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4.7.0-RC plus mitool integration #1643

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4.7.0-RC plus mitool integration #1643

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Commits on Apr 24, 2024

  1. using weight from read header

    @gnefedev
    gnefedev committed Apr 24, 2024
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  2. update version

    @gnefedev
    gnefedev committed Apr 24, 2024
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  3. fix tests

    @gnefedev
    gnefedev committed Apr 24, 2024
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  4. regression tests automated change

    @gnefedev @github-actions
    gnefedev authored and github-actions[bot] committed Apr 24, 2024
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  5. Merge pull request #1629 from milaboratory/mixcr-regression-tests/par… 

    …se-weight-from-header

Regression tests changes in the parse-weight-from-header
    @gnefedev
    gnefedev committed Apr 24, 2024
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Commits on Apr 25, 2024

  1. fix usage of pattern

    @gnefedev
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  2. Merge remote-tracking branch 'origin/parse-weight-from-header' into p… 

    …arse-weight-from-header
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Commits on Apr 26, 2024

  1. Merge branch 'optional-correction-of-tags' into 4-7-0-RC-plus-mitool-… 

    …integration

# Conflicts:
#	build.gradle.kts
#	regression/cli-help/align.txt
#	regression/cli-help/analyze.txt
    @gnefedev
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  2. Merge branch 'parse-weight-from-header' into 4-7-0-RC-plus-mitool-int… 

    …egration

# Conflicts:
#	build.gradle.kts
#	src/main/kotlin/com/milaboratory/mixcr/cli/CommandRefineTagsAndSort.kt
    @gnefedev
    gnefedev committed Apr 26, 2024
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  3. update version

    @gnefedev
    gnefedev committed Apr 26, 2024
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Commits on May 3, 2024

  1. Rename .java to .kt

    @gnefedev
    gnefedev committed May 3, 2024
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  2. split by tags on partial assembler

    @gnefedev
    gnefedev committed May 3, 2024
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  3. update version

    @gnefedev
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  4. update version

    @gnefedev
    gnefedev committed May 3, 2024
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  5. update version

    @gnefedev
    gnefedev committed May 3, 2024
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  6. update version

    @gnefedev
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  7. Merge branch 'parse-weight-from-header' into 4-7-0-RC-plus-mitool-int… 

    …egration

# Conflicts:
#	build.gradle.kts
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Commits on May 6, 2024

  1. Merge branch 'contigs-per-cell' into 4-7-0-RC-plus-mitool-integration 

    # Conflicts:
#	build.gradle.kts
#	regression/cli-help/align.txt
    @gnefedev
    gnefedev committed May 6, 2024
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  2. update version

    @gnefedev
    gnefedev committed May 6, 2024
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  3. actual use of alignment weight in MiXCR

    @gnefedev
    gnefedev committed May 6, 2024
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  4. actual use of alignment weight in MiXCR

    @gnefedev
    gnefedev committed May 6, 2024
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  5. archer kits

    @mizraelson
    mizraelson committed May 6, 2024
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  6. changelog

    @mizraelson
    mizraelson committed May 6, 2024
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  7. regression tests automated change

    @mizraelson @github-actions
    mizraelson authored and github-actions[bot] committed May 6, 2024
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  8. Merge pull request #1645 from milaboratory/mixcr-regression-tests/archer 

    Regression tests changes in the archer
    @mizraelson
    mizraelson committed May 6, 2024
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Commits on May 7, 2024

  1. Merge pull request #1644 from milaboratory/archer

    @mizraelson
    mizraelson committed May 7, 2024
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  2. ensure that tag types are the same in header and in records

    @gnefedev
    gnefedev committed May 7, 2024
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  3. update version

    @gnefedev
    gnefedev committed May 7, 2024
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  4. fix tests compilation

    @gnefedev
    gnefedev committed May 7, 2024
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  5. add reports and params to mic file

    @gnefedev
    gnefedev committed May 7, 2024
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Commits on May 8, 2024

  1. mitool params in mixcr

    @gnefedev
    gnefedev committed May 8, 2024
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  2. first version of analyze with mitool

    @gnefedev
    gnefedev committed May 8, 2024
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Commits on May 9, 2024

  1. multiple run of Consensus

    @gnefedev
    gnefedev committed May 9, 2024
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Commits on May 13, 2024

  1. new library version

    @gnefedev
    gnefedev committed May 13, 2024
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  2. Merge pull request #1655 from milaboratory/sheep 

    new library version
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    gnefedev committed May 13, 2024
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Commits on May 14, 2024

  1. support for samples from file name

    @gnefedev
    gnefedev committed May 14, 2024
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Commits on May 15, 2024

  1. fix case sensitivity of metadata in postanalysis

    @gnefedev
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  2. limit metadata format to tsv

