Commits · master · vgteam / vg

This project is mirrored from https://*****@github.com/vgteam/vg.git. Pull mirroring updated May 24, 2022.

23 May, 2022 1 commit
- Merge pull request #3665 from vgteam/long_read_giraffe_select_minimizers · 04775076
  Adam Novak authored May 23, 2022
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Enable capping number of minimizers and filtering of overlapping minimizers
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  04775076
21 May, 2022 1 commit
- Apply suggestions from code review · 26f49a79
  Adam Novak authored May 20, 2022
  
  26f49a79
20 May, 2022 2 commits
- Rename variable for number of selected minimizers. · 86bd3ff5
  StephenHwang authored May 20, 2022
  
  86bd3ff5
- Enable capping number of minimizers and filtering of overlapping minimizers. · ded8e2f3
  StephenHwang authored May 20, 2022
  
  ded8e2f3
19 May, 2022 1 commit
- Merge pull request #3658 from vgteam/retagging · 2ab89879
  Adam Novak authored May 19, 2022
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Allow manipulating GBWT tags to efficiently change references in a GBWT or GBZ
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  2ab89879
13 May, 2022 2 commits
- Merge pull request #3662 from vgteam/mp-surject-secondary · 2cea1e25
  Jordan Eizenga authored May 13, 2022
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Don't drop secondary alignment annotation on unmapped reads in surject
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  2cea1e25
- don't drop annotations on unmapped reads in surject · 132adf3c
  Jordan Eizenga authored May 13, 2022
  
  132adf3c
12 May, 2022 2 commits
- Merge pull request #3661 from vgteam/mp-surject-secondary · 0b6ac591
  Jordan Eizenga authored May 12, 2022
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preserve secondary annotations in mp surject
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  0b6ac591
- preserve secondary annotations in mp surject · 3bdeb37e
  Jordan Eizenga authored May 12, 2022
  
  3bdeb37e
11 May, 2022 2 commits
- Merge pull request #3660 from vgteam/gq-surject · 85efb279
  Jordan Eizenga authored May 11, 2022
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Add group MAPQ to surject output
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  85efb279
- add group mapq to surject output · 30ee1acd
  Jordan Eizenga authored May 11, 2022
  
  30ee1acd
06 May, 2022 3 commits
- Allow manipulating GBWT tags to efficiently change references in a GBWT or GBZ · cb6b598f
  Adam Novak authored May 06, 2022
  
  cb6b598f
- Merge pull request #3646 from vgteam/path-metadata · ffd49137
  Adam Novak authored May 06, 2022
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Path metadata support
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  ffd49137
- Merge pull request #3657 from vgteam/check-path-existence · 22d003c9
  Adam Novak authored May 06, 2022
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Protect against nonexistent paths when reading HTS formats
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  22d003c9
04 May, 2022 8 commits
- Keep read group around to apply to Alignment · 155bb9bd
  Adam Novak authored May 04, 2022
  
  155bb9bd
- Only look up read groups if actually present · 217eb72d
  Adam Novak authored May 04, 2022
  
  217eb72d
- Pre-find the paths that the BAM will use · 35792eeb
  Adam Novak authored May 04, 2022
  
  35792eeb
- Protect against nonexistent paths when reading HTS formats · 12d517cd
  Adam Novak authored May 04, 2022
  
  12d517cd
- Add seed to translate tests · fbf84b49
  Adam Novak authored May 04, 2022
  
  fbf84b49
- Make sure we emit paths and tags we can re-interpret · ba75467c
  Adam Novak authored May 04, 2022
  
  ba75467c
- Use GBWTGraph that also supports a * sample · 49e64acd
  Adam Novak authored May 04, 2022
  
  49e64acd
- Parse GFA RS tags like gbwtgraph · e12fc83b
  Adam Novak authored May 04, 2022
  
  e12fc83b
03 May, 2022 1 commit
- Start making vg's GFA parser agree with GBWTGraph's on defaulting P lines to haplotypes if possible · 99635661
  Adam Novak authored May 03, 2022
  
  99635661
29 Apr, 2022 1 commit
- Merge pull request #3654 from vgteam/gaf-support · 60763fb8
  Glenn Hickey authored Apr 29, 2022
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Patch gafkluge
```
  60763fb8
28 Apr, 2022 2 commits
- update libvgio for gafkluge patch · 2329339b
  Glenn Hickey authored Apr 28, 2022
  
  2329339b
- Use GBWTGraph accessors instead of our own helpers to get path metadata from a bare GBWT · 1bc86f17
  Adam Novak authored Apr 28, 2022
  
  1bc86f17
27 Apr, 2022 3 commits
- Start porting to gbwtgraph that uses tags for reference sense · 13620033
  Adam Novak authored Apr 27, 2022
  
  13620033
- Merge pull request #3651 from vgteam/gaf-support · ff9e777f
  Glenn Hickey authored Apr 27, 2022
```
Switch to vgteams's dozeu
```
  ff9e777f
- switch to vgteams's dozeu · ed68f6d7
  Glenn Hickey authored Apr 26, 2022
  
  ed68f6d7
21 Apr, 2022 2 commits
- Use toil-vg that will ask for GBWT threads with new names · 30a4eccd
  Adam Novak authored Apr 21, 2022
  
  30a4eccd
- Update libbdsg and libhandlegraph with even less int64_t · 42f48d29
  Adam Novak authored Apr 21, 2022
  
  42f48d29
20 Apr, 2022 9 commits
- Merge remote-tracking branch 'upstream/master' into path-metadata · 5fa88c1b
  Adam Novak authored Apr 20, 2022
  
  5fa88c1b
- Update libhandlegraph and libbdsg · 5fb577d1
  Adam Novak authored Apr 20, 2022
  
  5fb577d1
- Update with mainline libhandlegraph · b1a9df0d
  Adam Novak authored Apr 20, 2022
  
  b1a9df0d
- Use GBWTGraph that can actually safely add paths to a GBWTBuilder · 3db0ee65
  Adam Novak authored Apr 20, 2022
  
  3db0ee65
- Merge pull request #3643 from vgteam/count-walk-overflow · 7705d3c7
  Jordan Eizenga authored Apr 20, 2022
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Fix rare bug in mpmap that can make invalid alignments
```
  7705d3c7
- Stop testing --paths-as-samples · bc13f866
  Adam Novak authored Apr 20, 2022
  
  bc13f866
- also get xg version · 12619c2a
  Jordan Eizenga authored Apr 19, 2022
  
  12619c2a
- update dependency versions · 63e24e18
  Jordan Eizenga authored Apr 19, 2022
  
  63e24e18
- update xg and libbdsg for new libhandlegraph · 737bffd4
  Jordan Eizenga authored Apr 19, 2022
  
  737bffd4