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Merge branch 'master' of ssh://delangel@nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable

This commit is contained in:
Guillermo del Angel 2011-07-08 21:17:32 -04:00
parent 224574424e a3c9d9c3ff
commit 7fbc5987d0
6 changed files with 55 additions and 29 deletions
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70
build.xml
View File

@ -28,6 +28,7 @@
<property name="build.dir" value="build" />
<property name="dist.dir" value="dist" />
<property name="lib.dir" value="lib" />
<property name="external.dir" value="external" />
<property name="public.dir" value="public" />
<property name="private.dir" value="private" />
@ -44,11 +45,11 @@
<property name="queue-extensions.source.dir" value="${build.dir}/queue-extensions/src" />
<!-- Contracts for Java -->
<!-- uncomment out to enable building contracts -->
<property name="use.contracts" value="true" />
<!-- To disable, run with -Duse.contracts=false -->
<property name="use.contracts" value="true" />
<property name="java.contracts" value="${build.dir}/java/contracts" />
<property name="cofojaDir" value="settings/repository/com.google/"/>
<property name="cofoja.jar" value="${cofojaDir}/cofoja-1.0-20110609.jar"/>
<property name="contracts.version" value="1.0-20110609" />
<property name="cofoja.jar" value="${lib.dir}/cofoja-${contracts.version}.jar"/>
<!-- where to find the tribble distro -->
<property name="tribble.dir" value="tribble" />
@ -69,7 +70,7 @@
<property environment="env"/>
<property name="drmaa.jar" value="${env.SGE_ROOT}/lib/drmaa.jar" />
<property name="drmaa.jar" value="${env.SGE_ROOT}/${lib.dir}/drmaa.jar" />
<patternset id="java.source.pattern">
<include name="${java.public.source.dir}/**/*.java" />
@ -103,7 +104,7 @@
</patternset>
<path id="external.dependencies">
<fileset dir="lib">
<fileset dir="${lib.dir}">
<patternset refid="dependency.mask" />
</fileset>
</path>
@ -128,14 +129,14 @@
<!-- ivy properties -->
<property name="ivy.install.version" value="2.2.0"/>
<property name="ivy.home" value="${user.home}/.ant"/>
<property name="ivy.jar.dir" value="${ivy.home}/lib"/>
<property name="ivy.jar.dir" value="${ivy.home}/${lib.dir}"/>
<property name="ivy.jar.file" value="ivy-${ivy.install.version}.jar"/>
<property name="ivy.settings.dir" value="settings"/>
<property file="${ivy.settings.dir}/ivysettings.properties"/>
<mkdir dir="lib"/>
<mkdir dir="${lib.dir}"/>
<mkdir dir="${ivy.jar.dir}"/>
<copy file="${cofoja.jar}" toFile="lib/cofoja.jar"/>
<get src="http://repo1.maven.org/maven2/org/apache/ivy/ivy/${ivy.install.version}/${ivy.jar.file}"
dest="${ivy.jar.dir}/${ivy.jar.file}"
usetimestamp="true"/>
@ -147,7 +148,7 @@
</target>
<target name="init.gridengine" depends="init" if="include.gridengine">
<copy todir="lib" file="${drmaa.jar}"/>
<copy todir="${lib.dir}" file="${drmaa.jar}"/>
</target>
<target name="resolve" depends="init.resolve,init,init.gridengine"
@ -229,6 +230,10 @@
<equals arg1="${gatk.target}" arg2="private" casesensitive="false" />
</condition>
<condition property="include.contracts">
<equals arg1="${use.contracts}" arg2="true" />
</condition>
<!-- Create the build directory structure used by compile -->
<mkdir dir="${build.dir}"/>
<mkdir dir="${java.classes}"/>
@ -252,7 +257,7 @@
<target name="init.scala.compile" depends="resolve"
description="Initializes the scala ant tasks from scala-compiler.jar">
<path id="scala.classpath">
<fileset dir="lib">
<fileset dir="${lib.dir}">
<include name="scala-compiler-*.jar"/>
<include name="scala-library-*.jar"/>
</fileset>
@ -287,7 +292,7 @@
depends="gatk.compile.public.source,gatk.compile.private.source,gatk.compile.external.source"
description="compile the GATK source" />
<target name="gatk.contracts.public" depends="gatk.compile.source">
<target name="gatk.contracts.public" depends="gatk.compile.source" if="include.contracts">
<javac fork="true" memoryMaximumSize="512m" srcdir="${java.public.source.dir}" destdir="${java.contracts}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" >
<classpath>
<path refid="external.dependencies" />
@ -299,7 +304,16 @@
</javac>
</target>
<target name="gatk.contracts.private" depends="gatk.compile.source" if="include.private">
<target name="check.contracts.private" depends="gatk.contracts.public">
<condition property="include.contracts.private">
<and>
