vgteam/libbdsg issues and pull requests

#211 - bdsg install/compilation make a pybind11_tests fail on python-test.yml

Issue - State: closed - Opened by Plogeur about 1 month ago

#210 - Fix Binder for GCC 13

Pull Request - State: closed - Opened by adamnovak about 2 months ago

#209 - Take out unused function

Pull Request - State: closed - Opened by xchang1 about 2 months ago

#208 - Add implementations for the new sequence changing method in libhandlegraph.

Pull Request - State: closed - Opened by jeizenga about 2 months ago

#207 - Add some comments and instructions for making a new snarl index

Pull Request - State: closed - Opened by xchang1 about 2 months ago

#206 - Distance indexing

Pull Request - State: closed - Opened by xchang1 2 months ago

#205 - Allow hinting extra paths to index as reference paths

Pull Request - State: closed - Opened by adamnovak 4 months ago

#204 - Distance bugfix

Pull Request - State: closed - Opened by xchang1 5 months ago

#203 - upgrade libbdsg version from pip installation

Issue - State: open - Opened by Plogeur 6 months ago - 1 comment

#202 - Actually expose the PackedGraph batch path destroy function

Pull Request - State: closed - Opened by jeizenga 7 months ago

#201 - Implement batch delete functions for paths

Pull Request - State: closed - Opened by jeizenga 7 months ago

#200 - Odds and ends for reference path overlay

Pull Request - State: closed - Opened by jeizenga 7 months ago

#199 - A simpler overlay to speed up reference path queries

Pull Request - State: closed - Opened by jeizenga 8 months ago - 1 comment

#198 - Bump submodule to latest sdsl commit

Pull Request - State: closed - Opened by rlorigro 8 months ago

#197 - Build fails on Ubuntu 24

Issue - State: closed - Opened by rlorigro 8 months ago - 1 comment

#196 - Make overlay construction less parallel and lookup hopefully faster

Pull Request - State: closed - Opened by adamnovak 9 months ago

#195 - Zipcode support

Pull Request - State: closed - Opened by xchang1 11 months ago

#194 - When I use python bdsg to deal with a packedgraph, I found a question.

Issue - State: open - Opened by pioneer-pi about 1 year ago - 3 comments

#193 - Prevent uninitialized memory read during PackedPathPositionOverlay construction

Pull Request - State: closed - Opened by jeizenga about 1 year ago

#192 - Add missing jansson link in makefile

Pull Request - State: closed - Opened by jeizenga about 1 year ago

#191 - Enabled the creation of empty handles for PackedGraphs

Pull Request - State: closed - Opened by Robin-Rounthwaite about 1 year ago

#190 - Update net_handle_t bindings to include equality and hash

Pull Request - State: open - Opened by xchang1 over 1 year ago - 1 comment

#189 - Fix PackedGraph edge counting

Pull Request - State: closed - Opened by jeizenga over 1 year ago

#188 - PackedGraph::get_edge_count() doesn't work

Issue - State: closed - Opened by glennhickey over 1 year ago - 2 comments

#187 - Add extra wiggle room for bit width

Pull Request - State: closed - Opened by xchang1 almost 2 years ago

#186 - Predict bit width more accurately

Pull Request - State: closed - Opened by xchang1 almost 2 years ago

#185 - Long Read Giraffe

Pull Request - State: closed - Opened by adamnovak almost 2 years ago

#184 - Map read-only when needed

Pull Request - State: closed - Opened by adamnovak almost 2 years ago

#183 - add typedef for ReferencePathVectorizableOverlayHelper

Pull Request - State: closed - Opened by glennhickey almost 2 years ago

#182 - Allow preloading the distance index from disk

Pull Request - State: closed - Opened by adamnovak almost 2 years ago - 1 comment

