Code

Long Read Giraffe#3700

Code

Merged

adamnovak merged 104 commits intomastervgteam/vg:masterfrom lr-giraffevgteam/vg:lr-giraffeCopy head branch name to clipboardJul 29, 2022

+5,083-1,309

Commits

Commits on May 23, 2022

• Merge remote-tracking branch 'xian/distance-minimizer-caching' into lr-giraffe

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• Add MinimizerMapper::chain_extension_group that does half of the chaining problem

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Commits on May 24, 2022

• Rearrange and correct test cases and add debugging

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• Fix bug where overlaps were scored 1 too low

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• Fix more test cases and adjust debugging

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• Note that we don't actually enforce a containment ban

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Commits on May 25, 2022

• Implement some measurement and scoring of graph distances for chaining

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• Add some easy unit tests

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Commits on May 26, 2022

• Allow building individual dynamic unit test binaries

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• Add another test

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Commits on May 27, 2022

• Swap over to traits so we can define the DP once as a template

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• Hook up chaining into single-end Giraffe and get ready for the chain to alignment elaboration

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• Get build working with chaining

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• Merge Jouni's WFA-over-GBWT algorithm

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Commits on May 31, 2022

• Merge remote-tracking branch 'upstream/distance-minimizer-caching' into lr-giraffe

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• Add some tests for long read Giraffe that don't pass yet

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• Copy minimizer total limit and overlap detection over to old distance index codepath

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Commits on Jun 1, 2022

• Start implementing aligning between gapless extensions

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• Start on actually implementing the helpers and welding

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Commits on Jun 2, 2022

• Implement WFAAlignment to vg Alignment conversion

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• Act more like the existing alignment conversion logic

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• Get chaining to be attempted

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Commits on Jun 3, 2022

• Add some unit tests for alignment welding

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• Make easy join test pass

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• Make work-showing useful for long reads

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• Start at the right extension and make dropping overlapping extensions clear

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• Merge remote-tracking branch 'upstream/master' into lr-giraffe

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Commits on Jun 6, 2022

• Start trimming

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Commits on Jun 7, 2022

• Merge remote-tracking branch 'jouni/master' into lr-giraffe

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• Rename some variables to make making extensions optional make sense

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• Template out the extension logic

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• Unify seed finding with traits

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• Unify cluster scoring

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• Templatize chaining

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• Templatize best chain function

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• Start trying to chain raw seeds

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• Start factoring chaining into its own file

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• Hook up chaining as a parallel path to gapless extensions

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• Get the new chaining space system to compile

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Commits on Jun 8, 2022

• Split out chaining unit tests

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• Add cpp file for chaining code to hold non-templates

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• Merge remote-tracking branch 'upstream/master' into lr-giraffe

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• Templatize and deduplicate annotate_with_minimizer_statistics

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• Fix up gap length difference scoring

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• Flip around tail alignments to go the right way, but they're too slow because the chains are too tiny because the sweep line algorithm is not really considering long jumps between seeds as plausibl…

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Commits on Jun 13, 2022

• Chain with a finite lookback to previous items

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• Get chaining mostly working; splicing is still broken because connect doesn't guarantee anchoring matches

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• Trim trailing bases so we can splice alignments by abutment, but some seed hits are showing as not actual matches

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Commits on Jun 14, 2022

• Get seed to match run logic in the chaining space working properly for both minimizer orientations

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Commits on Jun 17, 2022

• Merge remote-tracking branch 'upstream/master' into lr-giraffe

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• Stop popping bases and also pass old_seeds where needed

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• Go back to the original sweep-line code for gapless extension set scoring only

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• Handle partial alignments from WFAAligner

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Commits on Jun 21, 2022

• Try to debug a busted read

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Commits on Jun 22, 2022

• Start brute-forcing path conversion

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• Check generated path sequence

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• Pass randomized tests for alignment round-trip

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• Simplify conversion function slightly

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• Improve comment and simplify error message

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Commits on Jun 23, 2022

• Don't do pathologically long tail or connection alignments that can make WFAExtender take too long

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• Shorten max connecting length and get Giraffe Facts to run when there are no stats

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• Get Giraffe Facts to report a speed

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• Handle empty tails

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Commits on Jun 27, 2022

• Merge remote-tracking branch 'courtyard/lr-giraffe' into lr-giraffe

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• Change unit tests to match the current lenient chaining

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• Add tests for distractability

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• Don't skip reachable things

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Commits on Jun 28, 2022

• Allow tuning connections and tails separately

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Commits on Jun 29, 2022

• Use a hashtable instead of a sorted list to find points by exact score and diagonal

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Commits on Jul 6, 2022

• Start on combining nodes into runs

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• Add a benchmark for connect()

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• Remember to start with empty alignment in test

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• Build positions in the right order

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• Benchmark quietly

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• Test 10 node sequence

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• Merge commit '8e090e64fba31bd89f4d1c9bfef6dbe9284273d6' into lr-giraffe

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• Merge remote-tracking branch 'courtyard/lr-giraffe' into lr-giraffe

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• Get coalesced WFANodes to build

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Commits on Jul 7, 2022

• Add some debugging prints

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• Revert "Add some debugging prints"

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• Add single test for working in a multi-node run

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• Revert "Revert "Add some debugging prints""

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• Add more debugging

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Commits on Jul 8, 2022

• Pass single node perfect match test

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• Change bound type to handle exact hits

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• Protect node_offset_of

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  db7cd1c

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• Fix some incorrect conversion of destination offset

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• Fix expected edit counts

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• Remove duplicate test cases

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• Turn off debug logging

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• Change to ImmutableList which is also taking all our time

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• Use a weird shared-middle list for paths

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• Try inlining 4 items in the path type

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• Set length limits to 5 kb

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Commits on Jul 11, 2022

• Add error model and low default limits for WFAExtender score

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• Merge remote-tracking branch 'origin/lr-giraffe' into lr-giraffe

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• Cap WFA scores aggressively

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• Remove debug prints

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• Don't look for unittest support headers that don't exist

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Commits on Jul 13, 2022

• Raise limits for benchmarking so it runs

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Commits on Jul 15, 2022

• Make sure to adopt the node offset when adopting the initial node

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Commits on Jul 21, 2022

• Merge remote-tracking branch 'upstream/master' into lr-giraffe

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• Drop unused print

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• Add a test for non-diverging multi-node cycles

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