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Dsl2/filter sv blacklist #965

Merged
merged 28 commits into from
Jul 25, 2022
Merged

Dsl2/filter sv blacklist #965

merged 28 commits into from
Jul 25, 2022

Commits on Jun 24, 2022

  1. change bedpe filtering script to handle both bedpe and bed regions fi… 

    …les, and renamed the python script to better reflect its purpose
    @anoronh4
    anoronh4 committed Jun 24, 2022
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  2. add pcawg blacklist filtering

    @anoronh4
    anoronh4 committed Jun 24, 2022
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  3. added reference definition for pcawg blacklist files for loading them… 

    … into referenceMap
    @anoronh4
    anoronh4 committed Jun 24, 2022
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  4. fixed filepaths for pcawg SV blacklist files

    @anoronh4
    anoronh4 committed Jun 24, 2022
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Commits on Jun 27, 2022

  1. bugfix of file name for germline annotation

    @anoronh4
    anoronh4 committed Jun 27, 2022
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  2. reorganized filter_regions_bedpe.py to be more modularized

    @anoronh4
    anoronh4 committed Jun 27, 2022
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  3. cleanup filter_regions_bedpe.py

    @anoronh4
    anoronh4 committed Jun 27, 2022
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  4. add notes

    @anoronh4
    anoronh4 committed Jun 27, 2022
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Commits on Jun 28, 2022

  1. fix filtering tags for sv annotation

    @anoronh4
    anoronh4 committed Jun 28, 2022
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Commits on Jun 29, 2022

  1. added pcawg blacklist filtering to Germline SV annotation, and fixed … 

    …publishing of files
    @anoronh4
    anoronh4 committed Jun 29, 2022
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  2. bugfixes

    @anoronh4
    anoronh4 committed Jun 29, 2022
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Commits on Jun 30, 2022

  1. bugfix for GermlineAnnotateSVBedpe inputs

    @anoronh4
    anoronh4 committed Jun 30, 2022
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  2. add reference for trasposable element filtering in SV

    @anoronh4
    anoronh4 committed Jun 30, 2022
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Commits on Jul 2, 2022

  1. added print statements for logging purposes, and made it so iannotate… 

    …sv processes only 1000 rows at a time
    @anoronh4
    anoronh4 committed Jul 2, 2022
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Commits on Jul 5, 2022

  1. bugfixes

    @anoronh4
    anoronh4 committed Jul 5, 2022
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  2. fix header of bedpe due to improper handling in svtools

    @anoronh4
    anoronh4 committed Jul 5, 2022
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  3. fix bedpe header

    @anoronh4
    anoronh4 committed Jul 5, 2022
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  4. parallelize iannotatesv

    @anoronh4
    anoronh4 committed Jul 5, 2022
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Commits on Jul 6, 2022

  1. add resource configuration for *AnnotateSVBedpe processes

    @anoronh4
    anoronh4 committed Jul 6, 2022
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Commits on Jul 11, 2022

  1. raise resources for *AnnotateSVBedpe

    @anoronh4
    anoronh4 committed Jul 11, 2022
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  2. edited travis test references for filtering SV events

    @anoronh4
    anoronh4 committed Jul 11, 2022
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  3. bugfix

    @anoronh4
    anoronh4 committed Jul 11, 2022
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  4. Merge branch 'dsl2/enhancement/WGS_SV' into dsl2/filterSVBlacklist

    @anoronh4
    anoronh4 authored Jul 11, 2022
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  5. remove duplicated line

    @anoronh4
    anoronh4 committed Jul 11, 2022
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Commits on Jul 22, 2022

  1. remove chunk parameter from run_iannotatesv.py because finetuning it … 

    …does not meaningfully impact run time
    @anoronh4
    anoronh4 committed Jul 22, 2022
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  2. Merge branch 'dsl2/filterSVBlacklist' of github.com:mskcc/tempo into … 

    …dsl2/filterSVBlacklist
    @anoronh4
    anoronh4 committed Jul 22, 2022
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  3. add note about sources for pcawg blacklist files

    @anoronh4
    anoronh4 committed Jul 22, 2022
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Commits on Jul 25, 2022

  1. add description and authorship info for each python file

    @anoronh4
    anoronh4 committed Jul 25, 2022
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