Push zunrplorkwkt #70
@@ -5,6 +5,7 @@
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.serena/
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.zed/
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memory/
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sandbox/
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src/target
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data-stress
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*.fasta
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@@ -1,167 +0,0 @@
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ratio_ceiling: 0.5
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cardinality_transitions:
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- from: 0
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to: 0
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count: 122014779
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probability: 0.870049812090934
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- from: 0
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||||
to: 1
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count: 17966272
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probability: 0.12811195254940888
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- from: 0
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to: 2
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count: 233683
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probability: 0.001666321505518981
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- from: 0
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||||
to: 3
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count: 24109
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probability: 0.00017191385413811494
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- from: 0
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to: 4
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count: 0
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probability: 0.0
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- from: 1
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to: 0
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count: 17966272
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probability: 0.967023782579572
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- from: 1
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to: 1
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count: 602798
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probability: 0.03244523972983381
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- from: 1
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to: 2
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count: 9562
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probability: 0.0005146688978673966
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- from: 1
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to: 3
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count: 303
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probability: 0.00001630879272681669
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- from: 1
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to: 4
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count: 0
|
||||
probability: 0.0
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||||
- from: 2
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to: 0
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count: 233683
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probability: 0.9585500516842502
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- from: 2
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to: 1
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count: 9562
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probability: 0.039222603245442765
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- from: 2
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to: 2
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count: 438
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probability: 0.0017966429848885097
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to: 3
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count: 105
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probability: 0.00043070208541847837
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to: 4
|
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count: 0
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||||
probability: 0.0
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||||
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to: 0
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||||
count: 24109
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probability: 0.9827171564831044
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||||
- from: 3
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||||
to: 1
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||||
count: 303
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||||
probability: 0.012350711286838137
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- from: 3
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to: 2
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count: 105
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probability: 0.004279949455834998
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- from: 3
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to: 3
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count: 16
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probability: 0.0006521827742224758
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- from: 3
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to: 4
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count: 0
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probability: 0.0
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- from: 4
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to: 0
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count: 0
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probability: 0.0
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- from: 4
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to: 1
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count: 0
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probability: 0.0
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- from: 4
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to: 2
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count: 0
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probability: 0.0
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- from: 4
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to: 3
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||||
count: 0
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probability: 0.0
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- from: 4
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to: 4
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count: 0
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probability: 0.0
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composition_transitions:
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- from: 'A'
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to: 'A'
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count: 0
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probability: 0.0
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- from: 'A'
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to: 'C'
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count: 0
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probability: 0.0
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count: 0
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probability: 0.0
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- from: 'A'
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count: 0
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probability: 0.0
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to: 'A'
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count: 0
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probability: 0.0
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- from: 'C'
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to: 'C'
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count: 96389
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probability: 0.9663832688335907
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- from: 'C'
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to: 'G'
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count: 1290
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probability: 0.012933368089671353
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- from: 'C'
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to: 'T'
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count: 2063
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probability: 0.020683363076737984
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- from: 'G'
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to: 'A'
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count: 0
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probability: 0.0
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- from: 'G'
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to: 'C'
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count: 1290
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probability: 0.005696948820201646
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- from: 'G'
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to: 'G'
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count: 222720
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probability: 0.9835848381669073
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- from: 'G'
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to: 'T'
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count: 2427
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probability: 0.010718213012891003
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- from: 'T'
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to: 'A'
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count: 0
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probability: 0.0
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- from: 'T'
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to: 'C'
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count: 2063
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probability: 0.007305266661709142
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- from: 'T'
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to: 'G'
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count: 2427
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probability: 0.008594223067362136
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- from: 'T'
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to: 'T'
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count: 277909
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probability: 0.9841005102709287
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@@ -1,167 +0,0 @@
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ratio_ceiling: 0.5
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cardinality_transitions:
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- from: 0
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to: 0
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count: 13019012
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probability: 0.8682962128540935
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- from: 0
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to: 1
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count: 1945560
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probability: 0.12975810913150784
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- from: 0
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to: 2
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count: 26381
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probability: 0.0017594670310852958
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- from: 0
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to: 3
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count: 2792
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probability: 0.000186210983313375
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- from: 0
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to: 4
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count: 0
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probability: 0.0
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- from: 1
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to: 0
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count: 1945560
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probability: 0.9666005228573729
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- from: 1
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to: 1
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count: 66078
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probability: 0.03282912341401421
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- from: 1
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to: 2
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count: 1123
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probability: 0.0005579331334776772
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- from: 1
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to: 3
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count: 25
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probability: 0.000012420595135300028
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- from: 1
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to: 4
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count: 0
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probability: 0.0
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- from: 2
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to: 0
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count: 26381
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probability: 0.9567346050627402
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count: 1123
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probability: 0.04072677159643142
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count: 51
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probability: 0.0018495684340320592
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to: 3
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count: 19
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probability: 0.0006890549067962574
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||||
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probability: 0.9841381741275996
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count: 25
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probability: 0.008812125484666901
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to: 2
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count: 19
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probability: 0.0066972153683468455
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count: 1
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probability: 0.00035248501938667606
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to: 4
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count: 0
|
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probability: 0.0
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||||
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||||
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probability: 0.0
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||||
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count: 0
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to: 3
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count: 0
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probability: 0.0
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||||
- from: 4
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||||
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count: 0
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probability: 0.0
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||||
composition_transitions:
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||||
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to: 'A'
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count: 0
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||||
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to: 'C'
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to: 'G'
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count: 0
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probability: 0.0
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||||
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||||
to: 'T'
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count: 0
