igvteam / hic-straw Goto Github PK

Hi Jim,

I am testing one file and the norm options did contain KR, while when I use KR to pull the data, I got error: Normalization vectors not present in this file. I used the code just pulled from master.

Hi, I started some experiments with using hic-straw in jbrowse and it's working quite well. I made a small wrapper so generic-filehandle can be used with it (adapts our read(buffer, offset, length, pos) to read(pos, length) which is of course much simpler...just a legacy of trying to adapt the nodejs file reader api) so this is great.

I did have one concern, I saw that commonjs require('hic-straw') was working but the es6 import wasn't (produced negative file offsets in file reading, etc)

Might be related to package.json having this?

"module": "dist/hic-straw_es6.js",

This file appears to not be involved in the current build though, yet it is being deployed in the NPM bundles, so I wonder if this should actually say this

"module": "dist/hic-straw.esm.js"

Hi Jim,

Previous version of straw seems works with file Blob as input when construct a new Straw instance, in this new version, how can I enable this?
I tried {file: fileBlob} which is not working.
Thanks.

Hi Jim,

Hope you are doing well and stay safe.

I recently upgrade hi-straw to 1.1.0, I found there are more errors on network tab trying to access same HiC file url

version 1.1.0:

version:0.9.4

fetched results are same though from my visual inspect..I don't see any usage update not sure if I did something wrong. Can you please check if I did something wrong? Thanks a lot.

Hi Jim,

Is it easy to support chromosome name 1 or chr1 automatically ? Thanks.

Hi there
We had a user of jbrowse 2 report that they got an error opening a hic file with a "RangeError: Out of bounds access" which appears to be due to reading a file that might have many scaffolds or something that makes it have a header that exceeds the boundary of 64000

I see in the source code it might make the assumption that the header can be obtained in a single fetch of 64000. It might need to do a larger fetch or perhaps re-fetch if it determines that the file is larger than that

Hi Jim,
Thanks for the nice library!
I am trying to including this library to our project, while trying the example, get following err:

I created an empty html page here and trying on the web console.

Thanks a lot.

Hi Jim,

Nice to see juicebox.js can access GEO hic files through web.
I also tried this link with latest hic-straw (0.9.3), i got following error:

same links works at juicebox.js site.
Did I miss any step? Thank you.