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Use multiplatform UMCCR gatk-bwamem-jni instead of org.broadinstitute.hellbender.* #691

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Use multiplatform UMCCR gatk-bwamem-jni instead of org.broadinstitute.hellbender.* #691

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e7511ca
Use multiplatform UMCCR gatk-bwamem-jni instead of org.broadinstitute…
brainstorm Apr 14, 2025
5aa91e6
Remove BwaUtils helper class, not needed anymore since binaries ship …
brainstorm Apr 14, 2025
980b33b
Merge branch 'master' into umccr_gatk_bwamem_jni
brainstorm Jun 26, 2025
5daed49
Merge branch 'master' into umccr_gatk_bwamem_jni
brainstorm Oct 29, 2025
24a104a
Merge branch 'master' into umccr_gatk_bwamem_jni
brainstorm Dec 5, 2025
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4 changes: 2 additions & 2 deletions bam-tools/pom.xml
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Expand Up @@ -36,9 +36,9 @@
<version>7.0.0</version>
</dependency>
<dependency>
<groupId>org.broadinstitute</groupId>
<groupId>org.umccr.java</groupId>
<artifactId>gatk-bwamem-jni</artifactId>
<version>1.0.5</version>
<version>1.2.0</version>
</dependency>

<dependency>
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2 changes: 1 addition & 1 deletion bam-tools/src/main/java/com/hartwig/hmftools/bamtools/remapper/AlignmentsList.java
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Expand Up @@ -3,7 +3,7 @@
import java.util.List;
import java.util.stream.Stream;

import org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment;
import org.umccr.java.hellbender.utils.bwa.BwaMemAlignment;

import htsjdk.samtools.SAMFlag;

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6 changes: 1 addition & 5 deletions bam-tools/src/main/java/com/hartwig/hmftools/bamtools/remapper/AltContigRemapperConfig.java
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Expand Up @@ -2,8 +2,6 @@

import static com.hartwig.hmftools.bamtools.common.CommonUtils.BT_LOGGER;
import static com.hartwig.hmftools.common.bamops.BamToolName.BAMTOOL_PATH;
import static com.hartwig.hmftools.common.bwa.BwaUtils.LIBBWA_PATH;
import static com.hartwig.hmftools.common.bwa.BwaUtils.loadAlignerLibrary;
import static com.hartwig.hmftools.common.genome.refgenome.RefGenomeSource.REF_GENOME;
import static com.hartwig.hmftools.common.genome.refgenome.RefGenomeSource.addRefGenomeFile;
import static com.hartwig.hmftools.common.perf.TaskExecutor.THREADS;
Expand All @@ -15,7 +13,7 @@
import com.hartwig.hmftools.common.genome.refgenome.RefGenomeVersion;
import com.hartwig.hmftools.common.utils.config.ConfigBuilder;

import org.broadinstitute.hellbender.utils.bwa.BwaMemIndex;
import org.umccr.java.hellbender.utils.bwa.BwaMemIndex;

import htsjdk.samtools.SAMFileHeader;

Expand Down Expand Up @@ -49,7 +47,6 @@ public AltContigRemapperConfig(final ConfigBuilder configBuilder)
OrigBamFile != null, OutputFile != null);
System.exit(1);
}
loadAlignerLibrary(null);

RefGenVersion = BamUtils.deriveRefGenomeVersion(OrigBamFile);

Expand All @@ -62,7 +59,6 @@ public static void addConfig(final ConfigBuilder configBuilder)
configBuilder.addConfigItem(OUTPUT_FILE, true, "Output comparison file");
configBuilder.addPath(ORIG_BAM_FILE, true, "Original BAM file");
configBuilder.addFlag(HLA_REGIONS_ONLY, "Slice HLA regions only");
configBuilder.addPath(LIBBWA_PATH, false, "Path to BWA library");
configBuilder.addPath(BAMTOOL_PATH, false, "Path to BWA library");

addRefGenomeFile(configBuilder, true);
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2 changes: 1 addition & 1 deletion bam-tools/src/main/java/com/hartwig/hmftools/bamtools/remapper/BwaHlaRecordPairAligner.java
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Expand Up @@ -13,7 +13,7 @@
import com.hartwig.hmftools.common.genome.refgenome.RefGenomeVersion;

import org.apache.commons.lang3.tuple.ImmutablePair;
import org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment;
import org.umccr.java.hellbender.utils.bwa.BwaMemAlignment;

import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMRecord;
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6 changes: 3 additions & 3 deletions bam-tools/src/main/java/com/hartwig/hmftools/bamtools/remapper/BwaPairAligner.java
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Expand Up @@ -3,9 +3,9 @@
import java.util.List;

