Alignment path in config files and new features

[4.12]

Added

• Accepts alignment_path in load config to pass bam/cram files
• Display all phenotypes on variant page
• Display hgvs coordinates on pinned and causatives
• Clear panel pending changes
• Adds option to setup the database with static files
• Adds cli command to download the resources from CLI that scout needs
• Adds dummy files for merged somatic SV and CNV; as well as merged SNV, and INDEL part of #1279
• Allows for upload of OMIM-AUTO gene panel from static files without api-key

Fixed

• Cancer case HPO panel variants link
• Fix so that some drop downs have correct size
• First IGV button in str variants page
• Cancer case activates on SNV variants
• Cases activate when STR variants are viewed
• Always calculate code coverage
• Pinned/Classification/comments in all types of variants pages
• Null values for panel's custom_inheritance_models
• Discrepancy between the manual disease transcripts and those in database in gene-edit page
• ACMG classification not showing for some causatives
• Fix bug which caused IGV.js to use hg19 reference files for hg38 data
• Bug when multiple bam files sources with non-null values are available

Changed

• Renamed requests file to scout_requests
• Cancer variant view shows two, instead of four, decimals for allele and normal