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probability: 0.0
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||||
to: 'A'
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count: 0
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probability: 0.0
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to: 'C'
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count: 10771
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probability: 0.9619540948468339
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to: 'G'
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count: 163
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||||
probability: 0.014557470751094042
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||||
to: 'T'
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count: 263
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probability: 0.023488434402071982
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||||
to: 'A'
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||||
count: 0
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||||
probability: 0.0
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||||
- from: 'G'
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||||
to: 'C'
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count: 163
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||||
probability: 0.006662851536952256
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||||
- from: 'G'
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||||
to: 'G'
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count: 24073
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probability: 0.9840173315892741
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- from: 'G'
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||||
to: 'T'
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||||
count: 228
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||||
probability: 0.009319816873773708
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||||
- from: 'T'
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||||
to: 'A'
|
||||
count: 0
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||||
probability: 0.0
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||||
- from: 'T'
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||||
to: 'C'
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||||
count: 263
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||||
probability: 0.008464484567603231
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||||
- from: 'T'
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||||
to: 'G'
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||||
count: 228
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||||
probability: 0.007338032248720672
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||||
- from: 'T'
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||||
to: 'T'
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count: 30580
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probability: 0.9841974831836761
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@@ -1,275 +0,0 @@
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[2m2026-04-27T20:36:04.208955Z[0m [32m INFO[0m [2mobikmer::cmd::partition[0m[2m:[0m dereplicating...
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[2m2026-04-27T20:36:11.471489Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 0/256
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[2m2026-04-27T20:36:11.471521Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 128/256
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[2m2026-04-27T20:36:11.471530Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 32/256
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[2m2026-04-27T20:36:11.471535Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 12/256
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[2m2026-04-27T20:36:11.471551Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 76/256
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[2m2026-04-27T20:36:11.471522Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 2/256
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[2m2026-04-27T20:36:11.471525Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 4/256
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[2m2026-04-27T20:36:11.471535Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 96/256
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[2m2026-04-27T20:36:11.471535Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 80/256
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[2m2026-04-27T20:36:11.471535Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 10/256
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[2m2026-04-27T20:36:11.471538Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 16/256
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[2m2026-04-27T20:36:11.471543Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 224/256
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[2m2026-04-27T20:36:11.471537Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 192/256
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[2m2026-04-27T20:36:11.471536Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 64/256
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[2m2026-04-27T20:36:11.471537Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 72/256
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[2m2026-04-27T20:36:11.471530Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 8/256
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[2m2026-04-27T20:36:12.831739Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 129/256
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[2m2026-04-27T20:36:13.555104Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 9/256
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[2m2026-04-27T20:36:14.077082Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 17/256
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[2m2026-04-27T20:36:14.203310Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 77/256
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[2m2026-04-27T20:36:14.316403Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 3/256
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||||
[2m2026-04-27T20:36:14.415177Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 33/256
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[2m2026-04-27T20:36:14.467689Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 97/256
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||||
[2m2026-04-27T20:36:14.559650Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 5/256
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||||
[2m2026-04-27T20:36:14.591431Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 81/256
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[2m2026-04-27T20:36:14.606508Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 193/256
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[2m2026-04-27T20:36:14.611406Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 73/256
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[2m2026-04-27T20:36:14.623813Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 11/256
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[2m2026-04-27T20:36:14.665058Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 65/256
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||||
[2m2026-04-27T20:36:14.666877Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 1/256
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[2m2026-04-27T20:36:14.667569Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 13/256
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[2m2026-04-27T20:36:14.697486Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 225/256
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[2m2026-04-27T20:36:14.698441Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 130/256
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[2m2026-04-27T20:36:14.998749Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 14/256
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[2m2026-04-27T20:36:15.485303Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 18/256
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||||
[2m2026-04-27T20:36:15.637613Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 78/256
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||||
[2m2026-04-27T20:36:15.722825Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 98/256
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[2m2026-04-27T20:36:15.831703Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 112/256
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[2m2026-04-27T20:36:16.161408Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 66/256
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[2m2026-04-27T20:36:16.340113Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 226/256
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[2m2026-04-27T20:36:16.506407Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 82/256
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[2m2026-04-27T20:36:16.542430Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 74/256
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[2m2026-04-27T20:36:16.550654Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 34/256
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[2m2026-04-27T20:36:16.634719Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 6/256
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[2m2026-04-27T20:36:16.763833Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 194/256
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[2m2026-04-27T20:36:16.813285Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 131/256
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[2m2026-04-27T20:36:16.913975Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 208/256
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[2m2026-04-27T20:36:16.993526Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 15/256
|
||||
[2m2026-04-27T20:36:17.092998Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 160/256
|
||||
[2m2026-04-27T20:36:17.114964Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 88/256
|
||||
[2m2026-04-27T20:36:17.148685Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 79/256
|
||||
[2m2026-04-27T20:36:17.161989Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 19/256
|
||||
[2m2026-04-27T20:36:17.180022Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 113/256
|
||||
[2m2026-04-27T20:36:17.397037Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 67/256
|
||||
[2m2026-04-27T20:36:17.484519Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 99/256
|
||||
[2m2026-04-27T20:36:17.906842Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 35/256
|
||||
[2m2026-04-27T20:36:18.146262Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 75/256
|
||||
[2m2026-04-27T20:36:18.247130Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 7/256
|
||||
[2m2026-04-27T20:36:18.303872Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 227/256
|
||||
[2m2026-04-27T20:36:18.374448Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 195/256
|
||||
[2m2026-04-27T20:36:18.382279Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 83/256
|
||||
[2m2026-04-27T20:36:18.428092Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 104/256
|
||||
[2m2026-04-27T20:36:18.442213Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 132/256
|
||||
[2m2026-04-27T20:36:18.621883Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 209/256
|
||||
[2m2026-04-27T20:36:18.784307Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 161/256
|
||||
[2m2026-04-27T20:36:18.796465Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 114/256
|
||||
[2m2026-04-27T20:36:18.877587Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 120/256
|
||||
[2m2026-04-27T20:36:18.888423Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 89/256
|
||||
[2m2026-04-27T20:36:18.918340Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 20/256
|
||||
[2m2026-04-27T20:36:18.985341Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 100/256
|
||||
[2m2026-04-27T20:36:19.080092Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 68/256
|
||||
[2m2026-04-27T20:36:19.282760Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 36/256
|
||||
[2m2026-04-27T20:36:19.485079Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 92/256
|
||||
[2m2026-04-27T20:36:19.692354Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 24/256
|
||||
[2m2026-04-27T20:36:19.746458Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 228/256
|
||||
[2m2026-04-27T20:36:20.004054Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 84/256
|
||||
[2m2026-04-27T20:36:20.164510Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 196/256
|
||||
[2m2026-04-27T20:36:20.277288Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 105/256
|
||||
[2m2026-04-27T20:36:20.349391Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 133/256
|
||||
[2m2026-04-27T20:36:20.511981Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 210/256
|
||||
[2m2026-04-27T20:36:20.709583Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 101/256
|
||||
[2m2026-04-27T20:36:20.715870Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 69/256
|
||||
[2m2026-04-27T20:36:20.728029Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 115/256
|
||||
[2m2026-04-27T20:36:20.822257Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 162/256
|
||||
[2m2026-04-27T20:36:20.982131Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 90/256
|
||||
[2m2026-04-27T20:36:20.990122Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 21/256
|
||||
[2m2026-04-27T20:36:21.030814Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 121/256
|
||||
[2m2026-04-27T20:36:21.088309Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 93/256
|
||||
[2m2026-04-27T20:36:21.134904Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 37/256
|
||||
[2m2026-04-27T20:36:21.196814Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 25/256
|
||||
[2m2026-04-27T20:36:21.444384Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 85/256
|
||||
[2m2026-04-27T20:36:21.605343Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 197/256
|
||||
[2m2026-04-27T20:36:21.954010Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 106/256
|
||||
[2m2026-04-27T20:36:22.026167Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 229/256
|
||||
[2m2026-04-27T20:36:22.194676Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 134/256
|
||||
[2m2026-04-27T20:36:22.209911Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 211/256
|
||||
[2m2026-04-27T20:36:22.281984Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 70/256
|
||||
[2m2026-04-27T20:36:22.440637Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 163/256
|
||||
[2m2026-04-27T20:36:22.481750Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 91/256
|
||||
[2m2026-04-27T20:36:22.522458Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 116/256
|
||||
[2m2026-04-27T20:36:22.775669Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 22/256
|
||||
[2m2026-04-27T20:36:23.095766Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 102/256
|
||||
[2m2026-04-27T20:36:23.119802Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 94/256
|
||||
[2m2026-04-27T20:36:23.183138Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 122/256
|
||||
[2m2026-04-27T20:36:23.186904Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 38/256
|
||||
[2m2026-04-27T20:36:23.196250Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 86/256
|
||||
[2m2026-04-27T20:36:23.206118Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 26/256
|
||||
[2m2026-04-27T20:36:23.314520Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 198/256
|
||||
[2m2026-04-27T20:36:23.355959Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 107/256
|
||||
[2m2026-04-27T20:36:23.526146Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 230/256
|
||||
[2m2026-04-27T20:36:23.723572Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 212/256
|
||||
[2m2026-04-27T20:36:23.856569Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 71/256
|
||||
[2m2026-04-27T20:36:23.910613Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 164/256
|
||||
[2m2026-04-27T20:36:23.945560Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 135/256
|
||||
[2m2026-04-27T20:36:24.085073Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 117/256
|
||||
[2m2026-04-27T20:36:24.111144Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 144/256
|
||||
[2m2026-04-27T20:36:24.188547Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 23/256
|
||||
[2m2026-04-27T20:36:24.573867Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 103/256
|
||||
[2m2026-04-27T20:36:24.604461Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 27/256
|
||||
[2m2026-04-27T20:36:24.670189Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 95/256
|
||||
[2m2026-04-27T20:36:24.935767Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 123/256
|
||||
[2m2026-04-27T20:36:25.031507Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 39/256
