Merge pull request #258 from samtools/cram3_rebase

Cram3 rebase
samtools · Jun 1, 2015 · 55af7bc · 55af7bc
2 parents 287b33f + d92460d
commit 55af7bc
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Showing 320 changed files with 35,901 additions and 14,566 deletions.
diff --git a/.idea/misc.xml b/.idea/misc.xml
diff --git a/build.xml b/build.xml
@@ -39,11 +39,7 @@
     <property name="javac.debug" value="true"/>
 
     <!-- Get GIT hash, if available, otherwise leave it blank.  -->
-    <exec executable="git" outputproperty="repository.revision" failifexecutionfails="true" errorproperty="">
-        <arg value="log"/>
-        <arg value="-1"/>
-        <arg value="--pretty=format:%H_%at"/>
-    </exec>
+
     <property name="repository.revision" value=""/>
     <property name="htsjdk-version" value="1.132"/>
     <property name="htsjdk-version-file" value="htsjdk.version.properties"/>

diff --git a/lib/apache-ant-1.8.2-bzip2.jar b/lib/apache-ant-1.8.2-bzip2.jar
diff --git a/lib/commons-compress-1.4.1.jar b/lib/commons-compress-1.4.1.jar
diff --git a/lib/xz-1.5.jar b/lib/xz-1.5.jar
diff --git a/src/java/htsjdk/samtools/BinaryTagCodec.java b/src/java/htsjdk/samtools/BinaryTagCodec.java
@@ -267,7 +267,7 @@ private void writeArray(final Object value, final boolean isUnsignedArray) {
      * @param length How many bytes in binaryRep are tag storage.
      */
     public static SAMBinaryTagAndValue readTags(final byte[] binaryRep, final int offset,
-                                         final int length, final ValidationStringency validationStringency) {
+                                                final int length, final ValidationStringency validationStringency) {
         final ByteBuffer byteBuffer = ByteBuffer.wrap(binaryRep, offset, length);
         byteBuffer.order(ByteOrder.LITTLE_ENDIAN);