6 +143,11 @@ public class PedReader {
         return parse(new FileReader(source), missingFields, sampleDB);
     }
 
+    public final List<Sample> parse(final String source, EnumSet<MissingPedField> missingFields, SampleDataSource sampleDB) {
+        logger.warn("Reading PED string: \"" + source + "\" with missing fields: " + missingFields);
+        return parse(new StringReader(source.replace(";", String.format("%n"))), missingFields, sampleDB);
+    }
+
     public final List<Sample> parse(Reader reader, EnumSet<MissingPedField> missingFields, SampleDataSource sampleDB) {
         final List<String> lines = new XReadLines(reader).readLines();
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/samples/PedReaderUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/samples/PedReaderUnitTest.java
index 35be45bc7..e68d169ea 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/samples/PedReaderUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/samples/PedReaderUnitTest.java
@@ -179,7 +179,7 @@ public class PedReaderUnitTest extends BaseTest {
         logger.warn("Test " + test);
         PedReader reader = new PedReader();
         SampleDataSource sampleDB = new SampleDataSource();
-        List<Sample> readSamples = reader.parse(new StringReader(myFileContents), missing, sampleDB);
+        List<Sample> readSamples = reader.parse(myFileContents, missing, sampleDB);
         Assert.assertEquals(new HashSet<Sample>(test.expectedSamples), new HashSet<Sample>(readSamples), "Parsed incorrect number of samples");
     }
 
@@ -188,11 +188,18 @@ public class PedReaderUnitTest extends BaseTest {
         runTest(test, test.fileContents, EnumSet.noneOf(PedReader.MissingPedField.class));
     }
 
-    @Test(enabled = true, dataProvider = "readerTest", dependsOnMethods = "testPedReader")
+    @Test(enabled = true, dataProvider = "readerTest")
     public void testPedReaderWithComments(PedReaderTest test) {
         runTest(test, String.format("#comment%n%s", test.fileContents), EnumSet.noneOf(PedReader.MissingPedField.class));
     }
 
+    @Test(enabled = true, dataProvider = "readerTest")
+    public void testPedReaderWithSemicolons(PedReaderTest test) {
+        runTest(test,
+                test.fileContents.replace(String.format("%n"), ";"),
+                EnumSet.noneOf(PedReader.MissingPedField.class));
+    }
+
     // -----------------------------------------------------------------
     // missing format field tests
     // -----------------------------------------------------------------
@@ -218,7 +225,6 @@ public class PedReaderUnitTest extends BaseTest {
 
     @DataProvider(name = "readerTestMissing")
     public Object[][] createPEDFilesWithMissing() {
-
         new PedReaderTestMissing("missingFam",
                 "fam1 kid dad mom 1 2",
                 EnumSet.of(PedReader.MissingPedField.NO_FAMILY_ID),
@@ -253,7 +259,7 @@ public class PedReaderUnitTest extends BaseTest {
         return PedReaderTestMissing.getTests(PedReaderTestMissing.class);
     }
 
-    @Test(enabled = true, dataProvider = "readerTestMissing", dependsOnMethods = "testPedReader")
+    @Test(enabled = true, dataProvider = "readerTestMissing")
     public void testPedReaderWithMissing(PedReaderTestMissing test) {
         final String contents = sliceContents(test.missingFields, test.fileContents);
         logger.warn("Test " + test);