|
||||
[2m2026-04-27T20:36:25.039809Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 108/256
|
||||
[2m2026-04-27T20:36:25.067950Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 199/256
|
||||
[2m2026-04-27T20:36:25.149100Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 231/256
|
||||
[2m2026-04-27T20:36:25.272346Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 213/256
|
||||
[2m2026-04-27T20:36:25.400111Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 165/256
|
||||
[2m2026-04-27T20:36:25.607381Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 136/256
|
||||
[2m2026-04-27T20:36:25.902415Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 152/256
|
||||
[2m2026-04-27T20:36:26.055400Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 118/256
|
||||
[2m2026-04-27T20:36:26.138877Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 119/256
|
||||
[2m2026-04-27T20:36:26.255235Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 87/256
|
||||
[2m2026-04-27T20:36:26.350364Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 148/256
|
||||
[2m2026-04-27T20:36:26.465089Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 145/256
|
||||
[2m2026-04-27T20:36:26.682375Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 40/256
|
||||
[2m2026-04-27T20:36:26.694729Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 216/256
|
||||
[2m2026-04-27T20:36:26.777197Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 28/256
|
||||
[2m2026-04-27T20:36:26.802996Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 124/256
|
||||
[2m2026-04-27T20:36:26.972099Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 200/256
|
||||
[2m2026-04-27T20:36:27.066713Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 232/256
|
||||
[2m2026-04-27T20:36:27.112569Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 166/256
|
||||
[2m2026-04-27T20:36:27.156124Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 214/256
|
||||
[2m2026-04-27T20:36:27.231214Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 137/256
|
||||
[2m2026-04-27T20:36:27.359784Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 109/256
|
||||
[2m2026-04-27T20:36:27.369743Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 153/256
|
||||
[2m2026-04-27T20:36:27.668409Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 204/256
|
||||
[2m2026-04-27T20:36:27.701887Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 202/256
|
||||
[2m2026-04-27T20:36:27.794402Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 215/256
|
||||
[2m2026-04-27T20:36:28.058391Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 149/256
|
||||
[2m2026-04-27T20:36:28.192195Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 217/256
|
||||
[2m2026-04-27T20:36:28.369717Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 125/256
|
||||
[2m2026-04-27T20:36:28.412339Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 41/256
|
||||
[2m2026-04-27T20:36:28.496068Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 29/256
|
||||
[2m2026-04-27T20:36:28.693510Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 167/256
|
||||
[2m2026-04-27T20:36:28.808495Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 201/256
|
||||
[2m2026-04-27T20:36:28.843564Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 233/256
|
||||
[2m2026-04-27T20:36:28.917920Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 140/256
|
||||
[2m2026-04-27T20:36:28.940416Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 138/256
|
||||
[2m2026-04-27T20:36:29.125956Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 110/256
|
||||
[2m2026-04-27T20:36:29.197246Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 154/256
|
||||
[2m2026-04-27T20:36:29.376894Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 203/256
|
||||
[2m2026-04-27T20:36:29.491887Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 176/256
|
||||
[2m2026-04-27T20:36:29.501763Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 205/256
|
||||
[2m2026-04-27T20:36:29.538499Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 150/256
|
||||
[2m2026-04-27T20:36:29.685646Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 218/256
|
||||
[2m2026-04-27T20:36:29.874786Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 126/256
|
||||
[2m2026-04-27T20:36:30.021059Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 42/256
|
||||
[2m2026-04-27T20:36:30.255780Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 240/256
|
||||
[2m2026-04-27T20:36:30.602468Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 141/256
|
||||
[2m2026-04-27T20:36:30.696718Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 234/256
|
||||
[2m2026-04-27T20:36:30.784522Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 139/256
|
||||
[2m2026-04-27T20:36:31.027016Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 155/256
|
||||
[2m2026-04-27T20:36:31.073326Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 30/256
|
||||
[2m2026-04-27T20:36:31.137264Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 111/256
|
||||
[2m2026-04-27T20:36:31.143413Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 168/256
|
||||
[2m2026-04-27T20:36:31.237329Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 206/256
|
||||
[2m2026-04-27T20:36:31.252908Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 236/256
|
||||
[2m2026-04-27T20:36:31.306110Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 177/256
|
||||
[2m2026-04-27T20:36:31.431064Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 151/256
|
||||
[2m2026-04-27T20:36:31.490837Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 127/256
|
||||
[2m2026-04-27T20:36:31.528815Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 43/256
|
||||
[2m2026-04-27T20:36:31.790858Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 219/256
|
||||
[2m2026-04-27T20:36:31.803934Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 241/256
|
||||
[2m2026-04-27T20:36:32.131051Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 156/256
|
||||
[2m2026-04-27T20:36:32.433342Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 235/256
|
||||
[2m2026-04-27T20:36:32.459699Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 142/256
|
||||
[2m2026-04-27T20:36:32.532717Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 31/256
|
||||
[2m2026-04-27T20:36:32.814909Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 184/256
|
||||
[2m2026-04-27T20:36:32.967090Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 169/256
|
||||
[2m2026-04-27T20:36:33.062660Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 178/256
|
||||
[2m2026-04-27T20:36:33.076014Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 237/256
|
||||
[2m2026-04-27T20:36:33.128961Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 207/256
|
||||
[2m2026-04-27T20:36:33.228734Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 180/256
|
||||
[2m2026-04-27T20:36:33.228905Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 143/256
|
||||
[2m2026-04-27T20:36:33.266931Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 44/256
|
||||
[2m2026-04-27T20:36:33.280333Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 158/256
|
||||
[2m2026-04-27T20:36:33.368740Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 220/256
|
||||
[2m2026-04-27T20:36:33.373469Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 179/256
|
||||
[2m2026-04-27T20:36:33.409455Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 157/256
|
||||
[2m2026-04-27T20:36:33.685036Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 242/256
|
||||
[2m2026-04-27T20:36:34.174714Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 182/256
|
||||
[2m2026-04-27T20:36:34.255362Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 146/256
|
||||
[2m2026-04-27T20:36:34.284053Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 170/256
|
||||
[2m2026-04-27T20:36:34.340602Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 185/256
|
||||
[2m2026-04-27T20:36:34.748830Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 45/256
|
||||
[2m2026-04-27T20:36:34.894515Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 172/256
|
||||
[2m2026-04-27T20:36:35.342815Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 238/256
|
||||
[2m2026-04-27T20:36:35.549647Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 159/256
|
||||
[2m2026-04-27T20:36:35.556431Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 181/256
|
||||
[2m2026-04-27T20:36:35.579877Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 188/256
|
||||
[2m2026-04-27T20:36:35.619438Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 221/256
|
||||
[2m2026-04-27T20:36:35.704344Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 174/256
|
||||
[2m2026-04-27T20:36:35.891634Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 190/256
|
||||
[2m2026-04-27T20:36:35.893065Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 239/256
|
||||
[2m2026-04-27T20:36:35.978053Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 183/256
|
||||
[2m2026-04-27T20:36:35.980835Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 186/256
|
||||
[2m2026-04-27T20:36:36.010364Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 243/256
|
||||
[2m2026-04-27T20:36:36.084972Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 171/256
|
||||
[2m2026-04-27T20:36:36.085806Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 147/256
|
||||
[2m2026-04-27T20:36:36.129893Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 48/256
|
||||
[2m2026-04-27T20:36:36.188339Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 46/256
|
||||
[2m2026-04-27T20:36:36.281975Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 173/256
|
||||
[2m2026-04-27T20:36:37.004395Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 187/256
|
||||
[2m2026-04-27T20:36:37.080479Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 222/256
|
||||
[2m2026-04-27T20:36:37.100573Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 189/256
|
||||
[2m2026-04-27T20:36:37.422152Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 248/256
|
||||
[2m2026-04-27T20:36:37.446786Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 175/256
|
||||
[2m2026-04-27T20:36:37.951518Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 244/256
|
||||
[2m2026-04-27T20:36:38.235613Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 191/256
|
||||
[2m2026-04-27T20:36:38.259288Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 47/256
|
||||
[2m2026-04-27T20:36:38.379966Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 252/256
|
||||
[2m2026-04-27T20:36:38.380690Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 223/256
|
||||
[2m2026-04-27T20:36:38.520398Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 56/256
|
||||
[2m2026-04-27T20:36:38.598256Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 49/256
|
||||
[2m2026-04-27T20:36:38.680704Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 254/256
|
||||
[2m2026-04-27T20:36:38.681038Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 246/256
|
||||
[2m2026-04-27T20:36:38.813533Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 247/256
|
||||
[2m2026-04-27T20:36:38.820199Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 60/256
|
||||
[2m2026-04-27T20:36:38.961240Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 52/256
|
||||
[2m2026-04-27T20:36:39.001585Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 58/256
|
||||
[2m2026-04-27T20:36:39.050047Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 249/256
|
||||
[2m2026-04-27T20:36:39.076449Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 57/256
|
||||
[2m2026-04-27T20:36:39.078254Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 250/256
|
||||
[2m2026-04-27T20:36:39.082390Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 251/256
|
||||
[2m2026-04-27T20:36:39.082697Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 245/256
|
||||
[2m2026-04-27T20:36:39.250465Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 50/256
|
||||
[2m2026-04-27T20:36:39.448799Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 54/256
|
||||
[2m2026-04-27T20:36:39.449166Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 62/256
|
||||
[2m2026-04-27T20:36:39.450954Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 63/256
|
||||
[2m2026-04-27T20:36:39.766480Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 253/256
|
||||
[2m2026-04-27T20:36:39.838346Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 59/256
|
||||
[2m2026-04-27T20:36:39.875987Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 255/256
|
||||
[2m2026-04-27T20:36:39.876798Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 55/256
|
||||
[2m2026-04-27T20:36:39.877292Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 51/256
|
||||
[2m2026-04-27T20:36:40.244598Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 61/256
|
||||
[2m2026-04-27T20:36:40.245589Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 53/256
|
||||
266.84 real 3776.35 user 115.80 sys
|
||||
2423504896 maximum resident set size
|
||||
0 average shared memory size
|
||||
0 average unshared data size
|
||||
0 average unshared stack size
|
||||
292303 page reclaims
|
||||
132311 page faults
|
||||
0 swaps
|
||||
0 block input operations
|
||||
0 block output operations
|
||||
0 messages sent
|
||||
0 messages received
|
||||
0 signals received
|
||||
4462 voluntary context switches
|
||||
1991864 involuntary context switches
|
||||
54933227607056 instructions retired
|
||||
11271230983971 cycles elapsed
|
||||
2210777320 peak memory footprint
|
||||
@@ -1 +0,0 @@
|
||||
(Escherichia_coli--CFT073:0.7973338454,(Escherichia_coli--EDL933:0.5132866305,(Escherichia_coli--K-12_MG1655:0.2990687226,Escherichia_coli--K-12_W3110:0.3006288477)100:0.1655629834)69:0.0000007189,(((Klebsiella_pneumoniae--ATCC_13883:0.9661675519,(Klebsiella_pneumoniae--MGH_78578:0.3148953385,Yersinia_ruckeri--YRB:0.3576917943)84:0.4568464394)83:0.0727808943,(Klebsiella_pneumoniae--HS11286:0.1397401144,Proteus_mirabilis--HI4320:0.2192824480)77:0.3686486712)76:0.1162295711,((Salmonella_enterica--AKU_12601:0.6158730439,(Salmonella_enterica--LT2:0.4371443730,Salmonella_enterica--P125109:0.5815549929)100:0.1012287522)100:0.0714169372,Salmonella_enterica--CT18:0.2058143021)76:0.3641489914)100:0.2900565429);
|
||||
@@ -1,62 +0,0 @@
|
||||
#nexus
|
||||
|
||||
BEGIN Taxa;
|
||||
DIMENSIONS ntax=13;
|
||||
TAXLABELS
|
||||
[1] 'Escherichia_coli--CFT073'
|
||||
[2] 'Escherichia_coli--EDL933'
|
||||
[3] 'Escherichia_coli--K-12_MG1655'
|
||||
[4] 'Escherichia_coli--K-12_W3110'
|
||||
[5] 'Klebsiella_pneumoniae--ATCC_13883'
|
||||
[6] 'Klebsiella_pneumoniae--HS11286'
|
||||
[7] 'Klebsiella_pneumoniae--MGH_78578'
|
||||
[8] 'Proteus_mirabilis--HI4320'
|
||||
[9] 'Salmonella_enterica--AKU_12601'
|
||||
[10] 'Salmonella_enterica--CT18'
|
||||
[11] 'Salmonella_enterica--LT2'
|
||||
[12] 'Salmonella_enterica--P125109'
|
||||
[13] 'Yersinia_ruckeri--YRB'
|
||||
;
|
||||
END; [Taxa]
|
||||
|
||||
BEGIN Splits;
|
||||
DIMENSIONS ntax=13 nsplits=34;
|
||||
FORMAT labels=no weights=yes confidences=no intervals=no;
|
||||
MATRIX
|
||||
100 2,
|
||||
100 3,
|
||||
100 4,
|
||||
100 3 4,
|
||||
69 2 3 4,
|
||||
100 5,
|
||||
100 7,
|
||||
16 5 7,
|
||||
100 6,
|
||||
100 13,
|
||||
16 6 13,
|
||||
23 5 6 7 13,
|
||||
100 8,
|
||||
100 10,
|
||||
23 8 10,
|
||||
100 9,
|
||||
100 11,
|
||||
100 12,
|
||||
100 11 12,
|
||||
100 9 11 12,
|
||||
23 8 9 10 11 12,
|
||||
100 1 2 3 4,
|
||||
100 1,
|
||||
84 7 13,
|
||||
83 5 7 13,
|
||||
77 6 8,
|
||||
76 5 6 7 8 13,
|
||||
76 9 10 11 12,
|
||||
31 1 2,
|
||||
1 5 6 7 8,
|
||||
1 10 13,
|
||||
1 9 10 11 12 13,
|
||||
1 5 6 13,
|
||||
1 5 6 8,
|
||||
;
|
||||
END; [Splits]
|
||||
|
||||
-1000
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@@ -1 +0,0 @@
|
||||
(((((((((((((Salmonella_enterica--P125109:0.009029074806027838,Salmonella_enterica--LT2:0.010374535686866677):0.00299392644685007,Salmonella_enterica--AKU_12601:0.010129090864056669):0.008889984754373365,Salmonella_enterica--CT18:0.029563522158784489):0.05178212639099835,(Escherichia_coli--CFT073:0.018265758526676266,(Escherichia_coli--EDL933:0.01586939152374907,(Escherichia_coli--K-12_MG1655:0.0043321525684933419,Escherichia_coli--K-12_W3110:0.004373581717010194):0.007835004272817602):0.005522415854494232):0.05395833543383322):0.007199364670842333,(Klebsiella_pneumoniae--HS11286:0.027306681424389149,(Klebsiella_pneumoniae--ATCC_13883:0.015176538442299506,Klebsiella_pneumoniae--MGH_78578:0.026462018414958045):0.0015885400482290244):0.060738462006352359):0.029481404183583916,Yersinia_ruckeri--YRB:0.10269826524749153):0.004316815340436764,Proteus_mirabilis--HI4320:0.11745645944715785):0.04439101156727093,Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1:0.17151356406519997):0.011344480816758762,Acidobacterium_capsulatum--ATCC_51196:0.17121217909071463):0.01869709592355495,Shouchella_clausii--KSM-K16:0.1554729916092201):0.04397682726757515,Bacillus_subtilis--168:0.10403127799132669):0.08828869671555731,Opitutus_terrae--PB90-1:0.06380512639846864):0.41655625366738377,Candidozyma_auris--GCF_003013715.1_ASM301371v2:0.22735026269091164,Saccharolobus_islandicus--M.16.4:0.21891918239548398);
|
||||
Binary file not shown.
