Resolve "IGV shows wrong alignments"
Description
Upgrade igv from current v2.5.4 to v2.7.9, where the bug https://github.com/igvteam/igv.js/issues/1280 has been resolved.
Related issues
Notes to review (code/docs/QA)
QA: Verify that IGV in VISUAL performs as expected. Also note any differences with current production version for docs.
New features in IGV.js v2.7.9 compared to v2.5.4 that might impact user experience:
- Insertions and deletions are now included in the "sort by base" option (issue 1244)
- Add "Sort by gap size" option to alignment track context (right-click) menu.
- Enable normalization of coverage tracks (1153).
- Add "squished view" option for BAM tracks (160).
- Support setting color (altColor) for negative strand features (1149)
- Make the "showAllChromosomes" option true by default. This option controls the chromosome pulldown. if false only the largest chromosomes will be shown. The intent is to filter out the thousands of small scaffolds and contigs sometimes present in fasta files.
See IGV releases for complete list of differences (including bug fixes).
Tests
General
-
Tests have been added that prove my fix is effective or that my feature works -
Related tests have been modified/removed
Hypothesis testing:
-
Soak testing has been done -
Distribution between positive / negative cases has been checked
Database
-
Includes changes to database schema -
Includes necessary database migrations
Configuration
-
Includes changes to configuration -
Includes configuration migration instructions in documentation
Merge checklist
-
Self-review of code has been performed. -
Feature review and validation against specification has been performed (if applicable). Apply label: QAdone -
Need for documentation has been evaluated and, if necessary, updated. Apply label: docsdone -
Code and implementation has been reviewed by other core developer (including any changes based on initial review). Apply label: code reviewdone
Closes #265 (closed)
Edited by Morten C. Eike