Aaron Quinlan comments

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                                            Aaron Quinlan

create fails on some cram/bams

I agree. I know it would be breaking, but I think it makes more sense to default to zero (filter nothing) and make it clear in the release. @38 -...

create fails on some cram/bams

Given the critical nature of this fix, I think we need a new 0.4.0 release for the CLI and pyd4.

[enhancement] stat for a region/list of regions

Hi Darek, This is possible with the `stat` command: d4tools stat -s median -r your.bed your.d4 If you want just one region, you can use UNIX `echo -e` to create...

[enhancement] stat for a region/list of regions

@38 can you look into why mean above is 0 and not 0.5 and explain the differences in behavior?

Allow view to accept a BED file of regions as input

Hi Anthony, absolutely. @38 is working on a new release that includes this functionality.

Allow view to accept a BED file of regions as input

Hi @af8 - this functionality is present in the current release.

Which d4utils version to use?

Currently, you should build from source, as the existing binary lacks recent bug fixes. @38 is working on new functionality for an imminent release, so stay tuned. @38 - is...

c-api doesn't allow setting parameters when writing a new d4 file

@brentp and @38 is this still an issue?

Add hts_open_cb() interface which allows callback function used as data source

For reference, this change is to help allow htslib integration into bedtools. If the htslib maintainers have any suggestions, please let us know.

bedtools merge error when handling reciporally overlap region

I see the error now. Could you share the contents of the original file, as you are requesting merge operations on 5 columns, but the input you show has only...