Binary file not shown.
@@ -1,167 +0,0 @@
|
||||
ratio_ceiling: 0.5
|
||||
cardinality_transitions:
|
||||
- from: 0
|
||||
to: 0
|
||||
count: 54999793
|
||||
probability: 0.7934021725308564
|
||||
- from: 0
|
||||
to: 1
|
||||
count: 8873859
|
||||
probability: 0.12801028195383377
|
||||
- from: 0
|
||||
to: 2
|
||||
count: 5305545
|
||||
probability: 0.07653539585976665
|
||||
- from: 0
|
||||
to: 3
|
||||
count: 126109
|
||||
probability: 0.001819191475424167
|
||||
- from: 0
|
||||
to: 4
|
||||
count: 16149
|
||||
probability: 0.00023295818011898336
|
||||
- from: 1
|
||||
to: 0
|
||||
count: 8873859
|
||||
probability: 0.8510749571674425
|
||||
- from: 1
|
||||
to: 1
|
||||
count: 1041044
|
||||
probability: 0.09984455215137214
|
||||
- from: 1
|
||||
to: 2
|
||||
count: 507272
|
||||
probability: 0.048651493749477304
|
||||
- from: 1
|
||||
to: 3
|
||||
count: 4248
|
||||
probability: 0.00040741760918753563
|
||||
- from: 1
|
||||
to: 4
|
||||
count: 225
|
||||
probability: 0.00002157932252052625
|
||||
- from: 2
|
||||
to: 0
|
||||
count: 5305545
|
||||
probability: 0.9117891245815953
|
||||
- from: 2
|
||||
to: 1
|
||||
count: 507272
|
||||
probability: 0.08717767784549091
|
||||
- from: 2
|
||||
to: 2
|
||||
count: 5227
|
||||
probability: 0.0008982907041949506
|
||||
- from: 2
|
||||
to: 3
|
||||
count: 689
|
||||
probability: 0.00011840870388182915
|
||||
- from: 2
|
||||
to: 4
|
||||
count: 96
|
||||
probability: 0.000016498164836945715
|
||||
- from: 3
|
||||
to: 0
|
||||
count: 126109
|
||||
probability: 0.9614164824273843
|
||||
- from: 3
|
||||
to: 1
|
||||
count: 4248
|
||||
probability: 0.03238545399100404
|
||||
- from: 3
|
||||
to: 2
|
||||
count: 689
|
||||
probability: 0.005252725470763132
|
||||
- from: 3
|
||||
to: 3
|
||||
count: 98
|
||||
probability: 0.0007471220553480217
|
||||
- from: 3
|
||||
to: 4
|
||||
count: 26
|
||||
probability: 0.00019821605550049553
|
||||
- from: 4
|
||||
to: 0
|
||||
count: 16149
|
||||
probability: 0.9781344639612356
|
||||
- from: 4
|
||||
to: 1
|
||||
count: 225
|
||||
probability: 0.013628104179285281
|
||||
- from: 4
|
||||
to: 2
|
||||
count: 96
|
||||
probability: 0.00581465778316172
|
||||
- from: 4
|
||||
to: 3
|
||||
count: 26
|
||||
probability: 0.0015748031496062992
|
||||
- from: 4
|
||||
to: 4
|
||||
count: 14
|
||||
probability: 0.0008479709267110841
|
||||
composition_transitions:
|
||||
- from: 'A'
|
||||
to: 'A'
|
||||
count: 161774
|
||||
probability: 0.4701762136303263
|
||||
- from: 'A'
|
||||
to: 'C'
|
||||
count: 27788
|
||||
probability: 0.0807624007835592
|
||||
- from: 'A'
|
||||
to: 'G'
|
||||
count: 130019
|
||||
probability: 0.3778842157577942
|
||||
- from: 'A'
|
||||
to: 'T'
|
||||
count: 24490
|
||||
probability: 0.07117716982832031
|
||||
- from: 'C'
|
||||
to: 'A'
|
||||
count: 27788
|
||||
probability: 0.0780165140757087
|
||||
- from: 'C'
|
||||
to: 'C'
|
||||
count: 184047
|
||||
probability: 0.5167232390273484
|
||||
- from: 'C'
|
||||
to: 'G'
|
||||
count: 19622
|
||||
probability: 0.05508996830263265
|
||||
- from: 'C'
|
||||
to: 'T'
|
||||
count: 124724
|
||||
probability: 0.3501702785943102
|
||||
- from: 'G'
|
||||
to: 'A'
|
||||
count: 130019
|
||||
probability: 0.3610094570655886
|
||||
- from: 'G'
|
||||
to: 'C'
|
||||
count: 19622
|
||||
probability: 0.05448224926003876
|
||||
- from: 'G'
|
||||
to: 'G'
|
||||
count: 183951
|
||||
probability: 0.5107565097152884
|
||||
- from: 'G'
|
||||
to: 'T'
|
||||
count: 26562
|
||||
probability: 0.07375178395908417
|
||||
- from: 'T'
|
||||
to: 'A'
|
||||
count: 24490
|
||||
probability: 0.07335783586895636
|
||||
- from: 'T'
|
||||
to: 'C'
|
||||
count: 124724
|
||||
probability: 0.37360076443118473
|
||||
- from: 'T'
|
||||
to: 'G'
|
||||
count: 26562
|
||||
probability: 0.07956434611479049
|
||||
- from: 'T'
|
||||
to: 'T'
|
||||
count: 158067
|
||||
probability: 0.4734770535850684
|
||||
@@ -1,660 +0,0 @@
|
||||
<h1 id="obikmer">obikmer</h1>
|
||||
<p><code>obikmer</code> is a Rust tool for manipulation, counting,
|
||||
indexing, and set operations on DNA sequences represented as kmer
|
||||
sets.</p>
|
||||
<h2 id="constraints">Constraints</h2>
|
||||
<ul>
|
||||
<li>Target scale: metagenomic data, tens of Gbases, billions of
|
||||
kmers</li>
|
||||
<li>Maximum efficiency in computation, memory, and disk usage</li>
|
||||
<li>k is odd, k ∈ [11, 31], fixed at runtime</li>
|
||||
<li>Input formats: FASTA, FASTQ, gzip, streaming stdin</li>
|
||||
</ul>
|
||||
<h2 id="input-processing">Input processing</h2>
|
||||
<p>For sequence files (FASTA/FASTQ):</p>
|
||||
<ul>
|
||||
<li>Cut sequence on non-ACGT nucleotides.</li>
|
||||
<li>Discard fragments < k.</li>
|
||||
<li>For sequences > 256 nt: cut at 256, start new with k-1 overlap
|
||||
(preserves all kmers, no duplicates).</li>
|
||||
</ul>
|
||||
<h2 id="super-kmers">Super-kmers</h2>
|
||||
<p>The fundamental stored unit is a <strong>canonical
|
||||
super-kmer</strong>: a maximal run of consecutive kmers sharing the same
|
||||
<strong>non-canonical</strong> (raw forward) minimizer, canonized at the
|
||||
end.</p>
|
||||
<h3 id="construction">Construction</h3>
|
||||
<p>Super-kmers are built using the <strong>non-canonical
|
||||
minimizer</strong> (minimum forward m-mer, no revcomp comparison). Two
|
||||
consecutive kmers belong to the same super-kmer if and only if their raw
|
||||
forward minimizer is identical.</p>
|
||||
<p>At the end of each super-kmer, the minimizer is canonized:
|
||||
<code>canonical(M) = min(M, revcomp(M))</code>.</p>
|
||||
<ul>
|
||||
<li>If <code>canonical(M) == M</code>: the super-kmer is already in
|
||||
canonical orientation — keep as-is.</li>
|
||||
<li>If <code>canonical(M) == revcomp(M)</code>: reverse-complement the
|
||||
entire super-kmer (and its minimizer).</li>
|
||||
</ul>
|
||||
<p>The reverse-complement step does not cause any additional splitting —
|
||||
it only flips the orientation.</p>
|
||||
<h3 id="why-non-canonical-minimizer">Why non-canonical minimizer?</h3>
|
||||
<p>Using the raw forward minimizer (rather than the canonical minimizer)
|
||||
means fewer candidates are considered at each position → the minimizer
|
||||
changes more often → super-kmers are <strong>shorter or equal</strong>,
|
||||
never longer, compared to the canonical-minimizer definition.</p>
|
||||
<p>The key benefit is at dereplication: a forward read and its
|
||||
reverse-complement covering the same genomic region both produce the
|
||||
<strong>same canonical super-kmer</strong> after the canonization step.
