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1.2 - development -> main#47

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mattgarner merged 121 commits intomastereastgenomics/athena:masterfrom developmenteastgenomics/athena:developmentCopy head branch name to clipboardJul 7, 2021

+1,708-21,667

Commits

Commits on Jun 11, 2021

• add UTF8 charset to template meta tag, fixes weird symbol rendering

  jethror1

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• add datatables functionality to gene and exon stats tables

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• fix table indexing

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• added % values to summary text

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Commits on Jun 14, 2021

• adding local js

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Commits on Jun 19, 2021

• changes to write all plots to array, reduce plot file size by ~1/2

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Commits on Jun 20, 2021

• modify template for new plot format

  jethror1

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• fix formatting of plot str to write

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• add functions for loading bed annotation files

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• fix plot row autosize

  jethror1

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Commits on Jun 21, 2021

• annotate_bed but its now in python

  jethror1

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• add to args

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• fix writing to file

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• fix window size on plots

  jethror1

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• increase plot size

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• improve plot labels

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Commits on Jun 23, 2021

• changes to accomdate moving plotly functionality to JS function, low exon data passed out in array and directly rendered with datatables & plotly in html

  jethror1

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Commits on Jun 26, 2021

• changes to JS for low exon plots to match current styling

  jethror1

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• fix sorting in low exon plot area

  jethror1

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• tidy up low_exon_plot() to remove old code

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Commits on Jun 27, 2021

• formatting and comments

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• update docstring

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• low exon plot formatting

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• comments for datatables/plotly script

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• remove unneeded JS

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• better styling on summary plot axis

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• revert commented line, remove print

  jethror1

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• remove ws

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Commits on Jun 28, 2021

• tidy up html template

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• tidy up python script

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• remove unneeded function from load_data.py

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• remove bad mouthing of pandas, set dtypes for everything

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• changes to move low exon table styling to JS

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• clean up style_sub_threshold()

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• update docstring

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• improve threshold column colouring

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• revert skipping figure

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• tweak report formatting

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• remove skipping plots

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• formatting, comments

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  2a6c356

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• Merge pull request #33 from eastgenomics/1.2-add-dataTables

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  Yu-jinKim

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• improve plot styling

  jethror1

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• Merge branch 'development' into 1.2-mod-plots

  jethror1

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• add check for empty bed file

  jethror1

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• fix assertion

  jethror1

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• remove ws

  jethror1

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• remove ws

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• remove ws

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Commits on Jun 29, 2021

• Merge pull request #31 from eastgenomics/1.2-summary-text

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• Merge branch 'development' into 1.2-fix-utf8

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• Merge pull request #32 from eastgenomics/1.2-fix-utf8

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• Merge branch 'development' into 1.2-low-exon-plots

  mattgarner

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• Merge pull request #36 from eastgenomics/1.2-low-exon-plots

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  mattgarner

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• Merge branch 'development' into 1.2-mod-plots

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• Merge pull request #34 from eastgenomics/1.2-mod-plots

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• - fix y-axis values on low exon plots sometimes being too low

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• comment & ws

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• Merge pull request #37 from eastgenomics/1.2-low-exon-plots

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  mattgarner

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• fix merge issues

  jethror1

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• move copy to clipboard function to head

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• change report text

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• adjust template

  jethror1

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• add multiprocessing to generate low exon plots

  jethror1

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• change example report in /data/example

  jethror1

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• remove old arg

  jethror1

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• remove ws

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• changes to summary text:

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• Merge branch '1.2-fix-merge-issues' of https://github.com/eastgenomics/athena into 1.2-fix-merge-issues

  jethror1

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• improve low exon threshold column colouring for nicer colours

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Commits on Jun 30, 2021

• Merge pull request #38 from eastgenomics/1.2-fix-merge-issues

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  mattgarner

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• remove call to generate sub threshold plots

  jethror1

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• Merge pull request #39 from eastgenomics/fix-plot-bug

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• add checks, output naming

  jethror1

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• comment

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• another comment

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• remove old annotate script

  jethror1

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• update readme

  jethror1

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• add extra check for missing transcripts on intersecting

  jethror1

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• remove testing lines

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• add arg to readme

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• readme typo

  jethror1

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• fix typo

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• readme update

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• switch to non reciprocal overlap, only require panel region covers transcript region & allow flanks

  jethror1

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• addition of --chunk-size arg to split per-base coverage up to not exceed available memory on intersecting

  jethror1

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• Merge pull request #40 from eastgenomics/1.2-annotate-bed

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  Aisha-D

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Commits on Jul 1, 2021

• changes to annotate_bed to match old output

  jethror1

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• Merge pull request #41 from eastgenomics/1.2-fix_annotate_bed-output

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• fix float precision of mean for gene stats

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• Merge pull request #42 from eastgenomics/fix-float-precision

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• fix missing hash on hex code

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• simplify version parsing

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• add newline to make pep8 overlord bot happy

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• Merge pull request #43 from eastgenomics/1.2-fixes

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• fix for appropriately exiting from multi processing on error in generating stats

  jethror1

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• added sorting for nicer output

  jethror1

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• move dropping exon column in gene stats table to stats script

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• Merge pull request #45 from eastgenomics/fix-making-child-kill-parent-successfully

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Commits on Jul 5, 2021

• switch variant tables to use datatables

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• add horizontal seperators

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• fix displaying variant vcfs in summary

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• clean up template

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• remove unneeded function

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• fix replacing empty tables with text, remove old css

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• remove whitespace from template

  jethror1

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• add function to confitionally hide low exon plots when empty

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• refactor template

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• PR tidying up

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• PR changes, JS tidy up, comments

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• Merge pull request #46 from eastgenomics/1.2-vcf_datatables

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Commits on Jul 6, 2021

• fix rounding for sub-threshold table

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• add comment for clarity

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• switch mean column to float in sub-threshold table

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• better comment, add type hints

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• Merge pull request #48 from eastgenomics/1.2-fix-rounding

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Commits on Jul 7, 2021

• add file formatting to readme

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• add link to page for generating transcript file to readme

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• tidy readme

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• readme typo

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• readme update

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• Merge pull request #50 from eastgenomics/1.2-update-readme

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