BiocPy/GenomicRanges

Issues

• Is GenomicRanges object open-ended?

  #132 opened a month ago by kijiy
  4

• Wrong dtypes used for seqnames in `GenomicRanges._sanitize_seqnames` and should use max value not len of unique values as `num_uniq`

  #120 opened 3 months ago by DiDeoxy
  2

• 8 bits is too little to store all contigs of hg38

  #127 opened 2 months ago by balwierz
  4

• `_combine_GenomicRanges` and `_fast_combine_GenomicRanges` return wrong results

  #129 opened 2 months ago by balwierz
  2

• `setdiff` fails on `reduce`d ranges

  #126 opened 2 months ago by balwierz
  0

• `IRanges.to_pandas` fails if there are mcols

  #125 opened 2 months ago by balwierz
  2

• Wrong value passed to `_validate_optional_attrs` when setting names in `GenomicRangesList`

  #119 opened 3 months ago by DiDeoxy
  0

• Should `GenomicRanges` and `GenomicRangesList` check that the row_names of `mcols` is the same as the name of the ranges in the parent object?

  #121 opened 4 months ago by DiDeoxy
  4

• when num of sequences > np.int8

  #117 opened 4 months ago by jkanche
  0

• subtract doesn't work as expected

  #116 opened 5 months ago by jkanche
  0

• Implement `psetdiff`

  #115 opened 5 months ago by jkanche
  0

• Overlaps between `GenomicRanges` and `GenomicRangesList`

  #113 opened 5 months ago by jkanche
  0

• Add `Hits` class

  #111 opened 5 months ago by jkanche
  0

• split `GenomicRanges` by a factor

  #108 opened 5 months ago by jkanche
  1

• "All objects to combine must have the same number of columns" should not be forced for intersect.

  #98 opened 6 months ago by ghuls
  9

• Add `distance` method

  #66 opened 6 months ago by jkanche
  1

• Integrate with granges for some of the interval operations

  #96 opened 6 months ago by jkanche
  1

• [feature request] Add _repr_html_() for visualistion in Jupyter Notebooks

  #94 opened 6 months ago by balwierz
  2

• coerce grangeslist to granges

  #19 opened a year ago by jkanche
  0

• missing option `equal` for `query_type` in `find_overlaps` and other associated methods

  #79 opened 8 months ago by jkanche
  0

• `read_gtf` function works slowly

  #84 opened 6 months ago by abearab
  8

• reduce function does not support hg19 seqnames

  #85 opened 7 months ago by maayanamid
  1

• `to_pandas()` coerces `seqnames` to integers

  #81 opened 8 months ago by tkoomar
  1

• Create more realistic examples

  #77 opened 9 months ago by mmokrejs
  8

• Add missing dependency on joblib

  #75 opened 9 months ago by mmokrejs
  2

• identify bug in `reduce` resulting in an in-place operation

  #49 opened a year ago by jkanche
  1

• Improve performance of `find_overlaps`

  #67 opened a year ago by jkanche
  1

• Fix printing method for empty GRL's

  #54 opened a year ago by jkanche
  1

• Documentation for version 0.4.1 is outdated

  #46 opened a year ago by nsheff
  1

• Improve generator function consistency with R packages

  #45 opened a year ago by mjsteinbaugh
  3

• bad version requirements leads to incompatibility with biocframe

  #41 opened a year ago by nsheff
  3

• Reading Gencode GTF failed

  #43 opened a year ago by Snowymint
  1

• Store strand as a NumPy array or Factor (probably)

  #39 opened a year ago by LTLA
  2

• Store the seqnames as indices into the Seqinfo

  #38 opened a year ago by LTLA
  1

• mcols should always be a `BiocFrame`

  #33 opened a year ago by LTLA
  1

• auto generate seqinfo object.

  #32 opened a year ago by jkanche
  1

• `GenomicRanges` should not inherit from a `BiocFrame`

  #35 opened a year ago by LTLA
  1

• Don't store the `seqinfo` in the `metadata`

  #36 opened a year ago by LTLA
  1

• module 'genomicranges' has no attribute 'from_gtf'

  #28 opened a year ago by onionpork
  2

• GRangesList should extend `biocframe`

  #20 opened a year ago by jkanche
  0

• need to be able to create an empty `genomicranges` object

  #21 opened a year ago by jkanche
  0

• Incorrect type hinting?

  #17 opened a year ago by DiDeoxy
  0

• GRangesList class

  #3 opened a year ago by jkanche
  0

• Can't import `genomicranges` with Python 3.11

  #11 opened a year ago by nleroy917
  1

• No way to set up an empty GenomicRanges like in BiocFrame

  #4 opened 2 years ago by DiDeoxy
  1