|
||||
Under the canonical-minimizer definition, they would share the same
|
||||
canonical minimizer but have different sequences (one being the revcomp
|
||||
of the other) — they would not dereplicate. Here they do, giving a
|
||||
compression factor of ~2× on paired or double-stranded data.</p>
|
||||
<h3 id="length">Length</h3>
|
||||
<p>For a random minimizer of length m over k-mers of length k, the
|
||||
density of minimizer positions is approximately 2/(k−m+2) <span
|
||||
class="citation" data-cites="Zheng2020-ji Golan2025-xf">[@Zheng2020-ji;
|
||||
@Golan2025-xf]</span>, giving an expected super-kmer length of (k+m)/2
|
||||
nucleotides. For k=31, m=13: expected ≈ 22 nt. In practice super-kmers
|
||||
rarely exceed a few dozen nucleotides — the 256 nt cap is almost never
|
||||
reached. When it is, the super-kmer is split at 256 nt with a k−1
|
||||
overlap, preserving all kmers without duplication.</p>
|
||||
<h2 id="binary-storage-format">Binary storage format</h2>
|
||||
<p>Memory-mappable binary format for sequence collections: store
|
||||
super-kmers end-to-end with u64-aligned headers (add padding if needed
|
||||
for 8-byte alignment). Include index blocks every B super-kmers
|
||||
(B=1000-10000) for fast jumping to position J (O(N/B + B) scan
|
||||
vs. separate index O(1) direct access), where N is total super-kmers in
|
||||
file. Represent header as union/struct for field access.</p>
|
||||
<h2 id="partitioning-and-indexing-architecture">Partitioning and
|
||||
indexing architecture</h2>
|
||||
<p>The canonical minimizer of a super-kmer is hashed to produce a
|
||||
<strong>p-bit routing value</strong> (p is a collection-level
|
||||
parameter):</p>
|
||||
<pre><code>canonical minimizer → hash(minimizer) → p-bit value → PART → partition directory</code></pre>
|
||||
<p>PART is computed once at phase 1 to open the correct partition file,
|
||||
then discarded. It is recomputed on the fly at query time. It is never
|
||||
stored in the super-kmer header.</p>
|
||||
<p>Each partition holds one BBHash instance (phase 6) that indexes kmers
|
||||
as plain u64 values — the minimizer plays no role inside the
|
||||
partition.</p>
|
||||
<p>Properties: - <strong>2^p partitions</strong>: p freely tunable at
|
||||
collection creation; not constrained to powers of 4 - <strong>Uniform
|
||||
distribution</strong>: hashing the canonical minimizer corrects the
|
||||
lexicographic bias inherent in minimizer selection <span
|
||||
class="citation"
|
||||
data-cites="Zheng2020-ji Zheng2021-cc Pan2024-hb Kille2023-px Golan2025-xf">[@Zheng2020-ji;
|
||||
@Zheng2021-cc; @Pan2024-hb; @Kille2023-px; @Golan2025-xf]</span> - The
|
||||
odd-length constraint on m only ensures canonical form correctness
|
||||
during minimizer computation — it does not affect the partition
|
||||
layout</p>
|
||||
<p><strong>Entropy constraint:</strong> the canonical minimizer has 2m
|
||||
bits of entropy. Requesting p bits from the hash requires 2m ≥ p,
|
||||
i.e. <strong>p ≤ 2m</strong>:</p>
|
||||
<table>
|
||||
<thead>
|
||||
<tr>
|
||||
<th>m</th>
|
||||
<th>p max</th>
|
||||
<th>Partitions max</th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody>
|
||||
<tr>
|
||||
<td>9</td>
|
||||
<td>2</td>
|
||||
<td>4</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td>11</td>
|
||||
<td>6</td>
|
||||
<td>64</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td>13</td>
|
||||
<td>10</td>
|
||||
<td>1 024</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td>15</td>
|
||||
<td>14</td>
|
||||
<td>16 384</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>For the typical configuration k=31, m=13: up to 1 024 partitions.
|
||||
Choosing p > 2m−16 is possible but produces artificially colliding
|
||||
PART values with no gain in routing granularity.</p>
|
||||
<h2 id="construction-pipeline">Construction pipeline</h2>
|
||||
<p>All phases after scatter are embarrassingly parallel across
|
||||
partitions.</p>
|
||||
<h3 id="phase-1-scatter">Phase 1 — Scatter</h3>
|
||||
<p>Single streaming pass over raw input files (FASTA/FASTQ, gzip). FASTQ
|
||||
quality scores are ignored. For each read:</p>
|
||||
<ol type="1">
|
||||
<li><strong>Ambiguous base filter</strong>: cut at any non-ACGT base;
|
||||
discard fragments shorter than k.</li>
|
||||
<li><strong>Entropy filter</strong>: scan each fragment with a sliding
|
||||
window of size k. When the kmer <span class="math inline">$K_i = S[i
|
||||
\mathinner{..} i+k-1]$</span> ended by nucleotide <span
|
||||
class="math inline"><em>S</em>[<em>j</em>]</span> (with <span
|
||||
class="math inline"><em>j</em> = <em>i</em> + <em>k</em> − 1</span>) has
|
||||
entropy below threshold <span class="math inline"><em>θ</em></span>,
|
||||
emit the current segment and start a new one (see algorithm below).
|
||||
<span class="math inline"><em>K</em><sub><em>i</em></sub></span> belongs
|
||||
to neither segment, and no valid kmer is lost.</li>
|
||||
<li><strong>Super-kmer extraction</strong>: for each clean segment,
|
||||
slide a minimizer window and group consecutive kmers sharing the same
|
||||
raw minimizer; canonise at the end.</li>
|
||||
<li><strong>Partition routing</strong>:
|
||||
<code>hash(canonical_minimizer) → PART</code> → append super-kmer to
|
||||
<code>partition/superkmers.bin.gz</code>.</li>
|
||||
</ol>
|
||||
<p><strong>Entropy filter algorithm:</strong></p>
|
||||
<p>When <span class="math inline"><em>K</em><sub><em>i</em></sub></span>
|
||||
(ended by <span class="math inline"><em>S</em>[<em>j</em>]</span>, <span
|
||||
class="math inline"><em>j</em> = <em>i</em> + <em>k</em> − 1</span>)
|
||||
fails the entropy threshold:</p>
|
||||
<ul>
|
||||
<li>Current segment <span class="math inline">$S[\textit{seg_start}
|
||||
\mathinner{..} j-1]$</span> is emitted (last valid kmer = <span
|
||||
class="math inline"><em>K</em><sub><em>i</em> − 1</sub></span>)</li>
|
||||
<li>New segment starts at <span
|
||||
class="math inline"><em>S</em>[<em>i</em> + 1]</span> (first new kmer =
|
||||
<span
|
||||
class="math inline"><em>K</em><sub><em>i</em> + 1</sub></span>)</li>
|
||||
<li><span class="math inline"><em>K</em><sub><em>i</em></sub></span> is
|
||||
excluded: current segment lacks <span
|
||||
class="math inline"><em>S</em>[<em>j</em>]</span>, new segment lacks
|
||||
<span class="math inline"><em>S</em>[<em>i</em>]</span></li>
|
||||
<li>Overlap = <span class="math inline">$S[i+1 \mathinner{..}
|
||||
j-1]$</span> = <span class="math inline"><em>k</em> − 2</span>
|
||||
nucleotides</li>
|
||||
</ul>
|
||||
<pre class="pseudocode"><code>\begin{algorithm}
|
||||
\caption{Entropy filter — sliding window segmentation}
|
||||
\begin{algorithmic}
|
||||
\PROCEDURE{EntropyFilter}{S, N, k, theta}
|
||||
\STATE seg_start <- 0
|
||||
\STATE window <- []
|
||||
\FOR{j <- 0 \TO N-1}
|
||||
\STATE window.push(S[j])
|
||||
\IF{|window| < k}
|
||||
\STATE continue
|
||||
\ENDIF
|
||||
\STATE i <- j - k + 1
|
||||
\IF{entropy(window) <= theta}
|
||||
\STATE emit S[seg_start .. j-1]
|
||||
\STATE seg_start <- i + 1
|
||||
\STATE window <- S[i+1 .. j]
|
||||
\ELSE
|
||||
\STATE window.pop_front()
|
||||
\ENDIF
|
||||
\ENDFOR
|
||||
\STATE emit S[seg_start .. N-1]
|
||||
\ENDPROCEDURE
|
||||
\end{algorithmic}
|
||||
\end{algorithm}</code></pre>
|
||||
<p>Writes are sequential and append-only — IO-friendly. Gzip applied at
|
||||
write time. Data volume ≈ raw genome size (2 bits/nt compaction offsets
|
||||
header overhead).</p>
|
||||
<h3 id="phase-2-dereplication">Phase 2 — Dereplication</h3>
|
||||
<p>Performed independently per partition. Identical super-kmers are
|
||||
consolidated and their COUNT accumulated — analogous to amplicon
|
||||
dereplication in metabarcoding. Uses external bucket sort to stay within
|
||||
RAM bounds:</p>
|
||||
<p><strong>Pass 1</strong> (streaming): hash the nucleotide payload of
|
||||
each super-kmer, route to one of B bucket files:</p>
|
||||
<pre><code>hash(sequence) % B → bucket_i.bin</code></pre>
|
||||
<p>B ≈ 100 is tunable; RAM needed ≈ partition_size / B.</p>
|
||||
<p><strong>Pass 2</strong>: for each bucket, load into an in-memory
|
||||
<code>HashMap<sequence, COUNT></code>, dereplicate by summing
|
||||
COUNT values, write consolidated super-kmers.</p>
|
||||
<p>After dereplication: at Nx coverage the partition shrinks by ~x
|
||||
(errors aside). The COUNT field in each super-kmer header = number of
|
||||
times that exact super-kmer sequence was observed across all input
|
||||
reads.</p>
|
||||
<p><strong>Important:</strong> super-kmer COUNT ≠ individual kmer count.