    @gnefedev
    gnefedev committed May 15, 2024
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  3. regression tests automated change

    @gnefedev @github-actions
    gnefedev authored and github-actions[bot] committed May 15, 2024
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  4. Merge pull request #1663 from milaboratory/mixcr-regression-tests/fix… 

    …-postanalyz

Regression tests changes in the fix-postanalyz
    @gnefedev
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  5. Merge pull request #1662 from milaboratory/fix-postanalyz 

    Fix postanalyz
    @gnefedev
    gnefedev committed May 15, 2024
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  6. support of {{IR}} and export of not aligned and not parsed reads

    @gnefedev
    gnefedev committed May 15, 2024
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Commits on May 16, 2024

  1. inherit reports and params from MIC file

    @gnefedev
    gnefedev committed May 16, 2024
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  2. actualize mixins

    @gnefedev
    gnefedev committed May 16, 2024
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  3. copy CriticalThresholdCollection from MIC

    @gnefedev
    gnefedev committed May 16, 2024
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  4. fix downsampling

    @gnefedev
    gnefedev committed May 16, 2024
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  5. update version

    @gnefedev
    gnefedev committed May 16, 2024
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  6. regression tests automated change

    @gnefedev @github-actions
    gnefedev authored and github-actions[bot] committed May 16, 2024
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  7. Merge pull request #1665 from milaboratory/mixcr-regression-tests/fix… 

    …-downsample

Regression tests changes in the fix-downsample
    @gnefedev
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  8. Merge pull request #1664 from milaboratory/fix-downsample 

    Fix downsample
    @gnefedev
    gnefedev committed May 16, 2024
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Commits on May 17, 2024

  1. resolve conflict of C gene on empiric assignment, parameterized Empir… 

    …icalAlignmentAssignment
    @gnefedev
    gnefedev committed May 17, 2024
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Commits on May 20, 2024

  1. add cmd args to mitool reports

    @gnefedev
    gnefedev committed May 20, 2024
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Commits on May 21, 2024

  1. fix align reports

    @gnefedev
    gnefedev committed May 21, 2024
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Commits on May 23, 2024

  1. update version

    @gnefedev
    gnefedev committed May 23, 2024
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  2. Merge pull request #1670 from milaboratory/fix-trees 

    update version
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Commits on May 29, 2024

  1. update version

    @gnefedev
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  2. fix test

    @gnefedev
    gnefedev committed May 29, 2024
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  3. regression tests automated change

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  4. Merge pull request #1677 from milaboratory/mixcr-regression-tests/fix… 

    …-trees

Regression tests changes in the fix-trees
    @gnefedev
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  5. Merge pull request #1676 from milaboratory/fix-trees 

    fix getNDN
    @gnefedev
    gnefedev committed May 29, 2024
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Commits on May 30, 2024

  1. add useOnlyFullAlignmentsIfPossible to assemble contigs

    @gnefedev
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  2. update version

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  3. Merge pull request #1679 from milaboratory/fix-tree-export 

    fix field header
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Commits on Jun 3, 2024

  1. fix assemble by already build consensuses

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Commits on Jun 13, 2024

  1. update version

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  2. regression tests automated change

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  3. Merge pull request #1693 from milaboratory/mixcr-regression-tests/kee… 

    …pTags

Regression tests changes in the keepTags
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Commits on Jun 14, 2024

  1. update version

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  2. Merge remote-tracking branch 'origin/keepTags' into keepTags

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  3. Merge pull request #1692 from milaboratory/keepTags 

    add keepTags
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Commits on Jun 21, 2024

  1. trim only specified tags on Parse

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Commits on Jun 24, 2024

  1. support --output-not-used-reads for bam files

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  2. Merge branch 'refs/heads/not-used-reads-for-bam' into 4-7-0-RC-plus-m… 

    …itool-integration

# Conflicts:
#	build.gradle.kts
#	src/main/kotlin/com/milaboratory/mixcr/cli/CommandAlign.kt
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  3. support --output-not-used-reads for bam files

    @gnefedev
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  4. fix reports (separation of alignment counts and read counts)

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  5. Merge branch 'refs/heads/develop' into not-used-reads-for-bam

    @gnefedev
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  6. update version

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  7. update version

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  8. update version

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  9. Merge pull request #1701 from milaboratory/not-used-reads-for-bam 

    fix bam
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Commits on Jun 25, 2024

  1. Merge branch 'refs/heads/develop' into 4-7-0-RC-plus-mitool-integration 

    # Conflicts:
#	build.gradle.kts
    @gnefedev
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  2. fix test compilation

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  3. update version

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  4. update version

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  5. fix itests

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  6. fix itests

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  7. fix tests

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