Comments (7)
I can reproduce this. I think I have a fix and will release a new version shortly, just need to make sure to test!
from bam-js.
@lidaof Ok I have made two changes that should fix this, mostly with regards to compatibility with the browser's native fetch. If you want to try updating to @gmod/[email protected] to give it a shot that would be great!
from bam-js.
hi @cmdcolin thanks for fast fix, i can confirm if it's bamUrl, it's fixed. if use a bamPath, a new error raised :)
from bam-js.
I think you can't use bamPath in the browser as that tries to access the filesystem directly via node.js file system calls and this does not exist in the browser.
If you want to access for example a file that a user opened in the browser, you might want to use the BlobFile class in https://github.com/GMOD/generic-filehandle and pass it to the bamFilehandle/baiFilehandle argument. The bamPath/bamUrl are just convenience methods for using the generic-filehandle class directly
from bam-js.
Note that some of your earlier comments about this topic of opening files actually motivated the creation of generic-filehandle so I hope it is useful :) feel free to provide feedback
from bam-js.
It's designed hopefully to be usable across multiple modules such as cram-js, bam-js, bbi-js, tabix-js, etc.
from bam-js.
oh...yeah..stupid me....what i was thinking using local path in browser....sorry!
Thank you!! @cmdcolin
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Related Issues (20)
- question on seq_id of returned feature 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
- Htsget unable to fetch header from some endpoints HOT 7
- 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
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