Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / vgteam/libvgio issues and pull requests

#71 - Fix multithreaded GAM read

Issue - State: open - Opened by adamnovak 5 months ago - 1 comment

#70 - Add support for progress reporting to the stream.hpp API

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

#69 - Allow extra data inline in GAM files

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

#68 - Use 8 decoding threads when reading BGZF files (GAM, etc.)

Pull Request - State: closed - Opened by adamnovak 12 months ago

#67 - Fix include references

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

#66 - Use installed libhandlegraph if available

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

#65 - Add debug logging and fix GAF end computation

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

#63 - Write fp/fn tags for unmapped reads too in GAF

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

#62 - Support build and large writes on Mac

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

#61 - Add test code to make sure Protobuf reflection works

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

#60 - Support big writes through stream encapsulation

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

#59 - fix logic bug introduced in prev commit wrt range translation

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

#58 - improve gam-to-gaf conversion for split alignments

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

#56 - Fix GAF parsing bug

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

#55 - Sync with latest libhandlegraph

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

#53 - Disallow trailing softclip-only mappings in GAM<=>GAF conversion

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

#52 - GAF support for GFA space

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

#51 - Enable snarls to talk about GFA coordinates

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

#50 - Support both 1- and 2-parameter versions of setTotalBytesLimit()

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

#48 - Use single-argument version of SetTotalBytesLimit

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

#47 - Pass through support from annotation to GAF AD tag

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

#47 - Pass through support from annotation to GAF AD tag

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

#46 - Make CMake minimum version reflect reality

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

#45 - Fix CMake build script

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

#44 - Use our own source dir when a subdirectory

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

#42 - Fix bad GAF parsing bug

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

#41 - Fix interval parsing bug in gafkluge

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

#40 - Replace load_all with try_load_first

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

#39 - Support cg cigars in GAF

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

#38 - fix gaf.path_end to be relative to the path, not last node

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

#37 - Generalize VPKG loader for GFA support

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

#36 - Properly paired tag

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

#35 - Explicit handlegraph dependency (fixes Mac build)

Pull Request - State: closed - Opened by Ellmen almost 4 years ago - 1 comment

#33 - Buffer standard input to allow putback

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

#32 - support fragment_next/prev in gaf<->gam conversion

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

#31 - Parallelize gam conversion when streaming in gaf

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

#30 - Add gaf interface that can use callbacks instead of graph

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

#29 - Use string Protobuf parser that takes big messages

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

#28 - Extend the schema for multipath alignments to accommodate splicing

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

#27 - Unable to install libvigo ?

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

#26 - Find Protobuf once and guess static lib

Pull Request - State: closed - Opened by adamnovak over 4 years ago - 2 comments

#25 - Move in a bunch of stuff from vg

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

#24 - don't throw away user provided CMAKE_CXX_FLAGS

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

#23 - Make max emitter message size static to silence clang warnings

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

#22 - Note that we need htslib 1.10 to avoid known bugs

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

#21 - Don't EOF streams by sniffing

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

#20 - Pull in StreamIndex from vg to support indexed GAM

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

#19 - Removed linking hack which caused incompatibility with other libraries

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

#18 - -isystem flag leads to standard library errors

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

#17 - Note that we need htslib

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

#16 - Multi magic

Pull Request - State: closed - Opened by adamnovak almost 5 years ago

#15 - Sniff Proto Streams and Allow Multiple Loaders

Pull Request - State: closed - Opened by adamnovak almost 5 years ago

#14 - explicitly share batch size variable with omp

Pull Request - State: closed - Opened by glennhickey about 5 years ago

#13 - Make streaming batch size a parameter

Pull Request - State: closed - Opened by glennhickey about 5 years ago

#12 - Severing Protobuf dependency

Issue - State: open - Opened by adamnovak about 5 years ago

#11 - Use C++14 standard

Pull Request - State: closed - Opened by adamnovak about 5 years ago

#10 - Magic numbers

Pull Request - State: closed - Opened by adamnovak about 5 years ago

#9 - Decompress vpkg

Pull Request - State: closed - Opened by adamnovak over 5 years ago

#8 - Implement stream multiplexing

Pull Request - State: closed - Opened by adamnovak over 5 years ago

#7 - correct overflow due to errant constant multiplication

Pull Request - State: closed - Opened by ekg over 5 years ago

#6 - Handle empty final batches

Pull Request - State: closed - Opened by adamnovak over 5 years ago

#5 - Adapt to message being a pointer

Pull Request - State: closed - Opened by adamnovak over 5 years ago

#4 - Allow loading of non-default-constructible types like abstract base classes

Pull Request - State: closed - Opened by adamnovak over 5 years ago - 2 comments

#3 - make compilation work when we haven't used namespace std

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

#2 - Bring back giant message parsing support

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

#1 - Document refpos semantics for Alignments

Pull Request - State: closed - Opened by adamnovak over 5 years ago