import org.apache.commons.lang3.tuple.ImmutablePair;
import org.broadinstitute.hellbender.utils.bwa.BwaMemAligner;
import org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment;
import org.broadinstitute.hellbender.utils.bwa.BwaMemIndex;
import org.umccr.java.hellbender.utils.bwa.BwaMemAligner;
import org.umccr.java.hellbender.utils.bwa.BwaMemAlignment;
import org.umccr.java.hellbender.utils.bwa.BwaMemIndex;

public class BwaPairAligner implements PairAligner
{
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6 changes: 3 additions & 3 deletions bam-tools/src/main/java/com/hartwig/hmftools/bamtools/remapper/BwaSingleRecordAligner.java
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Expand Up @@ -7,9 +7,9 @@
import com.hartwig.hmftools.common.codon.Nucleotides;
import com.hartwig.hmftools.common.utils.Arrays;

import org.broadinstitute.hellbender.utils.bwa.BwaMemAligner;
import org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment;
import org.broadinstitute.hellbender.utils.bwa.BwaMemIndex;
import org.umccr.java.hellbender.utils.bwa.BwaMemAligner;
import org.umccr.java.hellbender.utils.bwa.BwaMemAlignment;
import org.umccr.java.hellbender.utils.bwa.BwaMemIndex;

import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMRecord;
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2 changes: 1 addition & 1 deletion bam-tools/src/main/java/com/hartwig/hmftools/bamtools/remapper/HlaAlignment.java
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Expand Up @@ -12,7 +12,7 @@
import com.hartwig.hmftools.common.region.ChrBaseRegion;
import com.hartwig.hmftools.common.utils.Arrays;

import org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment;
import org.umccr.java.hellbender.utils.bwa.BwaMemAlignment;

import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMFlag;
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2 changes: 1 addition & 1 deletion bam-tools/src/main/java/com/hartwig/hmftools/bamtools/remapper/PairAligner.java
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Expand Up @@ -3,7 +3,7 @@
import java.util.List;

import org.apache.commons.lang3.tuple.ImmutablePair;
import org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment;
import org.umccr.java.hellbender.utils.bwa.BwaMemAlignment;

public interface PairAligner
{
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2 changes: 1 addition & 1 deletion ...ols/src/test/java/com/hartwig/hmftools/bamtools/remapper/BwaHlaRecordPairAlignerTest.java
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Expand Up @@ -17,7 +17,7 @@
import com.hartwig.hmftools.common.test.ReadIdGenerator;

import org.apache.commons.lang3.tuple.ImmutablePair;
import org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment;
import org.umccr.java.hellbender.utils.bwa.BwaMemAlignment;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
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2 changes: 1 addition & 1 deletion bam-tools/src/test/java/com/hartwig/hmftools/bamtools/remapper/HlaAligner.java
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Expand Up @@ -10,7 +10,7 @@
import com.hartwig.hmftools.common.codon.Nucleotides;

import org.apache.commons.lang3.tuple.ImmutablePair;
import org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment;
import org.umccr.java.hellbender.utils.bwa.BwaMemAlignment;
import org.junit.Assert;

import htsjdk.samtools.SAMRecord;
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2 changes: 1 addition & 1 deletion bam-tools/src/test/java/com/hartwig/hmftools/bamtools/remapper/HlaAlignmentPairTest.java
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Expand Up @@ -2,7 +2,7 @@

import static org.junit.Assert.assertEquals;

import org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment;
import org.umccr.java.hellbender.utils.bwa.BwaMemAlignment;
import org.junit.Test;

public class HlaAlignmentPairTest extends RemapperTestBase
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2 changes: 1 addition & 1 deletion bam-tools/src/test/java/com/hartwig/hmftools/bamtools/remapper/HlaAlignmentTest.java
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Expand Up @@ -4,7 +4,7 @@
import com.hartwig.hmftools.common.codon.Nucleotides;
import com.hartwig.hmftools.common.utils.Arrays;

import org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment;
import org.umccr.java.hellbender.utils.bwa.BwaMemAlignment;
import org.junit.Assert;
import org.junit.Test;

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2 changes: 1 addition & 1 deletion bam-tools/src/test/java/com/hartwig/hmftools/bamtools/remapper/RemapperTestBase.java
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Expand Up @@ -9,7 +9,7 @@
import java.util.List;
import java.util.Objects;

import org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment;
import org.umccr.java.hellbender.utils.bwa.BwaMemAlignment;
import org.junit.Assert;

import htsjdk.samtools.SAMFileHeader;
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4 changes: 2 additions & 2 deletions esvee/pom.xml
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Expand Up @@ -24,9 +24,9 @@
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.broadinstitute</groupId>
<groupId>org.umccr.java</groupId>
<artifactId>gatk-bwamem-jni</artifactId>
<version>1.0.5</version>
<version>1.2.0</version>
</dependency>

