Followed Khalid's suggestion for packing libVectorLoglessCaching into

the jar file with Maven

.gitignore

@@ -3,6 +3,7 @@
 /*.bed
 *~
 /*.vcf
+/*.vcf.idx
 /*.txt
 /*.csh
 /.*
@@ -40,3 +41,38 @@ perf
 verify
 maven-metadata-local.xml
 dependency-reduced-pom.xml
+private/gatk-private/private/
+private/gatk-private/public/
+private/gatk-private/target/
+private/na12878kb-utils/public/
+private/na12878kb-utils/target/
+private/queue-private/private/
+private/queue-private/public/
+private/queue-private/target/
+private/scala/
+private/testdata
+protected/gatk-protected/private/
+protected/gatk-protected/public/
+protected/gatk-protected/target/
+public/external-example/target/
+public/gatk-framework/private/
+public/gatk-framework/public/
+public/gatk-framework/target/
+public/gatk-package/private/
+public/gatk-package/public/
+public/gatk-package/target/
+public/gatk-queue-extgen/public/
+public/gatk-queue-extgen/target/
+public/gsalib/public/
+public/gsalib/target/
+public/queue-framework/private/
+public/queue-framework/public/
+public/queue-framework/target/
+public/queue-package/private/
+public/queue-package/public/
+public/queue-package/target/
+public/scala/
+public/sting-utils/public/
+public/sting-utils/target/
+public/testdata
+target/

protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java

@@ -155,4 +155,8 @@ public class GraphBasedLikelihoodCalculationEngine implements LikelihoodCalculat
             }
         }
     }
+
+    @Override
+    public void close() {
+    }
 }

protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java

@@ -170,9 +170,10 @@ public class PairHMMLikelihoodCalculationEngine implements LikelihoodCalculation
     @Override
     public void close() {
         if ( likelihoodsStream != null ) likelihoodsStream.close();
-	pairHMMThreadLocal.get().close();
+        pairHMMThreadLocal.get().close();
     }
 
+
     private void writeDebugLikelihoods(final GATKSAMRecord processedRead, final Haplotype haplotype, final double log10l){
         if ( WRITE_LIKELIHOODS_TO_FILE ) {
             likelihoodsStream.printf("%s %s %s %s %s %s %f%n",

protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java

@@ -79,4 +79,9 @@ public class RandomLikelihoodCalculationEngine implements LikelihoodCalculationE
 
         return result;
     }
+
+    @Override
+    public void close() {
+    }
+
 }

protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/DebugJNILoglessPairHMM.java

@@ -55,7 +55,7 @@ import org.broadinstitute.sting.utils.haplotype.Haplotype;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.variant.variantcontext.Allele;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-
+import static org.broadinstitute.sting.utils.pairhmm.PairHMMModel.*;
 
 import java.util.List;
 import java.util.Map;
@@ -258,7 +258,7 @@ public class DebugJNILoglessPairHMM extends LoglessPairHMM {
                         relative_error = 0;
                     else
                         relative_error = Math.abs(abs_error/mLikelihoodArray[i]);
-                    if(abs_error > 1e-6 && relative_error > 1e-6)
+                    if(abs_error > 1e-5 && relative_error > 1e-5)
                     {
                         toDump = true;
                         break;

protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM.java

@@ -67,8 +67,6 @@ import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
 
-
-
 /**
  * Created with IntelliJ IDEA.
  * User: rpoplin, carneiro

public/c++/VectorPairHMM/Makefile

@@ -58,7 +58,7 @@ $(AVX_OBJECTS): CXXFLAGS=$(COMMON_COMPILATION_FLAGS) -xAVX
 $(SSE_OBJECTS): CXXFLAGS=$(COMMON_COMPILATION_FLAGS) -xSSE4.2
 OBJECTS=$(NO_VECTOR_OBJECTS) $(AVX_OBJECTS) $(SSE_OBJECTS)
 
-all: $(BIN) Sandbox.class
+all: $(BIN) Sandbox.class copied_lib
 
 -include $(addprefix $(DEPDIR)/,$(SOURCES:.cc=.d))
 
@@ -79,5 +79,11 @@ $(OBJECTS): %.o: %.cc
 Sandbox.class: Sandbox.java
 	javac Sandbox.java
 
+copied_lib: libVectorLoglessPairHMM.so
+ifdef OUTPUT_DIR
+	mkdir -p $(OUTPUT_DIR)
+	rsync -a libVectorLoglessPairHMM.so $(OUTPUT_DIR)/
+endif
+
 clean:
 	rm -rf $(BIN) *.o $(DEPDIR) *.class

public/c++/VectorPairHMM/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc

@@ -191,8 +191,6 @@ inline JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_Vector
   }
 }
 
