vgteam/libhandlegraph issues and pull requests

#98 - Add a batch path destroy function with a default implementation

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

#98 - Add a batch path destroy function with a default implementation

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

#97 - Change to PanSN "scaffolds" with colon and dash coordinate ranges

Pull Request - State: open - Opened by adamnovak 10 months ago

#97 - Change to PanSN "scaffolds" with colon and dash coordinate ranges

Pull Request - State: open - Opened by adamnovak 10 months ago

#96 - Qualify std::move calls to avoid new warning

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

#96 - Qualify std::move calls to avoid new warning

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

#95 - Install a CMake config to enable find_package(libhandlegraph)

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

#95 - Install a CMake config to enable find_package(libhandlegraph)

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

#94 - Handle full parsing of two-part path names

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

#94 - Handle full parsing of two-part path names

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

#93 - Position of path step relative to the supporting node

Issue - State: closed - Opened by cgroza over 1 year ago - 1 comment

#93 - Position of path step relative to the supporting node

Issue - State: closed - Opened by cgroza over 1 year ago - 1 comment

#92 - undefined reference to `handlegraph::algorithms::dijkstra(handlegraph::HandleGraph const*, handlegraph::handle_t, std::function<bool (handlegraph::handle_t const&, unsigned long)>, bool)'

Issue - State: open - Opened by cgroza over 1 year ago - 2 comments

#92 - undefined reference to `handlegraph::algorithms::dijkstra(handlegraph::HandleGraph const*, handlegraph::handle_t, std::function<bool (handlegraph::handle_t const&, unsigned long)>, bool)'

Issue - State: open - Opened by cgroza over 1 year ago - 2 comments

#91 - Stop parsing `ARS_UCD12#hap0#6` as PanSN

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

#91 - Stop parsing `ARS_UCD12#hap0#6` as PanSN

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

#90 - enable GCC v13.1 compilation

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

#90 - enable GCC v13.1 compilation

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

#89 - Add a `dagify_from` algorithm

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

#89 - Add a `dagify_from` algorithm

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

#88 - add missing else to parse_path_name()

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

#88 - add missing else to parse_path_name()

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

#87 - Add more modes to Dijkstra search

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

#87 - Add more modes to Dijkstra search

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

#86 - Distance traceback

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

#86 - Distance traceback

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

#85 - Makefile:127: recipe for target 'all' failed

Issue - State: closed - Opened by 8banzhuan over 2 years ago - 3 comments

#85 - Makefile:127: recipe for target 'all' failed

Issue - State: closed - Opened by 8banzhuan over 2 years ago - 3 comments

#84 - Revise Path Metadata API

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

#84 - Revise Path Metadata API

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

#83 - Fix the bug I just made in count walks

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

#83 - Fix the bug I just made in count walks

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

#82 - Fix a bug in the overflow detection in count_walks

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

#82 - Fix a bug in the overflow detection in count_walks

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

#81 - Break out more entry points for path copy algorithm

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

#80 - Path metadata API

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

#80 - Path metadata API

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

#75 - Haplotype interface

Issue - State: closed - Opened by glennhickey almost 3 years ago - 15 comments

#75 - Haplotype interface

Issue - State: closed - Opened by glennhickey almost 3 years ago - 15 comments

#74 - Allow tracking nodes through chop

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

#74 - Allow tracking nodes through chop

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

#73 - Add NamedNodeBackTranslation and refactor BoolReturningWrapper

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

#73 - Add NamedNodeBackTranslation and refactor BoolReturningWrapper

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

#72 - Hash the net handle values in a way that compiles

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

#71 - Hash net_handle_t values instead of addresses

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

#70 - Const serialize

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

#70 - Const serialize

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

#69 - Fix bug in unchop

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

#69 - Fix bug in unchop

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

#68 - De-finalize TriviallySerializable

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

#68 - De-finalize TriviallySerializable

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

#67 - Snarls and distance

Pull Request - State: closed - Opened by xchang1 over 3 years ago

#67 - Snarls and distance

Pull Request - State: closed - Opened by xchang1 over 3 years ago

#66 - port over odgi's order-preserving chop

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

#66 - port over odgi's order-preserving chop

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

#65 - Add missing #includes

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

#65 - Add missing #includes

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

#64 - Migrate useful algorithm over from VG

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

#63 - Rip out the fiddly mmap code for libbdsg to own

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

#62 - Split source into multiple CPP files, and add SnarlDecomposition and TriviallySerializable

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

#62 - Split source into multiple CPP files, and add SnarlDecomposition and TriviallySerializable

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

#61 - Add a default implementation for handle get_step_count method

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

#61 - Add a default implementation for handle get_step_count method

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

#60 - Add a truncate method with a default implementation to DeletableHandleGraph interface

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

#60 - Add a truncate method with a default implementation to DeletableHandleGraph interface

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

#59 - Make usable from libbdsg for libbdsg Pip installation

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

#59 - Make usable from libbdsg for libbdsg Pip installation

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

#58 - allow getting the step count of a handle

Pull Request - State: closed - Opened by ekg over 4 years ago

#58 - allow getting the step count of a handle

Pull Request - State: closed - Opened by ekg over 4 years ago

#57 - making RankedHandleGraph part of the default HandleGraph implementation

Issue - State: open - Opened by ekg over 4 years ago

#57 - making RankedHandleGraph part of the default HandleGraph implementation

Issue - State: open - Opened by ekg over 4 years ago

#56 - breaking paths and using extents to maintain contiguity

Issue - State: open - Opened by ekg over 4 years ago

#55 - add specialization of increment_node_ids for long

Pull Request - State: closed - Opened by ekg over 4 years ago

#55 - add specialization of increment_node_ids for long

Pull Request - State: closed - Opened by ekg over 4 years ago

#54 - undefined reference to `increment_node_ids(long)`

Issue - State: closed - Opened by ekg over 4 years ago

#54 - undefined reference to `increment_node_ids(long)`

Issue - State: closed - Opened by ekg over 4 years ago

#53 - Change rewrite_segment semantics to match what libbdsg and vg implement

Pull Request - State: closed - Opened by adamnovak over 4 years ago - 1 comment

#53 - Change rewrite_segment semantics to match what libbdsg and vg implement

Pull Request - State: closed - Opened by adamnovak over 4 years ago - 1 comment

#52 - node naming interface

Issue - State: open - Opened by ekg over 4 years ago

#52 - node naming interface

Issue - State: open - Opened by ekg over 4 years ago