<isset property="include.contracts" />
<isset property="include.private" />
</and>
</condition>
</target>
<target name="gatk.contracts.private" depends="check.contracts.private" if="include.contracts.private">
<javac fork="true" memoryMaximumSize="512m" srcdir="${java.private.source.dir}" destdir="${java.contracts}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" >
<classpath>
<path refid="external.dependencies" />
@ -312,7 +326,7 @@
</target>
<target name="gatk.contracts" depends="gatk.contracts.public,gatk.contracts.private"
description="create GATK contracts" if="use.contracts" />
description="create GATK contracts" if="include.contracts" />
<target name="gatk.compile" depends="tribble,init,resolve,gatk.compile.source,gatk.contracts" />
@ -452,7 +466,7 @@
<target name="init.jar" depends="sting.compile,extracthelp">
<mkdir dir="${dist.dir}"/>
<copy todir="${dist.dir}">
<fileset dir="lib" includes="*.jar"/>
<fileset dir="${lib.dir}" includes="*.jar"/>
</copy>
</target>
@ -663,7 +677,7 @@
<path refid="external.dependencies" />
<pathelement location="${java.classes}"/>
<pathelement location="${java.contracts}"/>
<pathelement location="lib/testng-5.14.1.jar"/>
<pathelement location="${lib.dir}/testng-5.14.1.jar"/>
</classpath>
<compilerarg value="-proc:none"/>
<!--
@ -687,7 +701,7 @@
<path refid="scala.dependencies"/>
<pathelement location="${scala.test.classes}"/>
<pathelement location="${java.test.classes}"/>
<pathelement location="lib/testng-5.14.1.jar"/>
<pathelement location="${lib.dir}/testng-5.14.1.jar"/>
</classpath>
</scalac>
</target>
@ -727,9 +741,13 @@
<equals arg1="${pipeline.run}" arg2="$${pipeline.run}" />
</condition>
<condition property="cofoja.jvm.args" value="-javaagent:${cofoja.jar} -Dcom.google.java.contract.log.contract=false" else="">
<isset property="include.contracts" />
</condition>
<mkdir dir="${report}/@{testtype}"/>
<echo message="Sting: Running @{testtype} test cases!"/>
<taskdef resource="testngtasks" classpath="lib/testng-5.14.1.jar"/>
<taskdef resource="testngtasks" classpath="${lib.dir}/testng-5.14.1.jar"/>
<testng outputDir="${report}/@{testtype}"
haltOnFailure="false" failureProperty="test.failure"
verbose="2"
@ -740,9 +758,7 @@
<jvmarg value="-Djava.awt.headless=true" />
<jvmarg value="-Dpipeline.run=${pipeline.run}" />
<jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" />
<!-- needs to be if -->
<!--jvmarg value="-javaagent:lib/cofoja.jar"/-->
<!--jvmarg value="-Dcom.google.java.contract.log.contract=false"/-->
<jvmarg line="${cofoja.jvm.args}"/>
<!-- <jvmarg value="-Xdebug"/> -->
<!-- <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> -->
<classpath>
@ -820,7 +836,7 @@
<!-- copy the compiled library -->
<target name="tribble.compile.copy" description="Copies the compiled tribble library" depends="tribble.compile" if="tribble.compile.exists">
<copy todir="lib">
<copy todir="${lib.dir}">
<fileset dir="${tribble.dir}/dist" includes="*.jar"/>
</copy>
</target>
@ -828,7 +844,7 @@
<!-- copy the precompiled library -->
<target name="tribble.library.copy" description="Copies the precompiled tribble library" depends="tribble.init" unless="tribble.compile.exists">
<echo message="Copying the Tribble Library..."/>
<copy todir="lib">
<copy todir="${lib.dir}">
<fileset dir="settings/repository/org.broad" includes="tribble*.jar"/>
</copy>
</target>
@ -921,8 +937,8 @@
<pathconvert property="required.picard.jars" pathsep=":">
<fileset dir="${basedir}">
<include name="staging" />
<include name="lib/picard-*.*.*.jar" />
<include name="lib/sam-*.jar" />
<include name="${lib.dir}/picard-*.*.*.jar" />
<include name="${lib.dir}/sam-*.jar" />
</fileset>
</pathconvert>
<echo message="required.picard.jars=${required.picard.jars}" />
@ -944,7 +960,7 @@
<!-- Find bug tasks -->
<!-- ******************************************************************************** -->
<path id="findbugs.classpath">
<fileset dir="lib" erroronmissingdir="true" includes="*.jar"/>
<fileset dir="${lib.dir}" erroronmissingdir="true" includes="*.jar"/>
</path>
<target name="findbugs" depends="dist">
<antcall target ="resolve">
@ -969,7 +985,7 @@
<target name="clean" description="clean up" depends="tribble.clean,clean.javadoc">
<delete dir="out"/>
<delete dir="${build.dir}"/>
<delete dir="lib"/>
<delete dir="${lib.dir}"/>
<delete dir="staging"/>
<delete dir="${dist.dir}"/>
<delete dir="pipelinetests"/>