#181 - Python bindings install with pip raises legacy-install-failure

Issue - State: closed - Opened by Tharos-ux about 2 years ago - 1 comment

#180 - Add a maximum number of warnings about hitting the snarl size limit

Pull Request - State: closed - Opened by jeizenga about 2 years ago

#179 - Deal with Mac not really having libdl anymore

Pull Request - State: closed - Opened by adamnovak about 2 years ago

#178 - Long distances

Pull Request - State: closed - Opened by xchang1 about 2 years ago

#177 - Commit missing bindings file

Pull Request - State: closed - Opened by adamnovak about 2 years ago

#176 - Bump certifi from 2020.6.20 to 2022.12.7 in /bdsg/docs

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#175 - Remove ODGI

Pull Request - State: closed - Opened by adamnovak about 2 years ago

#174 - Parallelize step-to-path cache in ref overlay

Pull Request - State: closed - Opened by glennhickey about 2 years ago

#173 - Add step->path cache to the reference overlay

Pull Request - State: closed - Opened by glennhickey about 2 years ago

#172 - Deconstruction is still oddly slow with PackedReferencePathOverlay

Issue - State: closed - Opened by adamnovak about 2 years ago - 4 comments

#171 - Better jansson

Pull Request - State: closed - Opened by adamnovak about 2 years ago

#170 - Add and pass tests for multipel indexes

Pull Request - State: closed - Opened by adamnovak about 2 years ago

#169 - Add overlay that accelerates path lookup on nodes

Pull Request - State: closed - Opened by adamnovak about 2 years ago - 3 comments

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

Issue - State: closed - Opened by adamnovak over 2 years ago - 2 comments

#167 - Add some error checking to serialization/deserialization

Pull Request - State: closed - Opened by adamnovak over 2 years ago - 1 comment

#166 - Distance index error checking

Pull Request - State: closed - Opened by adamnovak over 2 years ago - 1 comment

#165 - Distance index

Pull Request - State: closed - Opened by xchang1 over 2 years ago - 2 comments

#164 - Unstatic get net handle

Pull Request - State: closed - Opened by xchang1 over 2 years ago

#163 - Update distance index

Pull Request - State: closed - Opened by xchang1 over 2 years ago

#161 - Docs don't seem to properly list C++ methods anymore

Issue - State: open - Opened by adamnovak over 2 years ago

#160 - Docs/Python bindings broke because of SnarlDistanceIndex

Issue - State: open - Opened by adamnovak over 2 years ago - 1 comment

#159 - Serialize distance index properly

Pull Request - State: closed - Opened by xchang1 over 2 years ago

#158 - Overlays don't work well with haplotype paths

Issue - State: open - Opened by adamnovak over 2 years ago

#157 - Overlays don't expose path metadata methods

Issue - State: open - Opened by adamnovak over 2 years ago

#156 - Distance index

Pull Request - State: closed - Opened by xchang1 over 2 years ago

#155 - Update to the newest libhandlegraph

Pull Request - State: closed - Opened by jeizenga almost 3 years ago

#154 - Fix PackedPositionOverlay multithreaded build

Pull Request - State: closed - Opened by adamnovak almost 3 years ago

#153 - Path metadata API implementation

Pull Request - State: closed - Opened by adamnovak almost 3 years ago - 1 comment

#139 - Use latest libhandlegraph

Pull Request - State: closed - Opened by adamnovak almost 3 years ago

#138 - Parallel overlays

Pull Request - State: closed - Opened by adamnovak almost 3 years ago

#137 - Speed up path position overlay

Issue - State: closed - Opened by glennhickey almost 3 years ago

#136 - Allow tracking nodes through apply_ordering

Pull Request - State: closed - Opened by adamnovak about 3 years ago

#135 - Make bit vector unpack() more like SDSL's get_int()

Pull Request - State: closed - Opened by adamnovak about 3 years ago

#134 - Public proxy

Pull Request - State: closed - Opened by adamnovak about 3 years ago

#133 - Prevent saved chains from being longer than they were when built in memory

Pull Request - State: closed - Opened by adamnovak about 3 years ago

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

Issue - State: open - Opened by adamnovak about 3 years ago

#131 - Fix non-optimized build

Pull Request - State: closed - Opened by adamnovak about 3 years ago - 1 comment

#130 - Bump babel from 2.8.0 to 2.9.1 in /bdsg/docs

Pull Request - State: open - Opened by dependabot[bot] over 3 years ago
Labels: dependencies

#129 - Add low level methods for handle graphs

Issue - State: open - Opened by rlorigro over 3 years ago - 2 comments
Labels: enhancement

