igv.js: "invalid stored block lengths" upgrading from 2.5.2 to 2.15.5

Hello, upgrading from IGV 2.5.2 to 2.15.5 I’m getting this error on an alignment track on a CRAM file (htsget protocol). This is the track (at runtime, so the request header, including the range, is generated by IGV)

{
    "type": "alignment",
    "sourceType": "htsget",
    "endpoint": "https://our.htsget.service",
    "id": "/reads/bypath/STUDY/by_name:SAMPLE_ID.cram",
    "name": "SAMPLE_ID.cram",
    "headers": {
        "Authorization": "Bearer token",
        "Eof": "true",
        "X-Subregion": "chr1:7365009-7383024",
        "Header-bytes-length": "118535"
    },
    "order": 1
}

Inspecting the htsget network requests, on our application running on 2.5.2 I see 3 of them:

https://our.htsget.service/reads/bypath/STUDY/by_name:SAMPLE_ID.cram?format=BAM&referenceName=chr1&start=7365009&end=7383024
https://our.htsget.service/data?format=CRAM&study=STUDY&fileId=12345&class=header
https://our.htsget.service/data?format=CRAM&study=STUDY&fileId=12345&class=body&referenceName=chr1&start=7365009&end=7383024

while in 2.15.5 I see IGV sends 5 requests:

https://our.htsget.service/reads/bypath/STUDY/by_name:SAMPLE_ID.cram?class=header&format=BAM
https://our.htsget.service/data?format=CRAM&study=STUDY&fileId=12345&class=header
https://our.htsget.service/reads/bypath/STUDY/by_name:SAMPLE_ID.cram?format=BAM&referenceName=chr1&start=7365009&end=7383024
https://our.htsget.service/data?format=CRAM&study=STUDY&fileId=12345&class=header
https://our.htsget.service/data?format=CRAM&study=STUDY&fileId=12345&class=body&referenceName=chr1&start=7365009&end=7383024

any suggestion on what could be throwing that error?

About this issue

  • Original URL
  • State: closed
  • Created 9 months ago
  • Comments: 24 (15 by maintainers)

Most upvoted comments

Jim, I just added the (temporary) public BAM endpoint you requested in our issue:

https://htsget.demo.umccr.org/reads/org.umccr.demo.htsget-rs-data/bam/htsnexus_test_NA12878