|
||||
A kmer can appear in multiple distinct super-kmers (same partition,
|
||||
different flanking context); its true count = sum of COUNT of all
|
||||
super-kmers containing it. A super-kmer with COUNT=1 may contain only
|
||||
high-abundance kmers, each appearing in many other super-kmers.
|
||||
Abundance filtering therefore cannot be applied at this phase.</p>
|
||||
<h3 id="phase-3-per-kmer-count-aggregation-and-quorum-filtering">Phase 3
|
||||
— Per-kmer count aggregation and quorum filtering</h3>
|
||||
<p>For each dereplicated super-kmer, enumerate its kmers and accumulate
|
||||
counts:</p>
|
||||
<pre><code>for each super-kmer (sequence, COUNT):
|
||||
for each kmer in sequence:
|
||||
kmer_counts[canonical(kmer)] += COUNT</code></pre>
|
||||
<p>Implemented as an external sort or a temporary HashMap, depending on
|
||||
partition size. At the end of this phase, each distinct canonical kmer
|
||||
has its exact total count.</p>
|
||||
<p>Abundance filter applied here: kmers with
|
||||
<code>total_count < q</code> are discarded. <code>q</code> is a
|
||||
collection parameter (0 = keep all, including singletons for ≤1x
|
||||
data).</p>
|
||||
<p>No pre-filter on super-kmer COUNT is possible at phase 2: a
|
||||
super-kmer with COUNT=1 may contain only high-abundance kmers, each
|
||||
present in many other super-kmers across the partition.</p>
|
||||
<h3 id="phase-4-super-kmer-compaction">Phase 4 — Super-kmer
|
||||
compaction</h3>
|
||||
<p>The valid kmer set from phase 3 is used as a mask to rewrite the
|
||||
super-kmer files:</p>
|
||||
<pre><code>for each dereplicated super-kmer:
|
||||
scan kmer by kmer
|
||||
kmer not in valid set → break point (terminates current super-kmer)
|
||||
kmer in valid set → extend current super-kmer</code></pre>
|
||||
<p>Three cases per super-kmer: - <strong>All kmers valid</strong> →
|
||||
copied as-is - <strong>No kmer valid</strong> → discarded -
|
||||
<strong>Mixed</strong> → split into sub-super-kmers at invalid
|
||||
boundaries; each sub-super-kmer inherits the original COUNT</p>
|
||||
<p>After splitting, re-apply dereplication (bucket sort, phase 2 method)
|
||||
— splitting can produce new identical super-kmers. This re-dereplication
|
||||
is cheap: the volume is already greatly reduced.</p>
|
||||
<p>Output: a clean super-kmer file where every kmer passes quorum. This
|
||||
file feeds phase 5.</p>
|
||||
<h3 id="phase-5-local-de-bruijn-graph-and-unitig-construction">Phase 5 —
|
||||
Local de Bruijn graph and unitig construction</h3>
|
||||
<p>Within each partition, build a <strong>local de Bruijn graph</strong>
|
||||
from the valid kmer set and compute its unitigs. All operations are
|
||||
local to the partition — no cross-partition communication.</p>
|
||||
<pre><code>valid kmers → HashSet<u64>
|
||||
|
||||
for each kmer K:
|
||||
out_degree = |{K[1:]+b | b ∈ {A,C,G,T}} ∩ HashSet|
|
||||
in_degree = |{b+K[:-1] | b ∈ {A,C,G,T}} ∩ HashSet|
|
||||
|
||||
internal node ↔ in_degree=1 AND out_degree=1
|
||||
branching / dead-end → unitig start or end</code></pre>
|
||||
<p>Traverse non-branching paths to assemble unitigs. Kmers whose
|
||||
neighbours fall in other partitions appear as dead ends locally — they
|
||||
terminate the unitig. The result: <strong>each kmer appears in exactly
|
||||
one unitig</strong> within the partition.</p>
|
||||
<p>The partition size (controlled by p) must be calibrated so that the
|
||||
HashSet fits in RAM during this phase.</p>
|
||||
<p>Output: <code>unitigs.bin</code> — the permanent evidence structure
|
||||
for the partition. Each kmer in the partition appears at exactly one
|
||||
(unitig_id, offset) location.</p>
|
||||
<p><strong>Scope of local unitigs:</strong> these are unitigs of the
|
||||
partition’s local de Bruijn graph, not global unitigs. A kmer whose k-1
|
||||
successor or predecessor falls in another partition appears as a dead
|
||||
end locally and terminates the unitig. This does not affect correctness
|
||||
of verification but means partition-local unitigs cannot be directly
|
||||
reused for global assembly.</p>
|
||||
<h3 id="phase-6-bbhash-construction-and-index-finalisation">Phase 6 —
|
||||
BBHash construction and index finalisation</h3>
|
||||
<p>Built once on the definitive kmer set (all kmers in all unitigs of
|
||||
the partition):</p>
|
||||
<pre><code>kmers from unitigs → BBHash → bbhash.bin
|
||||
→ counts.bin : packed n-bit array (or 1-bit for presence mode)
|
||||
→ refs.bin : (unitig_id: u32, kmer_offset: u8) per kmer</code></pre>
|
||||
<p>BBHash is built once — no rebuild. The n-bit width for
|
||||
<code>counts.bin</code> is chosen from the observed count distribution
|
||||
(n=5 covers ~97% of kmers at 15x; n=1 for presence mode). Counts
|
||||
exceeding 2ⁿ−1 go into <code>overflow.bin</code> as sorted
|
||||
<code>(bbhash_index: u32, count: u32)</code> pairs.</p>
|
||||
<p><strong>Exact verification via unitig evidence:</strong></p>
|
||||
<p><code>unitigs.bin</code> serves as the evidence structure: for any
|
||||
query kmer, the stored unitig provides the ground truth to confirm or
|
||||
deny its presence. BBHash maps every input to [0, N) including absent
|
||||
kmers — the unitig read-back is the only way to guarantee exactness.</p>
|
||||
<pre><code>query kmer q
|
||||
→ minimizer(q) → hash → PART, KEY → partition
|
||||
→ BBHash(q) → index i
|
||||
→ refs[i] = (unitig_id, offset)
|
||||
→ read unitig unitig_id from unitigs.bin
|
||||
→ extract kmer at offset → compare with q
|
||||
→ match : return counts[i] ← exact hit
|
||||
→ no match: kmer absent ← BBHash collision on absent kmer</code></pre>
|
||||
<p>One random disk access into <code>unitigs.bin</code> per query; the
|
||||
unitig is the minimal, non-redundant evidence (each kmer stored
|
||||
once).</p>
|
||||
<h2 id="on-disk-collection-structure">On-disk collection structure</h2>
|
||||
<p>Collections are too large to hold in RAM (hundreds of genomes,
|
||||
billions of kmers). The collection lives on disk as a directory of
|
||||
memory-mapped files:</p>
|
||||
<pre><code>collection/
|
||||
metadata.toml — collection parameters (see below)
|
||||
superkmers.bin — super-kmer sequences, end-to-end, memory-mappable
|
||||
superkmers.idx — index blocks every B super-kmers for fast seeking
|
||||
part_XXXX/
|
||||
bbhash.bin — BBHash function for this partition
|
||||
counts.bin — packed n-bit count array (or 1-bit presence array)
|
||||
refs.bin — back-references for exact verification</code></pre>
|
||||
<p><strong>Collection parameters</strong> (stored in
|
||||
<code>metadata.toml</code>):</p>
|
||||
<table>
|
||||
<thead>
|
||||
<tr>
|
||||
<th>Parameter</th>
|
||||
<th>Role</th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody>
|
||||
<tr>
|
||||
<td>k</td>
|
||||
<td>kmer length</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td>m</td>
|
||||
<td>minimizer length (odd, < k)</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td>p</td>
|
||||
<td>partition bits (0 ≤ p ≤ min(14, 2m−16))</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td>mode</td>
|
||||
<td><code>presence</code> (1 bit/kmer) or <code>count</code> (n
|
||||
bits/kmer)</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td>n</td>
|
||||
<td>bits per kmer in count mode (chosen at construction)</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td>min_count</td>
|
||||
<td>singleton filtering threshold (0 = keep all)</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td>hash_fn</td>
|
||||
<td>hash function identifier</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td>hash_seed</td>
|
||||
<td>seed for the hash function</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p><strong>Exact verification via back-reference:</strong></p>
|
||||
<p>BBHash maps any input to [0, N) — including absent kmers. To avoid
|
||||
false positives, <code>refs.bin</code> stores at each BBHash index a
|
||||
back-reference <code>(superkmer_id: u32, kmer_offset: u8)</code> = 5
|
||||
bytes. Query protocol:</p>
|
||||
<pre><code>query kmer q
|
||||
→ minimizer(q) → hash → PART, KEY → partition
|
||||
→ BBHash(q) → index i
|
||||
→ refs[i] = (sk_id, offset)
|
||||
→ read super-kmer sk_id from superkmers.bin
|
||||
→ extract kmer at offset → compare with q
|
||||
→ if match: return counts[i] (exact)
|
||||
→ if no match: kmer absent</code></pre>
|
||||
<p><strong>Count storage — two modes:</strong></p>
|
||||
<p><em>Presence mode</em> (coverage ≤ 1x, or when only presence/absence
|
||||
matters): - <code>counts.bin</code> is a packed 1-bit array — all bits
|
||||
set to 1 for indexed kmers - Singletons are the signal, not filtered</p>
|
||||
<p><em>Count mode</em> (coverage > 1x): - <code>counts.bin</code> is
|
||||
a packed n-bit array; n chosen at construction from the observed
|
||||
distribution - Value 0: absent sentinel; values 1..2ⁿ−2: direct count;
|
||||
value 2ⁿ−1: overflow - Overflow counts stored in a separate
|
||||
<code>overflow.bin</code> as sorted
|
||||
<code>(index: u32, count: u32)</code> pairs - Empirically (k=31, 15x
|
||||
coverage): n=5 covers 97% of real kmers, n=6 covers 99% - min_count
|
||||
threshold filters low-frequency kmers (errors) before indexing; for ≤1x,
|
||||
min_count=0</p>
|
||||
<p><strong>BBHash:</strong> operates on kmer u64 values directly within
|
||||
each partition. The minimizer plays no role inside the partition —
|
||||
BBHash receives the kmer and builds the perfect hash naturally.</p>
|
