Comments (7)
I suspect that's partly being tackled by @jb-adams in ga4gh/htsget-refserver#8 ?
from bam-js.
Could be! On some level, I think this code should figure out how to be more like samtools and figure it out but I'll certainly check the pr especially if it is deployed somewhere
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For dnanexus's webserver, we request a bogus refname because otherwise it says the "header" involves a download of 10GB of data, and we don't try to "subselect" the range that it gives us
We could consider dropping support for dnanexus's htsget server so that ga4gh's htsget server works, or we find a fix that accomodates both, or just leave as is
from bam-js.
See the behavior of the dnanexus server here
#range is the entire file, e.g. 140gb, which our code doesn't currently try to subselect from resulting in bad behavior if used
http://htsnexus.rnd.dnanex.us/v1/reads/BroadHiSeqX_b37/NA12878?class=header
#reasonable size, all data encoded in a data uri even
http://htsnexus.rnd.dnanex.us/v1/reads/BroadHiSeqX_b37/NA12878?class=header&referenceName=DOES_NOT_EXIST
from bam-js.
IIRC the htsnexus htsget server might not as up to date as the GA4GH reference htsget server? Please refer to the official public GA4GH server endpoints mentioned in here:
So yes, I'd consider dropping support for previous spec versions, tbh.
from bam-js.
Ya that was the impetus for the comment. However, my workaround to work with the dnanexus server (to add a random referenceName to the class=header request) does not work with the ga4gh server. I kind of figured the hacky behavior to add the random refname wouldn't be great but I got to figure out what to do next
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That page is now gone along with the deprecated endpoints. I was about to suggest using the official GA4GH htsget endpoint, but it seems to be undergoing some issues for a couple of weeks now?:
/cc @jb-adams can you tilt that one back up please?
/cc @victorskl @andrewpatto
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Related Issues (20)
- Support for Content-Encoding:gzip(?) HOT 2
- Support AN (alternative naming)
- Merge adjacent blocks code could result in large allocation HOT 2
- error with local uploaded file HOT 4
- Port intra-slice merging from tabix HOT 1
- Investigate split alignment data structures HOT 1
- Not fetching all reads HOT 1
- add SAM parsing
- Support BAI index aka BAM index index HOT 1
- Large amount of short reads bogs jbrowse down HOT 1
- All tags are stored in lower case, but technically lower case tags are distinct from upper case
- Wrong negative number values being reported for some tags
- Feature sequence is undefined HOT 2
- need explanation for usage HOT 5
- Missing end position in read mate? HOT 2
- fetch size limit error with `pairAcrossChr` HOT 2
- htsget auth support HOT 4
- LocalFile is not a constructor HOT 2
- Typing issues HOT 5
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