<dependency>
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8 changes: 2 additions & 6 deletions esvee/src/main/java/com/hartwig/hmftools/esvee/assembly/AssemblyConfig.java
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@@ -1,9 +1,6 @@
package com.hartwig.hmftools.esvee.assembly;

import static com.hartwig.hmftools.common.bamops.BamToolName.BAMTOOL_PATH;
import static com.hartwig.hmftools.common.bwa.BwaUtils.BWA_LIB_PATH;
import static com.hartwig.hmftools.common.bwa.BwaUtils.BWA_LIB_PATH_DESC;
import static com.hartwig.hmftools.common.bwa.BwaUtils.loadAlignerLibrary;
import static com.hartwig.hmftools.common.genome.refgenome.RefGenomeSource.REF_GENOME;
import static com.hartwig.hmftools.common.genome.refgenome.RefGenomeSource.addRefGenomeConfig;
import static com.hartwig.hmftools.common.genome.refgenome.RefGenomeSource.loadRefGenome;
Expand Down Expand Up @@ -269,8 +266,6 @@ else if(!asSubRoutine)

WriteTypes = WriteType.parseAssemblyTypes(configBuilder.getValue(WRITE_TYPES));

loadAlignerLibrary(configBuilder.getValue(BWA_LIB_PATH));

setSequencingType(configBuilder);
setSeqTechSpecifics();

Expand Down Expand Up @@ -377,7 +372,8 @@ public static void registerConfig(final ConfigBuilder configBuilder)
addRefGenomeConfig(configBuilder, true);
configBuilder.addPath(DECOY_GENOME, false, "Decoy genome image file");

configBuilder.addPath(BWA_LIB_PATH, false, BWA_LIB_PATH_DESC);
if(!configBuilder.isRegistered(WRITE_TYPES))
configBuilder.addConfigItem(WRITE_TYPES, false, enumValueSelectionAsStr(WriteType.values(), "Write types"));

configBuilder.addConfigItem(LOG_READ_IDS, false, LOG_READ_IDS_DESC);
configBuilder.addConfigItem(
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2 changes: 1 addition & 1 deletion esvee/src/main/java/com/hartwig/hmftools/esvee/assembly/alignment/AlignData.java
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Expand Up @@ -40,7 +40,7 @@
import com.hartwig.hmftools.common.region.ChrBaseRegion;
import com.hartwig.hmftools.esvee.assembly.types.RepeatInfo;

import org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment;
import org.umccr.java.hellbender.utils.bwa.BwaMemAlignment;

import htsjdk.samtools.CigarElement;

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2 changes: 1 addition & 1 deletion esvee/src/main/java/com/hartwig/hmftools/esvee/assembly/alignment/Aligner.java
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Expand Up @@ -2,7 +2,7 @@

import java.util.List;

import org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment;
import org.umccr.java.hellbender.utils.bwa.BwaMemAlignment;

public interface Aligner
{
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5 changes: 5 additions & 0 deletions esvee/src/main/java/com/hartwig/hmftools/esvee/assembly/alignment/Alignment.java
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Expand Up @@ -22,6 +22,11 @@
import com.hartwig.hmftools.common.perf.TaskQueue;
import com.hartwig.hmftools.esvee.common.WriteType;

import org.umccr.java.hellbender.utils.bwa.BwaMemAlignment;
import org.checkerframework.checker.units.qual.A;

import htsjdk.samtools.CigarOperator;

public class Alignment
{
private final AssemblyConfig mConfig;
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6 changes: 3 additions & 3 deletions esvee/src/main/java/com/hartwig/hmftools/esvee/assembly/alignment/AlignmentChecker.java
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Expand Up @@ -18,9 +18,9 @@
import com.hartwig.hmftools.esvee.assembly.types.JunctionAssembly;
import com.hartwig.hmftools.esvee.common.WriteType;

import org.broadinstitute.hellbender.utils.bwa.BwaMemAligner;
import org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment;
import org.broadinstitute.hellbender.utils.bwa.BwaMemIndex;
import org.umccr.java.hellbender.utils.bwa.BwaMemAligner;
import org.umccr.java.hellbender.utils.bwa.BwaMemAlignment;
import org.umccr.java.hellbender.utils.bwa.BwaMemIndex;

import htsjdk.samtools.Cigar;

