1.2 - development -> main

[jethror1]

Changes to functionality to improve usability and reduce file sizes. Adds a scrollable window, searching and deferred rendering to all tables and plots, allowing for large panels to not increase file size greatly and still load in similar time to smaller panels.

Component PRs included:

• 1.2 add gene % to summary text #31
• 1.2 fix UTF-8 encoding #32
• 1.2 Add dataTables to HTML tables #33
• 1.2 - Modify gene plots #34
• 1.2 - Modify sub-threshold plots #36
• 1.2 - Tweak low exon plots #37
• 1.2 Fix merge issues #38
• remove call to generate sub threshold plots #39
• 1.2 - Change annotation script to Python #40
• changes to annotate_bed to match old output #41
• fix float precision of mean for gene stats #42
• 1.2 - Fix missing hash, improve version parsing #43
• Fix making child kill parent successfully #45
• 1.2 - add dataTables functionality to variant tables from VCFs #46
• 1.2 - fix rounding for sub-threshold table #48
• 1.2 - Update readme #50

Issues fixed:

• Fixes change layout of subplot grid for small number of plots #2
• Fixes add check for annotated bed #19
• Fixes killing child causes map to hang #20
• Fixes rewrite annotate_bed.sh #21
• Fixes Limit low exon plots in report #24
• Fixes Conditionally hide low exon table and plots if everything covered at 100% #25
• Fixes Drop unneeded exon number col from gene_stats.tsv before writing to file #26
• Fixes Include absolute coverage values for genes in suboptimal coverage list of html report #28
• Fixes Fun characters in panel names #30

Full combined PR notes here

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This change is 

[pep8speaks]

Hello @jethror1! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file bin/annotate_bed.py:

Line 60:80: E501 line too long (80 > 79 characters)
Line 82:5: E303 too many blank lines (2)
Line 115:80: E501 line too long (83 > 79 characters)

• In the file bin/coverage_report_single.py:

Line 247:80: E501 line too long (80 > 79 characters)
Line 1084:80: E501 line too long (88 > 79 characters)
Line 1403:80: E501 line too long (82 > 79 characters)
Line 1410:80: E501 line too long (81 > 79 characters)

• In the file bin/coverage_stats_single.py:

Line 283:80: E501 line too long (80 > 79 characters)

• In the file bin/load_data.py:

Line 43:5: E303 too many blank lines (2)
Line 64:5: E303 too many blank lines (2)
Line 85:5: E303 too many blank lines (2)
Line 366:80: E501 line too long (80 > 79 characters)

Comment last updated at 2021-07-07 15:45:39 UTC

[mattgarner]

Fantastic work

[mattgarner]

Reviewed 9 of 10 files at r1, 1 of 1 files at r2.
Reviewable status: complete! all files reviewed, all discussions resolved (waiting on @jethror1)