fix: junctions extractor count overlapping read pairs once

griffithlab / regtools

Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.

https://regtools.readthedocs.org

MIT License

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fix: junctions extractor count overlapping read pairs once #196

Open TimD1 opened 2 months ago

TimD1 commented 2 months ago

closes #187, implemented by adding set of reads to Junction, and only incrementing read_count if read has not been seen yet
- this commit should also increase RegTools speed by removing the barcode updating bottleneck caused by repeatedly copying the barcode map
- updated regtools to v1.1.0

santataRU commented 1 month ago

closes bug report: junction extract tool should not count overlapping reads as double support for a junction #187, implemented by adding set of reads to Junction, and only incrementing read_count if read has not been seen yet

this commit should also increase RegTools speed by removing the barcode updating bottleneck caused by repeatedly copying the barcode map

updated regtools to v1.1.0

Dear TimD1,

Is the source code for Regtools version 1.1.0 available for download? I am currently using version 1.0.0 and would like to access the updated version so that the Regtools junctions extractor counts overlapping read pairs only once.

Thank you for your help.

Best regards, Xiao

TimD1 commented 1 month ago

The source code that counts overlapping read pairs only once is available from my fork of RegTools, at: https://github.com/fulcrumgenomics/regtools/tree/187/td/no-double-read-support

However, please note that this is not an official RegTools v1.1.0 release (I just suggested bumping the version due to several command-line parameter changes) and there are no guarantees on this fork being supported/maintained (it was only created to make this batch of PRs).

santataRU commented 1 month ago

The source code that counts overlapping read pairs only once is available from my fork of RegTools, at: https://github.com/fulcrumgenomics/regtools/tree/187/td/no-double-read-support

However, please note that this is not an official RegTools v1.1.0 release (I just suggested bumping the version due to several command-line parameter changes) and there are no guarantees on this fork being supported/maintained (it was only created to make this batch of PRs).

Hi, Tim,

Thank you very much for your help. Does this version address the strandedness issue mentioned in this post (https://github.com/griffithlab/regtools/issues/197)?

Xiao