deprecate adj-rc index, optimize and fix alignment to CanonicalDBG#454

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hmusta merged 82 commits intomasterfrom

hm/noderc_optim

Jul 28, 2023

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karasikov commented Jun 12, 2023

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hmusta added 12 commits

June 12, 2023 02:28


          fix compile error

983f938


          don't use mapping_ in NodeRC

316f428


          remove mapping computation

126095f


          simplify

cfd92a4


          split RC bit vector into two

a79de2c


          fix redundant suffix setting when making NodeRC index

f8e6b3f


          implement get_node_sequence in NodeFirstCache

b1b71fe


          Add pandas as a requirement

0dd53f3


          move some logic from CanonicalDBG into NodeRC

222864f


          take advantage of cache in more places

a5a5426


          extra checks

b303ca9


          if the rc_edge is a dead end, don't store it in rc_nodes_

3b12e61

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          fix for unmasked DBGSuccinct

b3ae307

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hmusta added 2 commits

June 13, 2023 12:39

fix

e469779


          precompute dummy edge mask if it doesn't exist already

10369ec

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hmusta added 2 commits

June 13, 2023 15:23


          give hints to get_first_char

3a8c8be


          get_first_char always passes a hint

4fc711c

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hmusta added 5 commits

June 13, 2023 17:59


          Avoid rank and select computation when making mask

ae9d15c


          ensure access to cache in noderc

5be2b4b


          missed a few

cc7b126


          pass spelling hints to canonicaldbg

c844133

fix

84c4354

hmusta changed the title ~~smaller adj-rc index~~ smaller adj-rc index, optimize alignment to CanonicalDBG


          cache index_range

bdbed29


          fixed asserts

82b9d42

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hmusta added 5 commits

July 2, 2023 21:54


          minor

0971f6e


          minor

345bb05


          bug fix: prevent traversing tto dummy k-mers on both strands

8fc4dbe


          simplify

af0477f


          minor

0c10426

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          Addressed reviewer comments

fdc78f1

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metagraph/src/graph/alignment/aligner_extender_methods.cpp Outdated Show resolved Hide resolved

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hmusta and others added 4 commits

July 19, 2023 13:09


          Added comments and an extra unit test

1bcb243


          added comments

f8b9504


          Merge remote-tracking branch 'origin/master' into hm/noderc_optim

1520f1a


          cleanup

638ea8a

karasikov force-pushed the hm/noderc_optim branch from 2fbea6a to 638ea8a Compare

July 26, 2023 15:40

karasikov and others added 7 commits

July 27, 2023 19:05


          changes

6215c94


          minor

7698f41


          minor

1d72c23


          Add extra unit tests

bb6f34a


          cleanup


          fix traversal to dummy nodes

c5d1d6d

fix

f9aba23

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hmusta and others added 3 commits

July 28, 2023 12:10


          Update metagraph/src/graph/representation/canonical_dbg.cpp

94378f9

Co-authored-by: Mikhail Karasikov <karasikov@users.noreply.github.com>


          Update metagraph/src/graph/representation/canonical_dbg.cpp

f3538c9

Co-authored-by: Mikhail Karasikov <karasikov@users.noreply.github.com>

fix

f361224

hmusta merged commit 1754312 into master

hmusta deleted the hm/noderc_optim branch

July 28, 2023 13:55

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