From dd080d7cb87d9d797801505c5eb6757b5bcdc4d9 Mon Sep 17 00:00:00 2001 From: imedina Date: Wed, 22 Jun 2022 02:08:19 +0100 Subject: [PATCH 01/10] Prepare new development version 2.5.0-SNAPSHOT --- biodata-external/pom.xml | 2 +- biodata-formats/pom.xml | 2 +- biodata-models/pom.xml | 2 +- biodata-tools/pom.xml | 2 +- pom.xml | 4 ++-- 5 files changed, 6 insertions(+), 6 deletions(-) diff --git a/biodata-external/pom.xml b/biodata-external/pom.xml index a2d461d3..54a395ff 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -6,7 +6,7 @@ biodata org.opencb.biodata - 2.4.1-SNAPSHOT + 2.5.0-SNAPSHOT ../pom.xml diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index 425341a3..5a105cde 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.4.1-SNAPSHOT + 2.5.0-SNAPSHOT ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index 516c7492..20b4957c 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.4.1-SNAPSHOT + 2.5.0-SNAPSHOT ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index dc93429e..98ca3d56 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.4.1-SNAPSHOT + 2.5.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 5ce97f26..7a35cdcc 100644 --- a/pom.xml +++ b/pom.xml @@ -20,7 +20,7 @@ org.opencb.biodata biodata - 2.4.1-SNAPSHOT + 2.5.0-SNAPSHOT pom Biodata @@ -35,7 +35,7 @@ - 4.4.0 + 4.5.0-SNAPSHOT 4.4 1.7.7 3.11.4 From 8b419a743e4bb33dce73ab69a8561a37be0112fa Mon Sep 17 00:00:00 2001 From: imedina Date: Fri, 24 Jun 2022 01:57:11 +0100 Subject: [PATCH 02/10] cicd: copy tests to server --- .github/workflows/develop.yml | 11 ++++++++++- .github/workflows/task.yml | 13 +++++++++++-- pom.xml | 15 +++++++++++++++ 3 files changed, 36 insertions(+), 3 deletions(-) diff --git a/.github/workflows/develop.yml b/.github/workflows/develop.yml index 81e82122..c8d292e6 100644 --- a/.github/workflows/develop.yml +++ b/.github/workflows/develop.yml @@ -35,7 +35,16 @@ jobs: - name: Install Samtools run: sudo apt-get install samtools - name: Run tests with Maven - run: mvn -T 2 clean install +# run: mvn -T 2 clean install + run: mvn surefire-report:report + - name: Deploy tests web recursively to remote + uses: garygrossgarten/github-action-scp@release + with: + local: target/site + remote: /mnt/resources/opencb/biodata/tests/${{ github.ref_name }}/${{ github.sha }} + host: 128.232.224.128 + username: ${{ secrets.SCP_SITE_USER }} + password: ${{ secrets.SCP_SITE_PASSWORD }} deploy-maven: uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop diff --git a/.github/workflows/task.yml b/.github/workflows/task.yml index a17b2311..c1c8a506 100644 --- a/.github/workflows/task.yml +++ b/.github/workflows/task.yml @@ -33,5 +33,14 @@ jobs: cache: 'maven' - name: Install Samtools run: sudo apt-get install samtools - - name: Run tests with Maven - run: mvn -T 2 clean install + - name: Run tests and create report with Maven +# run: mvn -T 2 clean install + run: mvn surefire-report:report + - name: Deploy tests web recursively to remote + uses: garygrossgarten/github-action-scp@release + with: + local: target/site + remote: /mnt/resources/opencb/biodata/tests/${{ github.ref_name }}/${{ github.sha }} + host: 128.232.224.128 + username: ${{ secrets.SCP_SITE_USER }} + password: ${{ secrets.SCP_SITE_PASSWORD }} diff --git a/pom.xml b/pom.xml index 7a35cdcc..bf966625 100644 --- a/pom.xml +++ b/pom.xml @@ -247,9 +247,24 @@ ${project.build.sourceEncoding} + + org.apache.maven.plugins + maven-surefire-plugin + 3.0.0-M7 + + + + + org.apache.maven.plugins + maven-surefire-report-plugin + 3.0.0-M7 + + + + deploy From 082817ddf007d28e18f2825f55bc316130f84633 Mon Sep 17 00:00:00 2001 From: imedina Date: Fri, 24 Jun 2022 02:03:10 +0100 Subject: [PATCH 03/10] cicd: fix copy tests to server --- .github/workflows/develop.