vgteam/libbdsg

Issues

• upgrade libbdsg version from pip installation

  #203 opened 2 months ago by Plogeur
  0

• Build fails on Ubuntu 24

  #197 opened 5 months ago by rlorigro
  0

• Python bindings install with pip raises legacy-install-failure

  #181 opened 10 months ago by dubssieg
  1

• When I use python bdsg to deal with a packedgraph, I found a question.

  #194 opened 10 months ago by pioneer-pi
  3

• PackedGraph::get_edge_count() doesn't work

  #188 opened a year ago by glennhickey
  2

• Deconstruction is still oddly slow with PackedReferencePathOverlay

  #172 opened 2 years ago by adamnovak
  4

• Speed up finding reference paths on a handle: Make PathPositionOverlay also implement its own for_each_step_on_handle_impl?

  #168 opened 2 years ago by adamnovak
  2

• Docs/Python bindings broke because of SnarlDistanceIndex

  #160 opened 2 years ago by adamnovak
  1

• Docs don't seem to properly list C++ methods anymore

  #161 opened 2 years ago by adamnovak
  0

• Overlays don't work well with haplotype paths

  #158 opened 2 years ago by adamnovak
  0

• Overlays don't expose path metadata methods

  #157 opened 2 years ago by adamnovak
  0

• Speed up path position overlay

  #137 opened 3 years ago by glennhickey
  0

• Add low level methods for handle graphs

  #129 opened 3 years ago by rlorigro
  2

• Building a big `bdsg::yomo::UniqueMappedPointer<bdsg::MappedIntVector>` and *then* saving it causes total chain size reported by `get_usage()` to increase

  #132 opened 3 years ago by adamnovak
  0

• Needs to be able to read GFA by itself

  #79 opened 4 years ago by adamnovak
  1

• BUILD_STATIC flag not working

  #123 opened 3 years ago by rlorigro
  0

• When running on (M1?) Mac, tests fail due to trying to refer across chains

  #116 opened 3 years ago by adamnovak
  0

• Graph implementations in libbdsg use copy constructors instead of move during vector reallocations

  #118 opened 3 years ago by jeizenga
  0

• Question on extracting non-reference nodes

  #106 opened 4 years ago by RenzoTale88
  2

• How to extract most likely position of series of nodes

  #104 opened 4 years ago by RenzoTale88
  5

• Deprecate libbdsg odgi

  #102 opened 4 years ago by adamnovak
  0

• PackedGraph fails to destroy handle after dividing

  #99 opened 4 years ago by glennhickey
  0

• divide_handle() doesn't properly update paths in PackedGraph

  #97 opened 4 years ago by glennhickey
  0

• divide_handle broken on rev. strand for PackedGraph and HashGraph

  #94 opened 4 years ago by glennhickey
  0

• Example of using bdsg.bdsg.PositionOverlay

  #93 opened 4 years ago by RenzoTale88
  1

• Question on extracted path with bdsg

  #92 opened 4 years ago by RenzoTale88
  1

• Installing the Python module on Mac claims to succeed at building the wheel, but ships a module file that can't find its libraries

  #83 opened 4 years ago by adamnovak
  0

• Needs to be pip installable

  #78 opened 4 years ago by adamnovak
  2

• We should be able to install via `pip` without checking the `python3` on the PATH

  #82 opened 4 years ago by adamnovak
  0

• reinterpret_cast should maybe be static_cast

  #76 opened 4 years ago by adamnovak
  1

• Too hard to use as an ExternalProject

  #73 opened 4 years ago by adamnovak
  1

• missing Python.h on system where it is present

  #65 opened 5 years ago by ekg
  1

• Who are the copyright holders of this code?

  #22 opened 4 years ago by mr-c
  2

• python documentation largely incomplete

  #66 opened 4 years ago by ekg
  3

• OverlayHelper ought to be apply()-able on const graphs

  #64 opened 4 years ago by adamnovak
  0

• Overlay helper get() ought to be const

  #63 opened 4 years ago by adamnovak
  0

• The ODGI graph does not pass the handle graph tests ported over from VG

  #19 opened 5 years ago by jeizenga
  9

• Incrementing ids leaves HashGraph is sorry state

  #51 opened 5 years ago by glennhickey
  3

• Python bindings don't bind any methods that use std::vector

  #50 opened 5 years ago by adamnovak
  6

• Resizing factor bug in PackedGraph

  #46 opened 5 years ago by jeizenga
  0

• HashGraph allows duplicate edges when it shouldn't.

  #39 opened 5 years ago by adamnovak
  3

• Vectoizable Overlays assume that graph iteration order is consistent and thus break vg pack

  #40 opened 5 years ago by adamnovak
  6

• Add magic numbers to the serialize/deserialize methods

  #24 opened 5 years ago by adamnovak
  2

• Deleting steps while looping through the steps on a node

  #35 opened 5 years ago by adamnovak
  0

• Looks for DYNAMIC in the wrong(?) place

  #23 opened 5 years ago by adamnovak
  1

• Let's get Travis running the unit tests

  #21 opened 5 years ago by glennhickey
  0

• Name Change

  #2 opened 5 years ago by adamnovak
  5