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Href passing to IGV too large - refactor jinja URL build

See original GitHub issue

Passing href to IGV is a large chunk of nearly identical information. Is there a way to make Jinja accept a higher order structure?

Reference: https://github.com/Clinical-Genomics/scout/pull/1548#discussion_r370552457

Example:

<a class="btn btn-outline-secondary btn-sm" href="/igv?sample=NA12878&amp;build=37&amp;bam=%2FUsers%2FMikael%2FWork%2Fgenomes%2FHG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam&amp;bam=%2FUsers%2FMikael%2FWork%2Fgenomes%2FHG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam&amp;bam=%2FUsers%2FMikael%2FWork%2Fgenomes%2FHG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam&amp;bai=%2FUsers%2FMikael%2FWork%2Fgenomes%2FHG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam.bai&amp;bai=%2FUsers%2FMikael%2FWork%2Fgenomes%2FHG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam.bai&amp;bai=%2FUsers%2FMikael%2FWork%2Fgenomes%2FHG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam.bai&amp;rhocall_bed=%2FUsers%2FMikael%2FWork%2Fscout_dev2%2Fscout%2Fscout%2Fdemo%2Ftest_upd.sites.bed&amp;rhocall_bed=%2FUsers%2FMikael%2FWork%2Fscout_dev2%2Fscout%2Fscout%2Fdemo%2Ftest_upd.sites.bed&amp;rhocall_bed=%2FUsers%2FMikael%2FWork%2Fscout_dev2%2Fscout%2Fscout%2Fdemo%2Ftest_upd.sites.bed&amp;rhocall_wig=%2FUsers%2FMikael%2FWork%2Fscout_dev2%2Fscout%2Fscout%2Fdemo%2Ftest.bw&amp;rhocall_wig=%2FUsers%2FMikael%2FWork%2Fscout_dev2%2Fscout%2Fscout%2Fdemo%2Ftest.bw&amp;rhocall_wig=%2FUsers%2FMikael%2FWork%2Fscout_dev2%2Fscout%2Fscout%2Fdemo%2Ftest.bw&amp;tiddit_coverage_wig=&amp;upd_regions_bed=%2FUsers%2FMikael%2FWork%2Fscout_dev2%2Fscout%2Fscout%2Fdemo%2Ftest_upd.sites.bed&amp;upd_regions_bed=%2FUsers%2FMikael%2FWork%2Fscout_dev2%2Fscout%2Fscout%2Fdemo%2Ftest_upd.sites.bed&amp;upd_regions_bed=%2FUsers%2FMikael%2FWork%2Fscout_dev2%2Fscout%2Fscout%2Fdemo%2Ftest_upd.sites.bed&amp;upd_sites_bed=%2FUsers%2FMikael%2FWork%2Fscout_dev2%2Fscout%2Fscout%2Fdemo%2Ftest_upd.sites.bed&amp;upd_sites_bed=%2FUsers%2FMikael%2FWork%2Fscout_dev2%2Fscout%2Fscout%2Fdemo%2Ftest_upd.sites.bed&amp;upd_sites_bed=%2FUsers%2FMikael%2FWork%2Fscout_dev2%2Fscout%2Fscout%2Fdemo%2Ftest_upd.sites.bed&amp;contig=7&amp;start=124491922&amp;stop=124492022&amp;center_guide=T" target="_blank">IGV viewer</a>

Issue Analytics

State:
Created 4 years ago
Reactions:1
Comments:7 (4 by maintainers)

Top GitHub Comments

1reaction

dnilcommented, Jan 24, 2020

Ah, actually it’s not the igv.js call directly that is the Problem. It’s one step before! We are quite free to modify our view in alignviewers to accept post requests, which would take care of the absolute length issue.

0reactions

northwestwitchcommented, Jan 24, 2020

What about creating a soft link to the folder where the data is?

But it’s not a good solution 😕

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