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/develop.yml b/.github/workflows/develop.yml index c8d292e6..71462403 100644 --- a/.github/workflows/develop.yml +++ b/.github/workflows/develop.yml @@ -42,9 +42,9 @@ jobs: with: local: target/site remote: /mnt/resources/opencb/biodata/tests/${{ github.ref_name }}/${{ github.sha }} - host: 128.232.224.128 - username: ${{ secrets.SCP_SITE_USER }} - password: ${{ secrets.SCP_SITE_PASSWORD }} + host: ${{ secrets.SSH_SWDEV_IP }} + username: ${{ secrets.SSH_SWDEV_USER }} + password: ${{ secrets.SSH_SWDEV_PASSWORD }} deploy-maven: uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop From 049a177286fe57cc8175c00e8e22f37b6b7c47df Mon Sep 17 00:00:00 2001 From: imedina Date: Fri, 24 Jun 2022 02:09:38 +0100 Subject: [PATCH 04/10] cicd: fix copy tests to server --- .github/workflows/develop.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/develop.yml b/.github/workflows/develop.yml index 71462403..6c5b73c5 100644 --- a/.github/workflows/develop.yml +++ b/.github/workflows/develop.yml @@ -41,7 +41,7 @@ jobs: uses: garygrossgarten/github-action-scp@release with: local: target/site - remote: /mnt/resources/opencb/biodata/tests/${{ github.ref_name }}/${{ github.sha }} + remote: /mnt/data/opencb/biodata/tests/${{ github.ref_name }}/${{ github.sha }} host: ${{ secrets.SSH_SWDEV_IP }} username: ${{ secrets.SSH_SWDEV_USER }} password: ${{ secrets.SSH_SWDEV_PASSWORD }} From 6789cef999476e72b38b71ef555b582893f06e38 Mon Sep 17 00:00:00 2001 From: imedina Date: Fri, 24 Jun 2022 02:11:33 +0100 Subject: [PATCH 05/10] cicd: add version when copy tests to server --- .github/workflows/develop.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/develop.yml b/.github/workflows/develop.yml index 6c5b73c5..ee5c4b84 100644 --- a/.github/workflows/develop.yml +++ b/.github/workflows/develop.yml @@ -41,7 +41,7 @@ jobs: uses: garygrossgarten/github-action-scp@release with: local: target/site - remote: /mnt/data/opencb/biodata/tests/${{ github.ref_name }}/${{ github.sha }} + remote: /mnt/data/opencb/biodata/tests/${{ needs.build.outputs.version }}/${{ github.ref_name }}/${{ github.sha }} host: ${{ secrets.SSH_SWDEV_IP }} username: ${{ secrets.SSH_SWDEV_USER }} password: ${{ secrets.SSH_SWDEV_PASSWORD }} From 9223bdcb5125cc7870548f89b889f985691467f7 Mon Sep 17 00:00:00 2001 From: imedina Date: Fri, 24 Jun 2022 02:18:34 +0100 Subject: [PATCH 06/10] cicd: add biodata-tools when copy tests to server --- .github/workflows/develop.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/develop.yml b/.github/workflows/develop.yml index ee5c4b84..55f0dec1 100644 --- a/.github/workflows/develop.yml +++ b/.github/workflows/develop.yml @@ -40,7 +40,7 @@ jobs: - name: Deploy tests web recursively to remote uses: garygrossgarten/github-action-scp@release with: - local: target/site + local: biodata-tools/target/site remote: /mnt/data/opencb/biodata/tests/${{ needs.build.outputs.version }}/${{ github.ref_name }}/${{ github.sha }} host: ${{ secrets.SSH_SWDEV_IP }} username: ${{ secrets.SSH_SWDEV_USER }} From 1b8796b4d10fdee471df32fdf26cb2f13ecc0f9b Mon Sep 17 00:00:00 2001 From: imedina Date: Fri, 24 Jun 2022 02:25:02 +0100 Subject: [PATCH 07/10] cicd: add biodata-tools target when copy tests to server --- .github/workflows/develop.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/develop.yml b/.github/workflows/develop.yml index 55f0dec1..7042dd44 100644 --- a/.github/workflows/develop.yml +++ b/.github/workflows/develop.yml @@ -40,7 +40,7 @@ jobs: - name: Deploy tests web recursively to remote uses: garygrossgarten/github-action-scp@release with: - local: biodata-tools/target/site + local: biodata-tools/target remote: /mnt/data/opencb/biodata/tests/${{ needs.build.outputs.version }}/${{ github.ref_name }}/${{ github.sha }} host: ${{ secrets.SSH_SWDEV_IP }} username: ${{ secrets.SSH_SWDEV_USER }} From aad4ce43d82d041e4e46bf08039ada2d17b46b9b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Wed, 29 Jun 2022 17:00:01 +0100 Subject: [PATCH 08/10] tools: Use ##SAMPLE names to map sample column names to actual sample names. #TASK-1215 --- .../tools/variant/VariantVcfHtsjdkReader.java | 24 +++-- ...VCFHeaderToVariantFileHeaderConverter.java | 4 +- ...FHeaderToVariantFileMetadataConverter.java | 97 +++++++++++++++++++ .../VariantContextToVariantConverter.java | 4 - .../metadata/VariantMetadataManager.java | 8 +- .../metadata/VariantMetadataUtils.java | 37 +++++-- .../VariantMetadataManagerTest.java | 2 +- .../metadata/VariantMetadataUtilsTest.java | 34 +++++++ .../src/test/resources/sampleMappingName.vcf | 8 ++ 9 files changed, 185 insertions(+), 33 deletions(-) create mode 100644 biodata-tools/src/main/java/org/opencb/biodata/tools/variant/converters/avro/VCFHeaderToVariantFileMetadataConverter.java rename biodata-tools/src/test/java/org/opencb/biodata/tools/variant/{ => metadata}/VariantMetadataManagerTest.java (99%) create mode 100644 biodata-tools/src/test/java/org/opencb/biodata/tools/variant/metadata/VariantMetadataUtilsTest.java create mode 100644 biodata-tools/src/test/resources/sampleMappingName.vcf diff --git a/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/VariantVcfHtsjdkReader.java b/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/VariantVcfHtsjdkReader.java index 4d29b815..7fcd4f0e 100644 --- a/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/VariantVcfHtsjdkReader.java +++ b/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/VariantVcfHtsjdkReader.java @@ -36,6 +36,7 @@ import org.opencb.biodata.models.variant.avro.FileEntry; import org.opencb.biodata.models.variant.metadata.VariantStudyMetadata; import org.opencb.biodata.tools.variant.converters.avro.VCFHeaderToVariantFileHeaderConverter; +import org.opencb.biodata.tools.variant.converters.avro.VCFHeaderToVariantFileMetadataConverter; import org.opencb.biodata.tools.variant.converters.avro.VariantContextToVariantConverter; import org.opencb.biodata.tools.variant.metadata.VariantMetadataManager; import org.opencb.commons.utils.FileUtils; @@ -178,23 +179,20 @@ public String readLine() throws IOException { @Override public void close() {} })); - // htsjdk automatically and inevitably sorts sample data in alphabetical order. Need to recover the original - // order in the VCF from the header and initialise the converter with the original order so that the order - // of samplesdata in CellBase output is exactly the same as in the original VCF - List samplesInOriginalOrder = Arrays.asList(new String[header.getSampleNameToOffset().size()]); - for (Map.Entry entry : header.getSampleNameToOffset().entrySet()) { - samplesInOriginalOrder.set(entry.getValue(), entry.getKey()); - } + VCFHeaderToVariantFileMetadataConverter fileMetadataConverter = new VCFHeaderToVariantFileMetadataConverter(); + fileMetadataConverter.convert(header, fileMetadata); + List samples = fileMetadata.getSampleIds(); + + header = new VCFHeader(header.getMetaDataInInputOrder(), samples); + codec.setVCFHeader(header, codec.getVCFHeaderVersion()); - // Create converters and fill VariantSource - converter = new VariantContextToVariantConverter(metadata.getId(), fileMetadata.getId(), samplesInOriginalOrder); - fileMetadata.setHeader(new VCFHeaderToVariantFileHeaderConverter().convert(header)); - fileMetadata.setSampleIds(samplesInOriginalOrder); + // Create converters + converter = new VariantContextToVariantConverter(metadata.getId(), fileMetadata.getId(), samples); if (metadata.getIndividuals() == null) { - metadata.setIndividuals(new ArrayList<>(samplesInOriginalOrder.size())); + metadata.setIndividuals(new ArrayList<>(samples.size())); } VariantMetadataManager metadataManager = new VariantMetadataManager(metadata); - for (String sample : samplesInOriginalOrder) { + for (String sample : samples) { metadataManager.addIndividual(sample, sample, metadata.getId()); } diff --git a/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/converters/avro/VCFHeaderToVariantFileHeaderConverter.java b/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/converters/avro/VCFHeaderToVariantFileHeaderConverter.java index 108aa598..3ef38a9c 100644 --- a/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/converters/avro/VCFHeaderToVariantFileHeaderConverter.java +++ b/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/converters/avro/VCFHeaderToVariantFileHeaderConverter.java @@ -6,7 +6,9 @@ import org.opencb.biodata.models.variant.metadata.VariantFileHeaderSimpleLine; import org.opencb.biodata.tools.commons.Converter; -import java.util.