From 93fba06cb545d331df4d2ebb67579987e1581cf7 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Mon, 3 Oct 2011 09:30:10 -0700 Subject: [PATCH] Support for whitespace only lines --- .../org/broadinstitute/sting/gatk/samples/PedReader.java | 4 +++- .../sting/gatk/samples/PedReaderUnitTest.java | 8 ++++++++ 2 files changed, 11 insertions(+), 1 deletion(-) 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 72c5ec12c..648637b09 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/samples/PedReader.java +++ b/public/java/src/org/broadinstitute/sting/gatk/samples/PedReader.java @@ -166,7 +166,9 @@ public class PedReader { final List splits = new ArrayList(lines.size()); for ( final String line : lines ) { if ( line.startsWith(commentMarker)) continue; - String[] parts = line.split("\\s+"); + if ( line.trim().equals("") ) continue; + + final String[] parts = line.split("\\s+"); if ( parts.length != nExpectedFields ) throw new UserException.MalformedFile(reader.toString(), "Bad PED line " + lineNo + ": wrong number of fields"); 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 e68d169ea..16c1d178b 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/samples/PedReaderUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/samples/PedReaderUnitTest.java @@ -107,6 +107,14 @@ public class PedReaderUnitTest extends BaseTest { "fam1 s1 0 0 1 1", "fam2 s2 0 0 2 2")); + new PedReaderTest("multipleUnrelatedExtraLine", + Arrays.asList( + new Sample("s1", "fam1", null, null, Gender.MALE, Affection.UNAFFECTED), + new Sample("s2", "fam2", null, null, Gender.FEMALE, Affection.AFFECTED)), + String.format("%s%n%s%n %n", // note extra newlines and whitespace + "fam1 s1 0 0 1 1", + "fam2 s2 0 0 2 2")); + new PedReaderTest("explicitTrio", Arrays.asList( new Sample("kid", "fam1", "dad", "mom", Gender.MALE, Affection.AFFECTED),