agalitsyna
agalitsyna
- [x] The major problem with pileups is that the pileup function does not know about regions and takes them from the input features dataframe. - [x] The creation of...
clever solution that immensely speeds up the expected_cis calculation is to do fast Fourier convolution for calculation of pairwise distances between bad bins ([here](https://github.com/open2c/cooltools/blob/ab5d775ee50fb3d4483520a40f758914348e89b7/cooltools/api/expected.py#L29)). However, at least with latest scipy...
Added `--count-dups` reporting mode for scipy and scikit-learn backends that report the number of duplicates (a little bit unfair, though, as the parent is counted there as well - it...
generate coverage in bedgraph/bigwig format with a given resolution from .pairs files. can be based on pairtools.filterbycov module. parameters to include: - resolution should be set up externally - output...
Premise: - `pysam` is fast but introduces multiple logistic complications. We may want to replace it with manual bam parser (Anton's style). `pysam`: - is complicated to link in isolated...
Are pairtools supported on OSX? It's removed in a recent conda recipe. Why?
#### Needs discussion/fix: - [ ] bam annotation? https://github.com/open2c/pairtools/issues/67 - [x] ~~report mapq in the stats: https://github.com/open2c/pairtools/issues/80 (or extend to any specified additional fields?)~~ This was actually implemented in the...
- [ ] definitions - [ ] functions - [ ] `regions_to_bins` to assign binspans to a set of bp spans - [ ] `align_tables` #37 - [ ] `adjust_view_to_bintable`...
Unexpected behavior while reproducing the docs: - Section of the docs is not running when working on a remote computer: http://docs-python.higlass.io/getting_started.html#numpy-matrix - Missing required argument for LocalTileset: datatype="matrix" - Plugin...