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CSI indexing #18

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MorexV3CAGE opened this issue Apr 23, 2024 · 3 comments
Open

CSI indexing #18

MorexV3CAGE opened this issue Apr 23, 2024 · 3 comments

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@MorexV3CAGE
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Hi,
I wanted to ask, is there an option to use csi indexing with PINTS? We are working on barley and when we tried running PINTS we got this error:
Snímek obrazovky z 2024-04-23 09-28-20
Am i missing some feature or is it currently not possible? Would you have any suggestions? We are working with NETCAGE data and wanted to give a PINTS a try but otherwise we are working with CAGEr/CAGEfightR.

Thanks,
Simon
@liyao001
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Hi Simon, thank you for reaching out and for your interest in using PINTS for your analysis! We appreciate your feedback and understand the importance of such features for your work. We'll look at this issue and see if we can add csi index support when tbi fails.

@liyao001
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We've developed a patch to address this issue. However, it relies on an update from one of our dependent packages. We've submitted a pull request to that repository and will conduct more systematic testing once the request is accepted. A new version will be released once the tests show no issue.

@MorexV3CAGE
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Thanks for the great news. Looking forward to the release.

liyao001 added a commit to liyao001/PINTS that referenced this issue Jul 21, 2024
@liyao001
[Changed]: improved IO performance by up to ~40% when working with bi…
101c0cb 
…gWig inputs

[Changed]: years in comments
[Added]: `pints_counter` for generating count matrix
[Fixing]: switched to csi index for better handling of large chromosomes. But more tests regarding memory pressure are needed (related to issue hyulab#18)
@liyao001 liyao001 mentioned this issue Jul 22, 2024
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2 participants
@liyao001 @MorexV3CAGE