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6 changes: 3 additions & 3 deletions esvee/src/main/java/com/hartwig/hmftools/esvee/assembly/alignment/BwaAligner.java
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Expand Up @@ -10,9 +10,9 @@
import java.util.Collections;
import java.util.List;

import org.broadinstitute.hellbender.utils.bwa.BwaMemAligner;
import org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment;
import org.broadinstitute.hellbender.utils.bwa.BwaMemIndex;
import org.umccr.java.hellbender.utils.bwa.BwaMemAligner;
import org.umccr.java.hellbender.utils.bwa.BwaMemAlignment;
import org.umccr.java.hellbender.utils.bwa.BwaMemIndex;

public class BwaAligner implements Aligner
{
Expand Down
4 changes: 2 additions & 2 deletions gene-utils/pom.xml
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Expand Up @@ -23,9 +23,9 @@
<artifactId>jooq</artifactId>
</dependency>
<dependency>
<groupId>org.broadinstitute</groupId>
<groupId>org.umccr.java</groupId>
<artifactId>gatk-bwamem-jni</artifactId>
<version>1.0.5</version>
<version>1.2.0</version>
</dependency>

<dependency>
Expand Down
9 changes: 3 additions & 6 deletions gene-utils/src/main/java/com/hartwig/hmftools/geneutils/mapping/BwaSeqTester.java
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@@ -1,8 +1,6 @@
package com.hartwig.hmftools.geneutils.mapping;

import static com.hartwig.hmftools.common.bam.CigarUtils.calcCigarAlignedLength;
import static com.hartwig.hmftools.common.bwa.BwaUtils.BWA_LIB_PATH;
import static com.hartwig.hmftools.common.bwa.BwaUtils.loadAlignerLibrary;
import static com.hartwig.hmftools.common.genome.refgenome.RefGenomeSource.REF_GENOME;
import static com.hartwig.hmftools.common.perf.PerformanceCounter.runTimeMinsStr;
import static com.hartwig.hmftools.common.utils.file.FileDelimiters.TSV_DELIM;
Expand All @@ -21,9 +19,9 @@
import com.hartwig.hmftools.common.region.ChrBaseRegion;
import com.hartwig.hmftools.common.utils.config.ConfigBuilder;

import org.broadinstitute.hellbender.utils.bwa.BwaMemAligner;
import org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment;
import org.broadinstitute.hellbender.utils.bwa.BwaMemIndex;
import org.umccr.java.hellbender.utils.bwa.BwaMemAligner;
import org.umccr.java.hellbender.utils.bwa.BwaMemAlignment;
import org.umccr.java.hellbender.utils.bwa.BwaMemIndex;

public class BwaSeqTester
{
Expand All @@ -36,7 +34,6 @@ public BwaSeqTester(final SeqTestConfig config, final ConfigBuilder configBuilde

String refGenomeImageFile = configBuilder.getValue(REF_GENOME) + ".img";

loadAlignerLibrary(configBuilder.getValue(BWA_LIB_PATH));
mAligner = initialiseBwaAligner(refGenomeImageFile);
}

Expand Down
3 changes: 0 additions & 3 deletions gene-utils/src/main/java/com/hartwig/hmftools/geneutils/mapping/SeqTestConfig.java
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@@ -1,8 +1,6 @@
package com.hartwig.hmftools.geneutils.mapping;

import static com.hartwig.hmftools.common.blastn.BlastnRunner.registerBlastn;
import static com.hartwig.hmftools.common.bwa.BwaUtils.BWA_LIB_PATH;
import static com.hartwig.hmftools.common.bwa.BwaUtils.BWA_LIB_PATH_DESC;
import static com.hartwig.hmftools.common.genome.refgenome.RefGenomeSource.REF_GENOME;
import static com.hartwig.hmftools.common.genome.refgenome.RefGenomeSource.addRefGenomeFile;
import static com.hartwig.hmftools.common.genome.refgenome.RefGenomeSource.deriveRefGenomeVersion;
Expand Down Expand Up @@ -47,7 +45,6 @@ public static void registerConfig(final ConfigBuilder configBuilder)
{
configBuilder.addPath(INPUT_FILE, true, "Input regions and sequences");

configBuilder.addPath(BWA_LIB_PATH, false, BWA_LIB_PATH_DESC);
registerBlastn(configBuilder, false);

addOutputOptions(configBuilder, false);
Expand Down
62 changes: 0 additions & 62 deletions hmf-common/src/main/java/com/hartwig/hmftools/common/bwa/BwaUtils.java
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