-
Notifications
You must be signed in to change notification settings - Fork 309
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Newbie questions - learning resources? Reading a range of records from Adam? #281
Comments
I faced same issue. Where is API doc like Javadoc or scaladoc and examples. 发自我的 iPhone 在 2014-6-28,上午10:11,pkondratyuk notifications@github.com 写道:
|
Hi @pkondratyuk and @alartin! We're glad to see you using the project; we're pushing towards a production release towards the end of this year where we have fully fleshed-out documentation. However, there has been a large demand for Scaladoc recently, so we will work to publish that. https://github.com/hammerlab has built an ipython notebook that documents how to setup ADAM, @massie @hammer @arahuja, can you post this link? If you have the repo checked out, you can generate scaladoc with:
@pkondratyuk there are two ways to filter on genomic region, depending on whether you want to filter on read from Parquet, or if you want to filter after you've read the data. Are you interested in a particular pattern? |
Thank you for your response. We don't really need to filter for this particular task, I think... We would just like to retrieve a set of records as AdamRecord when given the start record number and the end record number. I.e. retrieve records numbers 500 to 576 (contiguous), and possibly the SAM header from that Adam file. Or does it count as filtering on record number? |
The iPython notebook I mentioned above was hiding in plain sight! ;) For anyone interested, you can find it here. @pkondratyuk sorry for the slow response to your question above; I've been traveling the last few days, and a few other team members are out of the office as well. I'll try to post a more detailed reply tomorrow, but you may want to check out some of the code in the LocusPredicate, for an example of how we can use a predicate in Parquet to filter on records. In your case, I think you'd want to apply a predicate on the range of records you're looking to pull out. |
Thanks, that will definitely be helpful to us. We've built a simple program based on the adam-core API that reads from an ADAM file and tries to write a SAM file, and it compiles fine but for some reason fails at runtime with a strange-looking exception:
What could be going here? The code is below, it's pretty basic:
|
@fnothaft : do you mind if I post the |
@pkondratyuk yes, please! That would be great. |
Done! If you could help us with this issue, a bioinformatics company would be on its way to storing its data internally in the ADAM format :)) Thanks a lot for developing this product. |
Closing in favor of other documentation issues. |
Being totally new to Adam, I was wondering is there a set of learning resources to start teaching myself the Java/Scala API?
On a more specific note, what API functions would I need to read a range of records (say all records from number 5 to 637) from an adam file?
The text was updated successfully, but these errors were encountered: