From d36e639c92f7952045ae6920c498901849088591 Mon Sep 17 00:00:00 2001 From: Yossi Farjoun Date: Fri, 19 May 2017 23:54:31 -0400 Subject: [PATCH 1/2] -reved htsjdk to 2.9.1 --- build.gradle | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle b/build.gradle index 93f3cf651..a2da01c82 100644 --- a/build.gradle +++ b/build.gradle @@ -47,7 +47,7 @@ jacoco { toolVersion = "0.7.5.201505241946" } -final htsjdkVersion = System.getProperty('htsjdk.version', '2.9.0') +final htsjdkVersion = System.getProperty('htsjdk.version', '2.9.1') dependencies { compile 'com.google.guava:guava:15.0' From 004bf5eddc570f6718dd53235fafbae48697387e Mon Sep 17 00:00:00 2001 From: Yossi Farjoun Date: Fri, 26 May 2017 16:36:22 -0400 Subject: [PATCH 2/2] - fixed ambiguous constructor with null in test --- src/test/java/picard/util/FifoBufferTest.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/test/java/picard/util/FifoBufferTest.java b/src/test/java/picard/util/FifoBufferTest.java index 5f65bd68b..4f67877aa 100644 --- a/src/test/java/picard/util/FifoBufferTest.java +++ b/src/test/java/picard/util/FifoBufferTest.java @@ -57,8 +57,8 @@ public void test(final double megabytes) throws IOException { } // Run the input file through the FifoBuffer and back into another file - final Md5CalculatingInputStream in = new Md5CalculatingInputStream(new FileInputStream(inputFile), null); - final Md5CalculatingOutputStream out = new Md5CalculatingOutputStream(new FileOutputStream("/dev/null"), null); + final Md5CalculatingInputStream in = new Md5CalculatingInputStream(new FileInputStream(inputFile), (File)null); + final Md5CalculatingOutputStream out = new Md5CalculatingOutputStream(new FileOutputStream("/dev/null"), (File)null); final PrintStream outStream = new PrintStream(out); final FifoBuffer buffer = new FifoBuffer(in, outStream); buffer.BUFFER_SIZE = 128 * 1024 * 1024;