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Feature/revcomp #110

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Feature/revcomp #110

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Commits on Dec 17, 2021

  1. 3.6.1 hotfix changes

    Thomas Clarke committed Dec 17, 2021
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Commits on Dec 20, 2021

  1. Merge branch 'hotfix/3.6.1' 

    3.6.1
- Corrected logic of `FF019` and `FF020` to account for cases where FC > FD
    Thomas Clarke committed Dec 20, 2021
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  2. Merge tag '3.6.1' into dev 

    3.6.1
- Corrected logic of `FF019` and `FF020` to account for cases where FC > FD
    Thomas Clarke committed Dec 20, 2021
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Commits on Jan 6, 2022

  1. call checking against BWA more robust, lots of testing to do

    @keiranmraine
    keiranmraine committed Jan 6, 2022
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  2. Assess impact of excluding non-properly paired reads

    @keiranmraine
    keiranmraine committed Jan 6, 2022
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  3. Revert exclusion of reads not properly paired from call counts, too l… 

    …arge an impact on legacy data
    @keiranmraine
    keiranmraine committed Jan 6, 2022
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Commits on Jan 12, 2022

  1. Merge pull request #99 from cancerit/feature/invalidBwaCallInclusion 

    call checking against BWA more robust, lots of testing to do
    @keiranmraine
    keiranmraine authored Jan 12, 2022
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  2. Finalised release

    @keiranmraine
    keiranmraine committed Jan 12, 2022
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  3. Merge branch 'release/3.7.0'

    @keiranmraine
    keiranmraine committed Jan 12, 2022
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  4. Merge tag '3.7.0' into dev 

    Fix bug in BWA indel correlation counting
    @keiranmraine
    keiranmraine committed Jan 12, 2022
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Commits on Feb 10, 2022

  1. Addition of FF021 and update to normal panel generation script for cr… 

    …eation of relevant data, tests implemented
    @keiranmraine
    keiranmraine committed Feb 10, 2022
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  2. Add ability to run without flagging

    @keiranmraine
    keiranmraine committed Feb 10, 2022
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  3. Ensure both FF010 and FF021 don't attempt to run at the same time

    @keiranmraine
    keiranmraine committed Feb 10, 2022
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  4. correct expected file extension to gff3

    @keiranmraine
    keiranmraine committed Feb 10, 2022
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Commits on Feb 21, 2022

  1. Detail the use of nextflow

    @keiranmraine
    keiranmraine committed Feb 21, 2022
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  2. fixup licence check

    @keiranmraine
    keiranmraine committed Feb 21, 2022
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  3. Minor correction to docs [ci skip]

    @keiranmraine
    keiranmraine committed Feb 21, 2022
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  4. move nextflow files [ci skip]

    @keiranmraine
    keiranmraine committed Feb 21, 2022
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  5. fixup

    @keiranmraine
    keiranmraine committed Feb 21, 2022
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  6. Prevent bug from impacting NP

    @keiranmraine
    keiranmraine committed Feb 21, 2022
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  7. correct LSF queues

    @keiranmraine
    keiranmraine committed Feb 21, 2022
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Commits on Feb 22, 2022

  1. Merge pull request #105 from cancerit/feature/rangeBasedNormalPanel 

    Feature/range based normal panel
    @keiranmraine
    keiranmraine authored Feb 22, 2022
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  2. Detail changes, bump version

    @keiranmraine
    keiranmraine committed Feb 22, 2022
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  3. Merge branch 'release/3.8.0'

    @keiranmraine
    keiranmraine committed Feb 22, 2022
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  4. Merge tag '3.8.0' into dev 

    Finalise release
    @keiranmraine
    keiranmraine committed Feb 22, 2022
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Commits on Mar 10, 2022

  1. applied masking to pindel output

    Thomas Clarke committed Mar 10, 2022
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Commits on Mar 15, 2022

  1. Merge pull request #107 from cancerit/feature/masking 

    applied masking to pindel output
    @ThomasSClarke
    ThomasSClarke authored Mar 15, 2022
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Commits on Mar 16, 2022

  1. 3.9.0 updates

    Thomas Clarke committed Mar 16, 2022
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  2. Merge branch 'release/3.9.0' 

    - Masking of pindel calls where ref == alt implemented to remove invalid calls from pindel output
  - Core pindel fix required to resolve the underlying problem
    Thomas Clarke committed Mar 16, 2022
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  3. Merge tag '3.9.0' into dev 

    - Masking of pindel calls where ref == alt implemented to remove invalid calls from pindel output
  - Core pindel fix required to resolve the underlying problem
    Thomas Clarke committed Mar 16, 2022
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Commits on Mar 28, 2022

  1. Add option for exclude contigs file

    David Jones committed Mar 28, 2022
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  2. Adding tests and logic to deal with exclude sequence file

    David Jones committed Mar 28, 2022
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  3. Adding tests and logic to deal with exclude sequence file

    David Jones committed Mar 28, 2022
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  4. Adding tests and logic to deal with exclude sequence file

    David Jones committed Mar 28, 2022
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Commits on Mar 29, 2022

  1. Change to a loop checking for parameter clearing deletes in pindel.pl

    David Jones committed Mar 29, 2022
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  2. Add message to test is_deeply

    David Jones committed Mar 29, 2022
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  3. Add message to test is_deeply

    David Jones committed Mar 29, 2022
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  4. Add documnetation to script regarding new option

    David Jones committed Mar 29, 2022
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  5. Ensure arrays are declared and empty

    David Jones committed Mar 29, 2022
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  6. Merge pull request #108 from cancerit/feature/ignore_contigs_file 

    Feature/ignore contigs file
    @davidrajones
    davidrajones authored Mar 29, 2022
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  7. Update changes and version number

    David Jones committed Mar 29, 2022
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  8. Merge branch 'release/3.10.0'

    David Jones committed Mar 29, 2022
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  9. Merge tag '3.10.0' into dev 

    - Add commandline option for file containing exclude contigs
    David Jones committed Mar 29, 2022
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Commits on Jun 27, 2023

  1. revcomp initial changes

    Thomas Clarke committed Jun 27, 2023
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  2. tests removed for test runs

    Thomas Clarke committed Jun 27, 2023
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  3. adding feature/patientCohortAxt to branch

    Thomas Clarke committed Jun 27, 2023
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  4. Merge branch 'revcomp' into feature/revcomp

    Thomas Clarke committed Jun 27, 2023
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Commits on Jul 11, 2023

  1. revcomp completed code

    Thomas Clarke committed Jul 11, 2023
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