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Issue #7159 Create tool for producing genomic regions (as a BED file) #8942

Merged
merged 49 commits into from
Aug 29, 2024
Merged

Issue #7159 Create tool for producing genomic regions (as a BED file) #8942

merged 49 commits into from
Aug 29, 2024

Commits on Jul 10, 2024

  1. Initial commit and basic code to read gtf

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    sanashah007 committed Jul 10, 2024
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Commits on Jul 12, 2024

  1. add: code to write to bed & integration test

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    sanashah007 committed Jul 12, 2024
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Commits on Jul 15, 2024

  1. fix: make getAllFeatures public and use the nesting of features to ge… 

    …t to transcripts
    @sanashah007
    sanashah007 committed Jul 15, 2024
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Commits on Jul 17, 2024

  1. add: filtering transcripts by basic tag

    @sanashah007
    sanashah007 committed Jul 17, 2024
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Commits on Jul 18, 2024

  1. add: sorts by contig and start (need to fix - sorting lexicographically)

    @sanashah007
    sanashah007 committed Jul 18, 2024
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Commits on Jul 22, 2024

  1. fix: now sorts by contig then start & output is correct

    @sanashah007
    sanashah007 committed Jul 22, 2024
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  2. fix: make dictionary an arg

    @sanashah007
    sanashah007 committed Jul 22, 2024
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  3. add: comments + simplified CompareGtfInfo

    @sanashah007
    sanashah007 committed Jul 22, 2024
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Commits on Jul 24, 2024

  1. refactor: apply method 

    test: add separate tests for gene and transcript
    @sanashah007
    sanashah007 committed Jul 24, 2024
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  2. refactor: onTraversalSuccess and writeToBed

    @sanashah007
    sanashah007 committed Jul 24, 2024
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Commits on Jul 25, 2024

  1. add: more tests

    @sanashah007
    sanashah007 committed Jul 25, 2024
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  2. fix: test files in correct dir pt1. (files are too large)

    @sanashah007
    sanashah007 committed Jul 25, 2024
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  3. fix: test files in correct dir pt2.

    @sanashah007
    sanashah007 committed Jul 25, 2024
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Commits on Jul 30, 2024

  1. add: compareFiles and ground truth bed files

    @sanashah007
    sanashah007 committed Jul 30, 2024
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  2. fix: runGtfToBed assert

    @sanashah007
    sanashah007 committed Jul 30, 2024
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  3. add: comments to GtfToBed

    @sanashah007
    sanashah007 committed Jul 30, 2024
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Commits on Jul 31, 2024

  1. fix: error handling for different versions of gtf and dictionary

    @sanashah007
    sanashah007 committed Jul 31, 2024
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  2. fix: edited some bad conventions

    @sanashah007
    sanashah007 committed Jul 31, 2024
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Commits on Aug 1, 2024

  1. fix: remove spaces from input file fullName

    @sanashah007
    sanashah007 committed Aug 1, 2024
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  2. add: gtf file with MYT1L and MAPK1

    @sanashah007
    sanashah007 committed Aug 1, 2024
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Commits on Aug 2, 2024

  1. add: many transcripts unit test and refactoring

    @sanashah007
    sanashah007 committed Aug 2, 2024
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Commits on Aug 5, 2024

  1. add: tiebreaker sorting by id

    @sanashah007
    sanashah007 committed Aug 5, 2024
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  2. add: make sort by basic optional

    @sanashah007
    sanashah007 committed Aug 5, 2024
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  3. add: html doc comment

    @sanashah007
    sanashah007 committed Aug 5, 2024
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  4. fix: dictionary arg

    @sanashah007
    sanashah007 committed Aug 5, 2024
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Commits on Aug 7, 2024

  1. fix: add "Gencode" to description

    @sanashah007
    sanashah007 committed Aug 7, 2024
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  2. add: sample mouse gencode testing

    @sanashah007
    sanashah007 committed Aug 7, 2024
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Commits on Aug 9, 2024

  1. fix: Remove arg shortnames

    @sanashah007
    sanashah007 committed Aug 9, 2024
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  2. fix: rename and move CompareGtfInfo

    @sanashah007
    sanashah007 committed Aug 9, 2024
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  3. fix: kebab-case args

    @sanashah007
    sanashah007 committed Aug 9, 2024
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  4. fix: update html doc

    @sanashah007
    sanashah007 committed Aug 9, 2024
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  5. fix: use IntegrationTestSpec.assertEqualTextFiles()

    @sanashah007
    sanashah007 committed Aug 9, 2024
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  6. fix: remove unnecessary test of pik3ca

    @sanashah007
    sanashah007 committed Aug 9, 2024
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  7. fix: remove set functions in GtfInfo

    @sanashah007
    sanashah007 committed Aug 9, 2024
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  8. fix: style of comparator

    @sanashah007
    sanashah007 committed Aug 9, 2024
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  9. fix: style of comparator

    @sanashah007
    sanashah007 committed Aug 9, 2024
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Commits on Aug 13, 2024

  1. fix: use Files.newOutputStream() to write and logger for errors

    @sanashah007
    sanashah007 committed Aug 13, 2024
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  2. fix: use getBestAvailableSequenceDictionary()

    @sanashah007
    sanashah007 committed Aug 13, 2024
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  3. fix: use dataProvider for integration tests

    @sanashah007
    sanashah007 committed Aug 13, 2024
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  4. fix: better encapsulation

    @sanashah007
    sanashah007 committed Aug 13, 2024
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Commits on Aug 22, 2024

  1. fix: move mapk1.gtf to large dir

    @sanashah007
    sanashah007 committed Aug 22, 2024
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  2. fix: arg names

    @sanashah007
    sanashah007 committed Aug 22, 2024
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  3. fix: rename reference dict.

    @sanashah007
    sanashah007 committed Aug 22, 2024
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  4. fix: sequence-dictionary arg javadoc

    @sanashah007
    sanashah007 committed Aug 22, 2024
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  5. add: javadoc to GtfInfo

    @sanashah007
    sanashah007 committed Aug 22, 2024
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Commits on Aug 26, 2024

  1. add: dictionary exception and corresponding test

    @sanashah007
    sanashah007 committed Aug 26, 2024
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  2. add: test with fasta file as reference arg

    @sanashah007
    sanashah007 committed Aug 26, 2024
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Commits on Aug 27, 2024

  1. add: javadoc for fasta file

    @sanashah007
    sanashah007 committed Aug 27, 2024
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Commits on Aug 29, 2024

  1. fix: javadoc and onTraversalStart exception

    @sanashah007
    sanashah007 committed Aug 29, 2024
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