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Support reference panels in msav format and decay parameter #128

Merged
merged 39 commits into from
Dec 6, 2023
Merged

Support reference panels in msav format and decay parameter #128

merged 39 commits into from
Dec 6, 2023

Commits on Dec 2, 2021

  1. Add new minimac4 binary and adapt execution command

    @seppinho
    seppinho committed Dec 2, 2021
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  2. Add msav reference panels

    @seppinho
    seppinho committed Dec 2, 2021
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  3. Adapt test data to include GT tag

    @seppinho
    seppinho committed Dec 2, 2021
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Commits on Dec 3, 2021

  1. Fix input data

    @seppinho
    seppinho committed Dec 3, 2021
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  2. Fix input data for hg38 test cases

    @seppinho
    seppinho committed Dec 3, 2021
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  3. Ignore obsolete --myChromosome option

    @seppinho
    seppinho committed Dec 3, 2021
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  4. Update run-tests.yml

    @seppinho
    seppinho committed Dec 3, 2021
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  5. Merge pull request #71 from genepi/master 

    Update create-release.yml
    @seppinho
    seppinho committed Dec 3, 2021
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Commits on Dec 4, 2021

  1. Update run-tests.yml

    @seppinho
    seppinho committed Dec 4, 2021
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Commits on Dec 6, 2021

  1. Update to new parameter --sites for writing info files

    @seppinho
    seppinho committed Dec 6, 2021
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  2. Merge branch 'features/msav-support' of https://github.com/genepi/imp… 

    …utationserver.git into features/msav-support
    @seppinho
    seppinho committed Dec 6, 2021
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  3. Add new minR2 parameter to minimac4 and remove R2 pipeline filter

    @seppinho
    seppinho committed Dec 6, 2021
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  4. Add prefix mis_ to all MIS tags in VCF file

    @seppinho
    seppinho committed Dec 6, 2021
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  5. Fix VCF header test case with new prefix

    @seppinho
    seppinho committed Dec 6, 2021
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  6. Update to latest minimac4 binary

    @seppinho
    seppinho committed Dec 6, 2021
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  7. Add min-r2 parameter to command only if minR2 > 0

    @seppinho
    seppinho committed Dec 6, 2021
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Commits on Dec 13, 2021

  1. Merge branch 'features/update-pgs-calculation' into 

    features/msav-support

Conflicts:
	files/imputationserver-beagle.yaml
	files/imputationserver-hla.yaml
	files/imputationserver-pgs.yaml
	files/minimac4.yaml
	pom.xml
	src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java
    @seppinho
    seppinho committed Dec 13, 2021
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  2. Update to pgs-calc version v0.9.10

    @seppinho
    seppinho committed Dec 13, 2021
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  3. Prepare release v1.7.0-rc1

    @seppinho
    seppinho committed Dec 13, 2021
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Commits on Dec 15, 2021

  1. Update to latest minimac4 (commit 9c653eb)

    @seppinho
    seppinho committed Dec 15, 2021
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  2. Prepare release 1.7.0-rc2

    @seppinho
    seppinho committed Dec 15, 2021
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Commits on Dec 20, 2021

  1. Update minimac4 to 8498d

    @seppinho
    seppinho committed Dec 20, 2021
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Commits on Dec 23, 2021

  1. Add HTS tag to m4 format option

    @seppinho
    seppinho committed Dec 23, 2021
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Commits on Feb 14, 2022

  1. Merge remote-tracking branch 'origin/master' into features/msav-support 

    Conflicts:
	files/imputationserver-beagle.yaml
	files/imputationserver-hla.yaml
	files/imputationserver-pgs.yaml
	files/minimac4.yaml
	pom.xml
	src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java
    @seppinho
    seppinho committed Feb 14, 2022
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Commits on Feb 22, 2022

  1. Update minimac4 and rebuild msav files

    @seppinho
    seppinho committed Feb 22, 2022
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  2. Update DefaultPreferenceStore.java

    @seppinho
    seppinho committed Feb 22, 2022
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Commits on Oct 31, 2022

  1. Merge branch 'master' into features/msav-support 

    Conflicts:
	files/imputationserver-beagle.yaml
	files/imputationserver-hla.yaml
	files/imputationserver-pgs.yaml
	files/minimac4.yaml
	pom.xml
	src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java
	src/test/java/genepi/imputationserver/steps/ImputationTest.java
    @seppinho
    seppinho committed Oct 31, 2022
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  2. Fix line number in new test case (from master) due to new M4

    @seppinho
    seppinho committed Oct 31, 2022
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  3. Update to minimac v4.1.0

    @seppinho
    seppinho committed Oct 31, 2022
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Commits on Oct 24, 2023

  1. Update to minimac v4.1.4

    @seppinho
    seppinho committed Oct 24, 2023
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  2. Merge branch 'master' into features/msav-support

    @seppinho
    seppinho committed Oct 24, 2023
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Commits on Nov 8, 2023

  1. Add minimac4 decay option

    @seppinho
    seppinho committed Nov 8, 2023
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  2. Prepare release v1.8.0-beta1

    @seppinho
    seppinho committed Nov 8, 2023
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  3. Update imputation engine log to v4.1.4

    @seppinho
    seppinho committed Nov 8, 2023
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  4. Prepare release v1.8.0-beta2

    @seppinho
    seppinho committed Nov 8, 2023
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Commits on Nov 10, 2023

  1. Update to minimac v4.1.5

    @seppinho
    seppinho committed Nov 10, 2023
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  2. Prepare release v1.8.0-beta3

    @seppinho
    seppinho committed Nov 10, 2023
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Commits on Dec 6, 2023

  1. Prepare release v1.8.0-beta4 (#126) 

    Provenance: from installer script
https://github.com/statgen/Minimac4/releases/tag/v4.1.6
    @abought
    abought committed Dec 6, 2023
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  2. Merge branch 'master' into features/msav-support

    @seppinho
    seppinho committed Dec 6, 2023
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