-//#define DO_WARMUP
-//#define DO_REPEAT_PROFILING
 //Do compute over vector of testcase structs
 inline void compute_testcases(vector<testcase>& tc_array, unsigned numTestCases, double* likelihoodDoubleArray,
     unsigned maxNumThreadsToUse)

public/c++/VectorPairHMM/run.sh

@@ -8,7 +8,8 @@ then
 fi
 
 #-Djava.library.path is needed if you are using JNI_LOGLESS_CACHING, else not needed
-java  -Djava.library.path=${GSA_ROOT_DIR}/public/c++/VectorPairHMM -jar $GSA_ROOT_DIR/dist/GenomeAnalysisTK.jar   -T HaplotypeCaller \
+#java  -Djava.library.path=${GSA_ROOT_DIR}/public/c++/VectorPairHMM -jar $GSA_ROOT_DIR/target/GenomeAnalysisTK.jar   -T HaplotypeCaller \
+java -jar $GSA_ROOT_DIR/target/GenomeAnalysisTK.jar   -T HaplotypeCaller \
 --dbsnp /data/broad/samples/joint_variant_calling/dbSNP/00-All.vcf \
 -R /opt/Genomics/ohsu/dnapipeline/humanrefgenome/human_g1k_v37.fasta \
 -I /data/simulated/sim1M_pairs_final.bam \

public/c++/VectorPairHMM/utils.cc

@@ -306,15 +306,12 @@ uint64_t diff_time(struct timespec& prev_time)
   return (uint64_t)((curr_time.tv_sec-prev_time.tv_sec)*1000000000+(curr_time.tv_nsec-prev_time.tv_nsec));
 }
 
-#define DUMP_COMPUTE_VALUES 1
+
-//#define DO_REPEATS
 #ifdef USE_PAPI
 #include "papi.h"
 #define NUM_PAPI_COUNTERS 4
 #endif
 
-#define BATCH_SIZE  10000
-#define RUN_HYBRID
 void do_compute(char* filename, bool use_old_read_testcase, unsigned chunk_size, bool do_check)
 {
   FILE* fptr = 0;
@@ -370,7 +367,7 @@ void do_compute(char* filename, bool use_old_read_testcase, unsigned chunk_size,
 #endif
       get_time(&start_time);
 #pragma omp parallel for schedule(dynamic,chunk_size)  num_threads(12)
-#ifdef DO_REPEATS
+#ifdef DO_REPEAT_PROFILING
       for(unsigned z=0;z<10;++z)
 #endif
       {

public/c++/VectorPairHMM/utils.h

@@ -40,4 +40,11 @@ enum ProcessorCapabilitiesEnum
 uint64_t get_machine_capabilities();
 void initialize_function_pointers(uint64_t mask=ENABLE_ALL_HARDWARE_FEATURES);
 void do_compute(char* filename, bool use_old_read_testcase=true, unsigned chunk_size=10000, bool do_check=true);
+
+//#define DO_WARMUP
+//#define DO_REPEAT_PROFILING
+//#define DUMP_COMPUTE_VALUES 1
+#define BATCH_SIZE  10000
+#define RUN_HYBRID
+
 #endif