||||
<h2 id="kmer-entropy-filter">Kmer entropy filter</h2>
|
||||
<p>Low-complexity kmers (polyA, polyT, tandem repeats) are detected and
|
||||
excluded during phase 1. The filter computes a <strong>normalized
|
||||
Shannon entropy</strong> over sub-words of multiple sizes, corrected for
|
||||
two sources of bias: the small number of observations within a single
|
||||
kmer, and the unequal sizes of circular equivalence classes.</p>
|
||||
<h3 id="sub-word-frequencies">Sub-word frequencies</h3>
|
||||
<p>For a kmer of length k and a sub-word size ws (1 ≤ ws ≤ ws_max,
|
||||
typically ws_max = 6), extract the <span
|
||||
class="math inline"><em>n</em><sub>words</sub> = <em>k</em> − <em>w</em><em>s</em> + 1</span>
|
||||
overlapping sub-words by sliding a window of length ws:</p>
|
||||
<p><span class="math display">$$w_i = \text{kmer}[i \mathinner{..}
|
||||
i+ws-1], \quad i = 0, \ldots, n_{\text{words}}-1$$</span></p>
|
||||
<p>Each sub-word is mapped to its <strong>circular canonical
|
||||
form</strong>: the lexicographic minimum among all cyclic rotations of
|
||||
the word. Let <span
|
||||
class="math inline"><em>s</em><sub><em>j</em></sub></span> be the size
|
||||
of equivalence class <span class="math inline"><em>j</em></span> (number
|
||||
of distinct raw words mapping to canonical form <span
|
||||
class="math inline"><em>j</em></span>), and <span
|
||||
class="math inline"><em>f</em><sub><em>j</em></sub></span> the count of
|
||||
canonical form <span class="math inline"><em>j</em></span> among the
|
||||
<span class="math inline"><em>n</em><sub>words</sub></span> sub-words
|
||||
(<span
|
||||
class="math inline">∑<sub><em>j</em></sub><em>f</em><sub><em>j</em></sub> = <em>n</em><sub>words</sub></span>).</p>
|
||||
<h3 id="corrected-shannon-entropy">Corrected Shannon entropy</h3>
|
||||
<p>The circular equivalence classes have unequal sizes: under a uniform
|
||||
distribution over all <span
|
||||
class="math inline">4<sup><em>w</em><em>s</em></sup></span> raw words,
|
||||
class <span class="math inline"><em>j</em></span> is visited with
|
||||
probability <span
|
||||
class="math inline"><em>s</em><sub><em>j</em></sub>/4<sup><em>w</em><em>s</em></sup></span>,
|
||||
not <span class="math inline">1/<em>n</em><sub><em>a</em></sub></span>.
|
||||
Computing entropy directly over canonical classes therefore
|
||||
underestimates the entropy of a random sequence.</p>
|
||||
<p>The correction “unfolds” each canonical class back to its member raw
|
||||
words, redistributing each observation of class <span
|
||||
class="math inline"><em>j</em></span> equally among its <span
|
||||
class="math inline"><em>s</em><sub><em>j</em></sub></span> members:</p>
|
||||
<p><span class="math display">$$H_{\text{corr}} = \log(n_{\text{words}})
|
||||
- \frac{1}{n_{\text{words}}} \sum_j f_j \log f_j +
|
||||
\frac{1}{n_{\text{words}}} \sum_j f_j \log s_j$$</span></p>
|
||||
<p>The last term is the correction for unequal class sizes. For a
|
||||
uniformly random sequence (<span
|
||||
class="math inline"><em>f</em><sub><em>j</em></sub> ≈ <em>n</em><sub>words</sub> ⋅ <em>s</em><sub><em>j</em></sub>/4<sup><em>w</em><em>s</em></sup></span>),
|
||||
this gives <span
|
||||
class="math inline"><em>H</em><sub>corr</sub> ≈ log (4<sup><em>w</em><em>s</em></sup>) = 2 ⋅ <em>w</em><em>s</em> ⋅ log 2</span>,
|
||||
the maximum entropy over raw words.</p>
|
||||
<h3 id="maximum-entropy-correction-for-small-samples">Maximum entropy
|
||||
correction for small samples</h3>
|
||||
<p>With only <span class="math inline"><em>n</em><sub>words</sub></span>
|
||||
observations over <span
|
||||
class="math inline">4<sup><em>w</em><em>s</em></sup></span> possible raw
|
||||
words, the achievable maximum entropy is bounded by the most uniform
|
||||
integer distribution over <span
|
||||
class="math inline">4<sup><em>w</em><em>s</em></sup></span>
|
||||
categories.</p>
|
||||
<p>Let <span
|
||||
class="math inline"><em>c</em> = ⌊<em>n</em><sub>words</sub>/4<sup><em>w</em><em>s</em></sup>⌋</span>
|
||||
and <span
|
||||
class="math inline"><em>r</em> = <em>n</em><sub>words</sub> mod 4<sup><em>w</em><em>s</em></sup></span>.
|
||||
The most uniform integer distribution assigns frequency <span
|
||||
class="math inline"><em>c</em> + 1</span> to <span
|
||||
class="math inline"><em>r</em></span> categories and <span
|
||||
class="math inline"><em>c</em></span> to the remaining <span
|
||||
class="math inline">4<sup><em>w</em><em>s</em></sup> − <em>r</em></span>,
|
||||
with the convention <span class="math inline">0log 0 = 0</span>:</p>
|
||||
<p><span class="math display">$$H_{\max} = -\left[(4^{ws} -
|
||||
r)\,\frac{c}{n_{\text{words}}}\log\frac{c}{n_{\text{words}}} +
|
||||
r\,\frac{c+1}{n_{\text{words}}}\log\frac{c+1}{n_{\text{words}}}\right]$$</span></p>
|
||||
<p>When <span
|
||||
class="math inline"><em>n</em><sub>words</sub> < 4<sup><em>w</em><em>s</em></sup></span>:
|
||||
<span class="math inline"><em>c</em> = 0</span>, <span
|
||||
class="math inline"><em>r</em> = <em>n</em><sub>words</sub></span>, and
|
||||
the formula reduces to <span
|
||||
class="math inline"><em>H</em><sub>max</sub> = log (<em>n</em><sub>words</sub>)</span>
|
||||
— a single unified expression covers both regimes. A truly random
|
||||
sequence achieves <span
|
||||
class="math inline"><em>H</em><sub>corr</sub> ≈ <em>H</em><sub>max</sub></span>.</p>
|
||||
<h3 id="normalized-entropy">Normalized entropy</h3>
|
||||
<p><span class="math display">$$\hat{H}(ws) =
|
||||
\frac{H_{\text{corr}}}{H_{\max}} \in [0, 1]$$</span></p>
|
||||
<h3 id="final-score">Final score</h3>
|
||||
<p>The filter computes <span
|
||||
class="math inline"><em>Ĥ</em>(<em>w</em><em>s</em>)</span> for each
|
||||
word size ws from 1 to ws_max and returns the
|
||||
<strong>minimum</strong>:</p>
|
||||
<p><span class="math display">$$\text{entropy}(kmer) =
|
||||
\min_{ws=1}^{ws_{\max}} \hat{H}(ws)$$</span></p>
|
||||
<p>A value near 0 indicates low complexity (e.g. AAAA…); near 1
|
||||
indicates high complexity. A kmer is rejected if <span
|
||||
class="math inline">entropy(<em>k</em><em>m</em><em>e</em><em>r</em>) ≤ <em>θ</em></span>,
|
||||
where <span class="math inline"><em>θ</em></span> is a collection
|
||||
parameter. The minimum across word sizes ensures that any scale of
|
||||
repetition is detected independently: polyA is caught at ws=1,
|
||||
dinucleotide repeats at ws=2, etc.</p>
|
||||
<h2 id="priority-operations">Priority operations</h2>
|
||||
<ul>
|
||||
<li>Kmer counting (frequencies)</li>
|
||||
<li>Fast search / query</li>
|
||||
<li>Set operations: union, intersection, difference</li>
|
||||
</ul>
|
||||
<h2 id="data-types">Data types</h2>
|
||||
<p>Two types of DNA are represented:</p>
|
||||
<ul>
|
||||
<li><strong>Super-kmers</strong>: stored as a nucleotide sequence (2
|
||||
bits/base, byte-aligned, no padding). Max length: 256 nucleotides (512
|
||||
bits, 64 bytes). Each super-kmer has a <strong>32-bit
|
||||
header</strong>:</li>
|
||||
</ul>
|
||||
<table>
|
||||
<thead>
|
||||
<tr>
|
||||
<th>Field</th>
|
||||
<th>Bits</th>
|
||||
<th>Role</th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody>
|
||||
<tr>
|
||||
<td>COUNT</td>
|
||||
<td>24</td>
|
||||
<td>Occurrence count (≤ 16 M)</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td>SEQL</td>
|
||||
<td>8</td>
|
||||
<td>Sequence length in nucleotides (≤ 256)</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>Bit layout (MSB to LSB):</p>
|
||||
<pre><code>[31:8] COUNT [7:0] SEQL</code></pre>
|
||||
<p>Getters:</p>
|
||||
<div class="sourceCode" id="cb12"><pre
|
||||
class="sourceCode rust"><code class="sourceCode rust"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a><span class="kw">fn</span> seql(<span class="op">&</span><span class="kw">self</span>) <span class="op">-></span> <span class="dt">u8</span> <span class="op">{</span> <span class="kw">self</span><span class="op">.</span><span class="dv">0</span> <span class="kw">as</span> <span class="dt">u8</span> <span class="op">}</span></span>
|
||||
<span id="cb12-2"><a href="#cb12-2" aria-hidden="true" tabindex="-1"></a><span class="kw">fn</span> count(<span class="op">&</span><span class="kw">self</span>) <span class="op">-></span> <span class="dt">u32</span> <span class="op">{</span> <span class="kw">self</span><span class="op">.</span><span class="dv">0</span> <span class="op">>></span> <span class="dv">8</span> <span class="op">}</span></span>
|
||||
<span id="cb12-3"><a href="#cb12-3" aria-hidden="true" tabindex="-1"></a><span class="kw">fn</span> increment(<span class="op">&</span><span class="kw">mut</span> <span class="kw">self</span>) <span class="op">{</span> <span class="kw">self</span><span class="op">.</span><span class="dv">0</span> <span class="op">+=</span> <span class="dv">1</span> <span class="op"><<</span> <span class="dv">8</span><span class="op">;</span> <span class="op">}</span></span></code></pre></div>
|
||||
<p>PART and KEY were considered as routing fields derived from
|
||||
<code>hash(minimizer)</code> but are single-use at phase 1 only —
|
||||
neither is stored. The nucleotide sequence is always byte-aligned (no
|
||||
offset): after reverse-complementing a super-kmer, a single bit-shift
|
||||
realigns the sequence so that nucleotide 0 always starts at bit 0 of
|
||||
word[0]. This shift is paid once at canonisation (phase 1, at most half
|
||||
of super-kmers) and eliminates any need for an alignment offset field.