4
ivy.xml
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@ -60,6 +60,10 @@
<dependency org="net.sourceforge.findbugs" name="jsr305" rev="1.3.2" conf="test"/>
<dependency org="com.google.code.caliper" name="caliper" rev="1.0-SNAPSHOT" conf="test" />
<!-- Contracts for Java and dependencies -->
<dependency org="com.google.code.cofoja" name="cofoja" rev="1.0-20110609" />
<dependency org="asm" name="asm-all" rev="3.3.1" />
<!-- POI, for reading pipeline files -->
<dependency org="org.apache.poi" name="poi" rev="3.8-beta3" />
<dependency org="org.apache.poi" name="poi-ooxml" rev="3.8-beta3" />

6
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
View File

@ -225,7 +225,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
loc = pos + alleles.get(0).length() - 1;
} else if ( !isSingleNucleotideEvent(alleles) ) {
ArrayList<Allele> newAlleles = new ArrayList<Allele>();
loc = clipAlleles(pos, ref, alleles, newAlleles);
loc = clipAlleles(pos, ref, alleles, newAlleles, lineNo);
alleles = newAlleles;
}
@ -504,7 +504,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
* @param clippedAlleles output list of clipped alleles
* @return a list of alleles, clipped to the reference
*/
protected static long clipAlleles(long position, String ref, List<Allele> unclippedAlleles, List<Allele> clippedAlleles) {
protected static long clipAlleles(long position, String ref, List<Allele> unclippedAlleles, List<Allele> clippedAlleles, int lineNo) {
// Note that the computation of forward clipping here is meant only to see whether there is a common
// base to all alleles, and to correctly compute reverse clipping,
@ -522,6 +522,8 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
}
if (a.length() - reverseClipped <= forwardClipping || a.length() - forwardClipping == 0)
clipping = false;
else if (ref.length() == reverseClipped)
generateException("bad alleles encountered", lineNo);
else if (a.getBases()[a.length()-reverseClipped-1] != ref.getBytes()[ref.length()-reverseClipped-1])
clipping = false;
}

1
settings/ivysettings.xml
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@ -25,5 +25,6 @@
<module organisation="javax.activation" resolver="java.net" />
<module organisation="net.java.dev.jna" resolver="maven2-repository.dev.java.net" />
<module organisation="com.google.code.caliper" resolver="projects" />
<module organisation="com.google.code.cofoja" resolver="projects" />
</modules>
</ivysettings>

0
settings/repository/com.google/cofoja-1.0-20110609.jar → settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.jar
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3
settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.xml 100644
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@ -0,0 +1,3 @@
<ivy-module version="1.0">
<info organisation="com.google.code.cofoja" module="cofoja" revision="1.0-20110609" status="integration" publication="20110609114800" />
</ivy-module>