public/c++/pom.xml

@@ -0,0 +1,167 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <parent>
+        <groupId>org.broadinstitute.sting</groupId>
+        <artifactId>sting-root</artifactId>
+        <version>2.8-SNAPSHOT</version>
+        <relativePath>../../public/sting-root</relativePath>
+    </parent>
+
+    <artifactId>pairhmm-native</artifactId>
+    <packaging>pom</packaging>
+    <name>PairHMM Native Libraries</name>
+
+    <description>Builds a platform dependent version of pairhmm. During install, copies it into sting-utils.</description>
+
+    <properties>
+        <sourceEncoding>UTF-8</sourceEncoding>
+        <project.build.sourceEncoding>${sourceEncoding}</project.build.sourceEncoding>
+        <project.reporting.outputEncoding>${sourceEncoding}</project.reporting.outputEncoding>
+        <sting.basedir>${project.basedir}/../..</sting.basedir>
+        <sting-utils.basedir>${sting.basedir}/public/sting-utils</sting-utils.basedir>
+        <!-- Where to place the library in sting-utils -->
+        <pairhmm.resources.directory>${sting-utils.basedir}/src/main/resources/org/broadinstitute/sting/utils/pairhmm</pairhmm.resources.directory>
+
+        <!-- Per architecture properties, overriden in profiles below -->
+        <!--
+        NOTE: cxxflags is for currently only for -fPIC on linux.
+        For other architectures still have to pass something, until possibly
+        switching to command line arguments with exec-maven-plugin 1.3
+        http://jira.codehaus.org/browse/MEXEC-104
+        -->
+        <pairhmm.build.architecture>x86_64</pairhmm.build.architecture>
+        <pairhmm.build.extension>so</pairhmm.build.extension>
+        <pairhmm.build.cxxflags>-Wall</pairhmm.build.cxxflags>
+        <pairhmm.build.ldflags>-dynamiclib</pairhmm.build.ldflags>
+    </properties>
+    <build>
+        <plugins>
+            <!-- Print out the current architecture, to know which profile is being activated. -->
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-enforcer-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <goals>
+                            <goal>display-info</goal>
+                        </goals>
+                        <phase>validate</phase>
+                    </execution>
+                </executions>
+            </plugin>
+
+            <!-- Run make -->
+            <plugin>
+                <groupId>org.codehaus.mojo</groupId>
+                <artifactId>exec-maven-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <goals>
+                            <goal>exec</goal>
+                        </goals>
+                        <phase>compile</phase>
+                        <configuration>
+                            <executable>make</executable>
+                            <workingDirectory>VectorPairHMM</workingDirectory>
+                            <environmentVariables>
+                                <ARCHITECTURE>${pairhmm.build.architecture}</ARCHITECTURE>
+                                <LIB_EXT>${pairhmm.build.extension}</LIB_EXT>
+                                <CXXFLAGS>${pairhmm.build.cxxflags}</CXXFLAGS>
+                                <LDFLAGS>${pairhmm.build.ldflags}</LDFLAGS>
+                                <OUTPUT_DIR>${project.build.directory}</OUTPUT_DIR>
+                            </environmentVariables>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+
+            <!-- Don't actually install this artifact into the user's repo -->
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-install-plugin</artifactId>
+                <configuration>
+                    <skip>true</skip>
+                </configuration>
+            </plugin>
+
+            <!-- Copy the built library into sting-utils -->
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-resources-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>default-install</id>
+                        <goals>
+                            <goal>copy-resources</goal>
+                        </goals>
+                        <phase>install</phase>
+                        <configuration>
+                            <outputDirectory>${pairhmm.resources.directory}</outputDirectory>
+                            <resources>
+                                <resource>
+                                    <directory>${project.build.directory}</directory>
+                                    <includes>
+                                        <include>**/*</include>
+                                    </includes>
+                                </resource>
+                            </resources>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+
+            <!-- pom.xml cleanup, always sort according to the definitions in sting-root -->
+            <plugin>
+                <groupId>com.google.code.sortpom</groupId>
+                <artifactId>maven-sortpom-plugin</artifactId>
+                <configuration>
+                    <createBackupFile>false</createBackupFile>
+                    <predefinedSortOrder>custom_1</predefinedSortOrder>
+                    <lineSeparator>\n</lineSeparator>
+                    <encoding>${sourceEncoding}</encoding>
+                    <keepBlankLines>true</keepBlankLines>
+                    <sortDependencies>scope</sortDependencies>
+                    <nrOfIndentSpace>4</nrOfIndentSpace>
+                    <expandEmptyElements>false</expandEmptyElements>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+
+    <profiles>
+
+        <profile>
+            <id>mac_x86_64</id>
+            <activation>
+                <os>
+                    <family>mac</family>
+                    <arch>x86_64</arch>
+                </os>
+            </activation>
+            <properties>
+                <pairhmm.build.architecture>mac_x86_64</pairhmm.build.architecture>
+                <pairhmm.build.extension>jnilib</pairhmm.build.extension>
+                <pairhmm.build.ldflags>-dynamiclib</pairhmm.build.ldflags>
+            </properties>
+        </profile>
+
+        <profile>
+            <id>linux_x86_64</id>
+            <activation>
+                <os>
+                    <name>linux</name>
+                    <arch>amd64</arch>
+                </os>
+            </activation>
+            <properties>
+                <pairhmm.build.architecture>linux_x86_64</pairhmm.build.architecture>
+                <pairhmm.build.extension>jnilib</pairhmm.build.extension>
+                <pairhmm.build.cxxflags>-fPIC</pairhmm.build.cxxflags>
+                <pairhmm.build.ldflags>-shared</pairhmm.build.ldflags>
+            </properties>
+        </profile>
+
+    </profiles>
+</project>

public/sting-root/pom.xml

@@ -332,7 +332,11 @@
                     <artifactId>maven-assembly-plugin</artifactId>
                     <version>2.4</version>
                 </plugin>
-
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-enforcer-plugin</artifactId>
+                    <version>1.3.1</version>
+                </plugin>
                 <!--
                 surefire/failsafe configurations are global, even across poms
                 not directly aggregated, for example package-tests/pom.xml