Rewrite generate_bam_index() #2718

hackdna · 2018-04-11T18:16:48Z

FIXME refers to standalone IGV that is no longer used (v1.6.3)
pysam.index() generates .bai file inside FILE_STORE_BASE_DIR which will not work with S3 storage backend since it circumvents file_store API (https://github.com/refinery-platform/refinery-platform/blob/v1.6.3/refinery/data_set_manager/tasks.py#L471)
getting bai extension from FileExtension object is redundant

See also #2210

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hackdna added bug files technical debt important server cloud labels Apr 11, 2018

hackdna added this to To Do in AWS S3 as a storage backend Apr 18, 2018

jkmarx added this to Backlog in Technical Debt via automation Apr 26, 2018

jkmarx assigned scottx611x Apr 26, 2018

hackdna mentioned this issue May 23, 2018

Avoid generating BAM index file under FILE_STORE_BASE_DIR tree #2713

Closed

hackdna added this to the Release 1.6.6 milestone Jul 31, 2018

jkmarx modified the milestones: Release 1.6.6, Release 1.6.7 Aug 28, 2018

ngehlenborg modified the milestones: Release 1.6.7, Release 1.6.9 Sep 17, 2018

ngehlenborg unassigned scottx611x Sep 17, 2018

hackdna mentioned this issue Sep 27, 2018

Remove generate_bam_index() #3037

Closed

hackdna moved this from To Do to Backlog in AWS S3 as a storage backend Oct 1, 2018

hackdna moved this from Backlog to Code in Technical Debt Mar 21, 2019

hackdna modified the milestones: Release 1.6.9, Next Apr 9, 2019

ilan-gold mentioned this issue Oct 11, 2019

Bam File IGV Not Working #3465

Closed

hackdna mentioned this issue Oct 15, 2019

Python2 Package Updates/Changes #3464

Merged

ilan-gold mentioned this issue Oct 25, 2019

Add index file for bam visualizations refinery-platform/docker_igv_js#32

Merged

ngehlenborg modified the milestones: Next, Release 1.7.2 Oct 28, 2019

ilan-gold mentioned this issue Nov 1, 2019

Fix .bam file handling for visualizations #3484

Merged

ilan-gold self-assigned this Nov 13, 2019

ilan-gold closed this as completed Nov 13, 2019

Technical Debt automation moved this from Code to Done Nov 13, 2019

hackdna moved this from Backlog to QA in AWS S3 as a storage backend Dec 9, 2019

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