#128 - Fast mem map

Pull Request - State: closed - Opened by adamnovak over 3 years ago - 1 comment

#127 - Check chains and distance index

Pull Request - State: closed - Opened by adamnovak over 3 years ago - 1 comment

#126 - Check chains for corruption

Pull Request - State: closed - Opened by adamnovak over 3 years ago

#125 - Pull in SubgraphOverlay and PathSubgraphOverlay from vg

Pull Request - State: closed - Opened by adamnovak over 3 years ago

#124 - Trim unused memory and add memory reporting

Pull Request - State: closed - Opened by adamnovak over 3 years ago - 1 comment

#123 - BUILD_STATIC flag not working

Issue - State: open - Opened by rlorigro over 3 years ago

#122 - Fix MacOS empty CMAKE_INSTALL_LIBDIR when using CMAKE_INSTALL_PREFIX variable

Pull Request - State: closed - Opened by rlorigro over 3 years ago - 5 comments

#121 - Fix Github Actions YAML

Pull Request - State: closed - Opened by adamnovak over 3 years ago - 1 comment

#120 - Mac test

Pull Request - State: closed - Opened by adamnovak over 3 years ago

#119 - Mac build alone

Pull Request - State: closed - Opened by adamnovak over 3 years ago

#118 - Graph implementations in libbdsg use copy constructors instead of move during vector reallocations

Issue - State: open - Opened by jeizenga over 3 years ago

#117 - Fix HashGraph moving and copying

Pull Request - State: closed - Opened by jeizenga over 3 years ago

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

Issue - State: closed - Opened by adamnovak over 3 years ago

#115 - Correct bug in PackedGraph's formula for edge count after deleting nodes

Pull Request - State: closed - Opened by jeizenga over 3 years ago

#114 - Fix bug with deleting down to empty PackedGraph

Pull Request - State: closed - Opened by jeizenga over 3 years ago

#113 - Simplify serialization when magic number/prefix is handled elsewhere

Pull Request - State: closed - Opened by adamnovak over 3 years ago

#112 - Check width for int vector

Pull Request - State: closed - Opened by adamnovak over 3 years ago

#111 - vg reintegration

Pull Request - State: closed - Opened by adamnovak over 3 years ago

#110 - Drop packed-structs.o from the build

Pull Request - State: closed - Opened by adamnovak over 3 years ago

#109 - MappedPackedGraph

Pull Request - State: closed - Opened by adamnovak over 3 years ago

#108 - Bump urllib3 from 1.25.11 to 1.26.5 in /bdsg/docs

Pull Request - State: open - Opened by dependabot[bot] over 3 years ago
Labels: dependencies

#107 - Actually pack the memory-mapped int vectors

Pull Request - State: closed - Opened by adamnovak over 3 years ago - 2 comments

#106 - Question on extracting non-reference nodes

Issue - State: closed - Opened by RenzoTale88 almost 4 years ago - 2 comments

#105 - Bump pygments from 2.7.2 to 2.7.4 in /bdsg/docs

Pull Request - State: open - Opened by dependabot[bot] almost 4 years ago
Labels: dependencies

#104 - How to extract most likely position of series of nodes

Issue - State: open - Opened by RenzoTale88 almost 4 years ago - 5 comments

#103 - Bump jinja2 from 2.11.2 to 2.11.3 in /bdsg/docs

Pull Request - State: open - Opened by dependabot[bot] almost 4 years ago
Labels: dependencies

#102 - Deprecate libbdsg odgi

Issue - State: open - Opened by adamnovak almost 4 years ago

#101 - Add memory mapping support data structures

Pull Request - State: closed - Opened by adamnovak almost 4 years ago

#100 - Fix edge-handling in PackedGraph when dividing backward handles

Pull Request - State: closed - Opened by jeizenga about 4 years ago

#99 - PackedGraph fails to destroy handle after dividing

Issue - State: closed - Opened by glennhickey about 4 years ago

#98 - Update the head and tail of PackedGraph paths during divide_handle

Pull Request - State: closed - Opened by jeizenga about 4 years ago

GitHub / vgteam/libbdsg issues and pull requests