|
||||
The direct consequence for dereplication: the byte array can be hashed
|
||||
directly without any offset adjustment.</p>
|
||||
<p>Note: minimizer selection (window minimum) biases the raw minimizer
|
||||
distribution toward lexicographically small values <span
|
||||
class="citation"
|
||||
data-cites="Zheng2020-ji Zheng2021-cc Pan2024-hb Kille2023-px Golan2025-xf">[@Zheng2020-ji;
|
||||
@Zheng2021-cc; @Pan2024-hb; @Kille2023-px; @Golan2025-xf]</span>;
|
||||
hashing corrects this before partition routing.</p>
|
||||
<ul>
|
||||
<li><strong>Kmers</strong>: short DNA subsequences (k bases),
|
||||
represented in <code>u64</code>.</li>
|
||||
</ul>
|
||||
<h2 id="kmer-representation">Kmer representation</h2>
|
||||
<p>Each base is encoded on 2 bits, so any kmer with k ≤ 31 fits in a
|
||||
<code>u64</code>.</p>
|
||||
<h3 id="bit-layout">Bit layout</h3>
|
||||
<p>Nucleotide <code>i</code> occupies bits <code>64-i</code> and
|
||||
<code>63-i</code>. For a kmer of length k, 2k bits are used; the
|
||||
low-order 64 - 2k bits of the u64 are kept at 0 and have no meaning.</p>
|
||||
<ul>
|
||||
<li>Extraction of nuc[i]:
|
||||
<code>(word >> (63 - 2*i)) & 0b11</code>.</li>
|
||||
</ul>
|
||||
<p>For kmers (k ≤ 31), the whole sequence fits in a single
|
||||
<code>u64</code>. For longer sequences up to 256 nucleotides (512 bits),
|
||||
the representation extends across multiple words.</p>
|
||||
<h3 id="complement-and-reverse-complement">Complement and reverse
|
||||
complement</h3>
|
||||
<p>The encoding is chosen so that the Watson-Crick complement of any
|
||||
base is its bitwise NOT (on 2 bits):</p>
|
||||
<table>
|
||||
<thead>
|
||||
<tr>
|
||||
<th>Base</th>
|
||||
<th>Encoding</th>
|
||||
<th>Complement</th>
|
||||
<th>NOT</th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody>
|
||||
<tr>
|
||||
<td>A</td>
|
||||
<td><code>00</code></td>
|
||||
<td>T</td>
|
||||
<td><code>11</code></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td>C</td>
|
||||
<td><code>01</code></td>
|
||||
<td>G</td>
|
||||
<td><code>10</code></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td>G</td>
|
||||
<td><code>10</code></td>
|
||||
<td>C</td>
|
||||
<td><code>01</code></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td>T</td>
|
||||
<td><code>11</code></td>
|
||||
<td>A</td>
|
||||
<td><code>00</code></td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>This means <code>complement(base) = ~base & 0b11</code>, and the
|
||||
reverse complement of a kmer reduces to two cheap operations:</p>
|
||||
<pre><code>revcomp(kmer) = reverse_bases(~kmer & mask_2k)</code></pre>
|
||||
<p>where <code>mask_2k = (1 << 2k) - 1</code> zeros the unused
|
||||
high bits, and <code>reverse_bases</code> reorders the 2-bit chunks from
|
||||
LSB to MSB. No lookup table needed.</p>
|
||||
<p>DNA being double-stranded, each kmer and its reverse complement are
|
||||
equivalent. The canonical form is defined as:</p>
|
||||
<pre><code>canonical(kmer) = min(kmer, revcomp(kmer))</code></pre>
|
||||
<p>This halves the kmer space and ensures strand-independent
|
||||
counting.</p>
|
||||
<h2 id="sequence-operations">Sequence operations</h2>
|
||||
<h3 id="reverse-complement">Reverse complement</h3>
|
||||
<p>Reverse complement of a super-kmer sequence (used at most once per
|
||||
super-kmer, during phase 1 canonisation):</p>
|
||||
<ol type="1">
|
||||
<li>Reverse byte order</li>
|
||||
<li>Apply 256-entry lookup table (precomputed reverse-complemented
|
||||
bytes) to each byte</li>
|
||||
<li>Bit-shift the result to realign nucleotide 0 to bit 0 of
|
||||
word[0]</li>
|
||||
</ol>
|
||||
<p>The shift amount depends only on the sequence length:
|
||||
<code>shift = (len % 4) * 2</code> bits. After the shift, the sequence
|
||||
is byte-aligned with no offset — the same invariant as the original.</p>
|
||||
<div class="sourceCode" id="cb15"><pre
|
||||
class="sourceCode rust"><code class="sourceCode rust"><span id="cb15-1"><a href="#cb15-1" aria-hidden="true" tabindex="-1"></a><span class="kw">fn</span> reverse_complement(words<span class="op">:</span> <span class="op">&</span>[<span class="dt">u64</span>]<span class="op">,</span> len<span class="op">:</span> <span class="dt">usize</span>) <span class="op">-></span> <span class="dt">Vec</span><span class="op"><</span><span class="dt">u64</span><span class="op">></span> <span class="op">{</span></span>
|
||||
<span id="cb15-2"><a href="#cb15-2" aria-hidden="true" tabindex="-1"></a> <span class="kw">let</span> bytes <span class="op">=</span> words_to_bytes(words)<span class="op">;</span></span>
|
||||
<span id="cb15-3"><a href="#cb15-3" aria-hidden="true" tabindex="-1"></a> <span class="kw">let</span> <span class="kw">mut</span> rev<span class="op">:</span> <span class="dt">Vec</span><span class="op"><</span><span class="dt">u8</span><span class="op">></span> <span class="op">=</span> bytes<span class="op">.</span>iter()<span class="op">.</span>rev()<span class="op">.</span>map(<span class="op">|&</span>b<span class="op">|</span> LOOKUP_TABLE[b <span class="kw">as</span> <span class="dt">usize</span>])<span class="op">.</span>collect()<span class="op">;</span></span>
|
||||
<span id="cb15-4"><a href="#cb15-4" aria-hidden="true" tabindex="-1"></a> <span class="kw">let</span> shift <span class="op">=</span> (len <span class="op">%</span> <span class="dv">4</span>) <span class="op">*</span> <span class="dv">2</span><span class="op">;</span></span>
|
||||
<span id="cb15-5"><a href="#cb15-5" aria-hidden="true" tabindex="-1"></a> <span class="cf">if</span> shift <span class="op">></span> <span class="dv">0</span> <span class="op">{</span> bit_shift_left(<span class="op">&</span><span class="kw">mut</span> rev<span class="op">,</span> shift)<span class="op">;</span> <span class="op">}</span></span>
|
||||
<span id="cb15-6"><a href="#cb15-6" aria-hidden="true" tabindex="-1"></a> bytes_to_words(rev)</span>
|
||||
<span id="cb15-7"><a href="#cb15-7" aria-hidden="true" tabindex="-1"></a><span class="op">}</span></span></code></pre></div>
|
||||
<h2 id="multithreading">Multithreading</h2>
|
||||
<p>For HPC with 100+ cores: use Rayon for data parallelism (parallel
|
||||
iterators), std::thread for custom threading, or async with Tokio for
|
||||
I/O-bound tasks. Equivalent to Go’s goroutines but with
|
||||
ownership/borrowing safety.</p>
|
||||
<p>Rayon: Rust crate for automatic data parallelism. Provides parallel
|
||||
iterators (par_iter) that distribute work across CPU cores, e.g.,
|
||||
vec.par_iter().map(|x| x*2).collect(). Handles thread
|
||||
spawning/synchronization transparently. Widely used and maintained by
|
||||
the Rust project. Orthogonal to Tokio (async runtime): Rayon for CPU
|
||||
parallelism, Tokio for async I/O.</p>
|
||||
<p>Data pipelines: use Crossbeam channels (MPMC) with threads/async,
|
||||
equivalent to Go’s channels + goroutines.</p>
|
||||
<p>Channels: std::sync::mpsc (built-in, MPSC, simple); crossbeam (crate,
|
||||
MPMC, faster, more features like select). Use Crossbeam for
|
||||
multi-producer/multi-consumer scenarios.</p>
|
||||
<h1 id="bibliographie">Bibliographie</h1>
|
||||
<p>\bibliography</p>
|
||||
Reference in New Issue
Block a user