*; +import java.util.ArrayList; +import java.util.List; +import java.util.Map; import java.util.function.Function; /** diff --git a/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/converters/avro/VCFHeaderToVariantFileMetadataConverter.java b/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/converters/avro/VCFHeaderToVariantFileMetadataConverter.java new file mode 100644 index 00000000..f59e64a6 --- /dev/null +++ b/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/converters/avro/VCFHeaderToVariantFileMetadataConverter.java @@ -0,0 +1,97 @@ +package org.opencb.biodata.tools.variant.converters.avro; + +import htsjdk.variant.vcf.VCFConstants; +import htsjdk.variant.vcf.VCFHeader; +import htsjdk.variant.vcf.VCFHeaderLine; +import htsjdk.variant.vcf.VCFSampleHeaderLine; +import org.apache.commons.lang3.StringUtils; +import org.opencb.biodata.models.variant.VariantFileMetadata; +import org.opencb.biodata.models.variant.metadata.VariantFileHeader; +import org.opencb.biodata.models.variant.metadata.VariantFileHeaderComplexLine; + +import java.util.*; +import java.util.stream.Collectors; + +public class VCFHeaderToVariantFileMetadataConverter { + + public VariantFileMetadata convert(VCFHeader header, String id, String path) { + return convert(header, new VariantFileMetadata(id, path)); + } + + public VariantFileMetadata convert(VCFHeader header, VariantFileMetadata variantFileMetadata) { + VariantFileHeader variantFileHeader = new VCFHeaderToVariantFileHeaderConverter().convert(header); + Map sampleMapping = getSampleMapping(variantFileHeader); + List samples = getSamples(header, sampleMapping); + + // Create converters and fill VariantSource + variantFileMetadata.setHeader(variantFileHeader); + variantFileMetadata.setSampleIds(samples); + if (variantFileMetadata.getAttributes() == null) { + variantFileMetadata.setAttributes(new HashMap<>()); + } + variantFileMetadata.getAttributes().put("originalSamples", String.join(",", header.getGenotypeSamples())); + + return variantFileMetadata; + } + + public List getSamples(VCFHeader header, Map sampleNameMapping) { + if (sampleNameMapping == null) { + sampleNameMapping = Collections.emptyMap(); + } + + List samplesInOriginalOrder = header.getGenotypeSamples(); + List renamedSamples = new ArrayList<>(samplesInOriginalOrder.size()); + for (String sample : samplesInOriginalOrder) { + renamedSamples.add(sampleNameMapping.getOrDefault(sample, sample)); + } + + return renamedSamples; + } + + public Map getSampleMapping(VCFHeader header) { + Map sampleNameMapping = new HashMap<>(); + for (VCFHeaderLine line : header.getMetaDataInInputOrder()) { + if (line instanceof VCFSampleHeaderLine) { + VCFSampleHeaderLine sampleHeaderLine = (VCFSampleHeaderLine) line; + getActualSampleName(sampleHeaderLine.getID(), sampleHeaderLine.getGenericFields(), sampleNameMapping); + } + } + return sampleNameMapping; + } + + public Map getSampleMapping(VariantFileHeader header) { + Map sampleNameMapping = new HashMap<>(); + for (VariantFileHeaderComplexLine line : header.getComplexLines()) { + if (line.getKey().equals(VCFConstants.SAMPLE_HEADER_KEY)) { + getActualSampleName(line.getId(), line.getGenericFields(), sampleNameMapping); + } + } + return sampleNameMapping; + } + + private void getActualSampleName(String id, Map genericFields, Map sampleNameMapping) { + String sampleName = getValueIgnoreCase(genericFields, "SampleName"); + if (sampleName == null) { + sampleName = getValueIgnoreCase(genericFields, "SampleId"); + } + if (sampleName == null) { + sampleName = getValueIgnoreCase(genericFields, "Name"); + } + if (sampleName != null) { + sampleNameMapping.put(id, sampleName); + } + } + + private String getValueIgnoreCase(Map map, String key) { + for (Map.Entry entry : map.entrySet()) { + if (entry.getKey().equalsIgnoreCase(key)) { + String value = entry.getValue(); + if (StringUtils.isNotEmpty(value)) { + return value; + } + } + } + return null; + } + +} diff --git a/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/converters/avro/VariantContextToVariantConverter.java b/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/converters/avro/VariantContextToVariantConverter.java index e0da1934..e825d273 100644 --- a/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/converters/avro/VariantContextToVariantConverter.java +++ b/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/converters/avro/VariantContextToVariantConverter.java @@ -48,7 +48,6 @@ public class VariantContextToVariantConverter implements Converter samplesPosition; - private List consequenceTypeFields; protected Logger logger = LoggerFactory.getLogger(this.getClass().toString()); @@ -65,9 +64,6 @@ public VariantContextToVariantConverter(String studyId, String fileId, List +##SAMPLE= +##SAMPLE= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TUMOR NORMAL OTHER +chr1 28494 . T C 100 PASS . GT:NAME 0|0:TUMOR 1|0:NORMAL 1|0:OTHER +chr1 99166 . C T 100 PASS . GT:NAME 0|1:TUMOR 0|1:NORMAL 0|1:OTHER +chr1 99580 . T C 100 PASS . GT:NAME 0|1:TUMOR 0|0:NORMAL 1|1:OTHER From 71b87da225d6efe91819cecd9431e3ccb66133d5 Mon Sep 17 00:00:00 2001 From: imedina Date: Fri, 19 Aug 2022 15:49:06 +0200 Subject: [PATCH 09/10] pom: increase version to 2.4.3-SNAPSHOT --- biodata-external/pom.xml | 2 +- biodata-formats/pom.xml | 2 +- biodata-models/pom.xml | 2 +- biodata-tools/pom.xml | 2 +- pom.xml | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/biodata-external/pom.xml b/biodata-external/pom.xml index a9ce2743..2d27183f 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -6,7 +6,7 @@ biodata org.opencb.biodata - 2.4.2 + 2.4.3-SNAPSHOT ../pom.xml diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index e13816e9..a1fec23d 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.4.2 + 2.4.3-SNAPSHOT ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index 627c87ef..7eb94e43 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.4.2 + 2.4.3-SNAPSHOT ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index ca21a256..c12c0440 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.4.2 + 2.4.3-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 90dfcd40..51de6dfe 100644 --- a/pom.xml +++ b/pom.xml @@ -20,7 +20,7 @@ org.opencb.biodata biodata - 2.4.2 + 2.4.3-SNAPSHOT pom Biodata From 7b1bb056b44ea5d19f73cefac6e5d567655db888 Mon Sep 17 00:00:00 2001 From: imedina Date: Wed, 7 Sep 2022 03:01:28 +0100 Subject: [PATCH 10/10] Prepare release 2.4.3 --- biodata-external/pom.xml | 2 +- biodata-formats/pom.xml | 2 +- biodata-models/pom.xml | 2 +- biodata-tools/pom.xml | 2 +- pom.xml | 4 ++-- 5 files changed, 6 insertions(+), 6 deletions(-) diff --git a/biodata-external/pom.xml b/biodata-external/pom.xml index 54a395ff..d8459c9a 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -6,7 +6,7 @@ biodata org.opencb.biodata - 2.5.0-SNAPSHOT + 2.4.3 ../pom.xml diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index 5a105cde..59a61d48 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.5.0-SNAPSHOT + 2.4.3 ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index 20b4957c..1783af81 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.5.0-SNAPSHOT + 2.4.3 ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index 15f11675..75cdfc87 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.5.0-SNAPSHOT + 2.4.3 ../pom.xml diff --git a/pom.xml b/pom.xml index cf97c597..41b6b693 100644 --- a/pom.xml +++ b/pom.xml @@ -20,7 +20,7 @@ org.opencb.biodata biodata - 2.5.0-SNAPSHOT + 2.4.3 pom @@ -36,7 +36,7 @@ - 4.5.0-SNAPSHOT + 4.4.1 4.4 1.7.7 3.11.4