Aaron Quinlan issues

Results 43 issues of


                                            Aaron Quinlan

Allow view to accept a BED file of regions as input

Currently, the `view` command will accept a list of regions in ... format on the CL. It would be a nice addition to allow a BED file to be specified...

Add a 'shift' tool.

`shift` should move an interval left or right by either a fixed number of bases or a specific fraction of a chromosome.

Add -split option to tag sub command

https://groups.google.com/forum/?fromgroups=#!topic/bedtools-discuss/_2ky6yqmxEQ

Bug in slop if chrom not present in genome file?

https://groups.google.com/forum/?fromgroups=#!topic/bedtools-discuss/PTalkUVQbwk

shuffle -bedpe ignores the -chrom option.

Finding closest intervals on _both_ sides of a query interval

https://groups.google.com/forum/?fromgroups=#!topic/bedtools-discuss/_Pinr6dLG1E While closest doesn't do this in one fell swoop, it should be able to do it in two steps via -D, -id, and -iu. However, I cannot get a...

Support for remote files.

Self explanatory. Use curlib? boost::asio? We would prefer to not use boost::asio in order to minimize external dependencies. Is there a stable C++ library for reading remote files?

Add a 'flip' tool.

Like bit flipping, this would flip the strand of every interval.

Aaron Quinlan