First pass at picard gradle build file.

.gitignore

@@ -13,4 +13,5 @@ htsjdk
 target
 report
 jacoco.data
-
+.gradle
+build

.travis.yml

@@ -1,11 +1,15 @@
 language: java
+before_cache:
+  - rm -f $HOME/.gradle/caches/modules-2/modules-2.lock
+cache:
+  directories:
+    - $HOME/.gradle/caches/
+    - $HOME/.gradle/wrapper/
+    - $HOME/.m2
 jdk:
   - oraclejdk8
 before_install:
+  - wget -q -O - https://dl.google.com/linux/linux_signing_key.pub | sudo apt-key add -
   - sudo apt-get -qq update
   - sudo apt-get install -y --no-install-recommends r-base-dev r-recommended qpdf
-  - sed -i -e 's_git@github.com:_https://github.com/_' build.xml
-script:
-  - ant -lib lib/ant clone-htsjdk 
-  - ant
-  - ant test
+script: ./gradlew jacocoTestReport

Picard-public.fbp

@@ -1,18 +0,0 @@
-<Project filename="&lt;&lt;unnamed project&gt;&gt;" projectName="Picard-public">
-  <Jar>/Users/alecw/Documents/Picard/Picard-public/classes</Jar>
-  <SrcDir>/Users/alecw/Documents/Picard/Picard-public/src/java</SrcDir>
-  <SuppressionFilter>
-    <LastVersion value="-1" relOp="NEQ"/>
-    <Designation designation="NOT_A_BUG"/>
-    <And>
-      <Priority value="2"/>
-      <Bug category="MALICIOUS_CODE"/>
-      <Bug code="EI"/>
-    </And>
-    <And>
-      <Priority value="2"/>
-      <Bug category="MALICIOUS_CODE"/>
-      <Bug code="EI2"/>
-    </And>
-  </SuppressionFilter>
-</Project>

Picard-public.iml

@@ -1,54 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module relativePaths="true" type="JAVA_MODULE" version="4">
-  <component name="FacetManager">
-    <facet type="Python" name="Python">
-      <configuration sdkName="" />
-    </facet>
-  </component>
-  <component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8" inherit-compiler-output="false">
-    <output url="file://$MODULE_DIR$/intellij.classes" />
-    <output-test url="file://$MODULE_DIR$/intellij.testclasses" />
-    <exclude-output />
-    <content url="file://$MODULE_DIR$">
-      <sourceFolder url="file://$MODULE_DIR$/src/java" isTestSource="false" />
-      <sourceFolder url="file://$MODULE_DIR$/src/tests/java" isTestSource="true" />
-      <sourceFolder url="file://$MODULE_DIR$/htsjdk/src/java" isTestSource="false" />
-      <sourceFolder url="file://$MODULE_DIR$/htsjdk/src/tests/java" isTestSource="true" />
-      <excludeFolder url="file://$MODULE_DIR$/.command_tmp" />
-      <excludeFolder url="file://$MODULE_DIR$/classes" />
-    </content>
-    <orderEntry type="inheritedJdk" />
-    <orderEntry type="sourceFolder" forTests="false" />
-    <orderEntry type="module-library">
-      <library>
-        <CLASSES>
-          <root url="file://$MODULE_DIR$/htsjdk/lib" />
-        </CLASSES>
-        <JAVADOC />
-        <SOURCES />
-        <jarDirectory url="file://$MODULE_DIR$/htsjdk/lib" recursive="false" />
-      </library>
-    </orderEntry>
-    <orderEntry type="module-library">
-      <library>
-        <CLASSES>
-          <root url="file://$MODULE_DIR$/htsjdk/lib/cofoja" />
-        </CLASSES>
-        <JAVADOC />
-        <SOURCES />
-        <jarDirectory url="file://$MODULE_DIR$/htsjdk/lib/cofoja" recursive="false" />
-      </library>
-    </orderEntry>
-    <orderEntry type="module-library">
-      <library>
-        <CLASSES>
-          <root url="file://$MODULE_DIR$/htsjdk/lib/testng" />
-        </CLASSES>
-        <JAVADOC />
-        <SOURCES />
-        <jarDirectory url="file://$MODULE_DIR$/htsjdk/lib/testng" recursive="false" />
-      </library>
-    </orderEntry>
-    <orderEntry type="library" name="guava-15.0" level="project" />
-  </component>
-</module>