Refactor: Extract utility function for string reversal
Extracted `inverser_chaine` into a reusable utility function with docstring and added unit test to ensure correctness.
This commit is contained in:
Eric Coissac
@@ -5,3 +5,5 @@ data-stress
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*.zst
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*.zst.meta
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*.pb
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*.json
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*.bin
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@@ -0,0 +1,275 @@
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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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|
||||
[2m2026-04-27T20:36:25.272346Z[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
|
||||
@@ -1,6 +1,29 @@
|
||||
# MPHF selection — analysis in progress
|
||||
# MPHF selection — two-phase indexing architecture
|
||||
|
||||
The choice of Minimal Perfect Hash Function for phase 6 is not yet settled. Three candidates were evaluated.
|
||||
## Indexing architecture
|
||||
|
||||
Kmer indexing per partition proceeds in two phases. The separation is necessary because the exact number of unique kmers in a partition is not known until after counting and filtering.
|
||||
|
||||
### Superkmer vs kmer counts
|
||||
|
||||
The `SKFileMeta` sidecar written by `SKFileWriter` records `instances` (unique superkmers) and `length_sum` (total nucleotides). A superkmer of length L contains L − k + 1 kmers, so the kmer count per partition can be estimated as `length_sum − instances × (k − 1)`. This is an **overestimate** of unique kmers: two distinct superkmers (different flanking contexts, same minimizer) can share kmers. The exact count of unique kmers is only known after enumerating and deduplicating them.
|
||||
|
||||
Note: two superkmers sharing a kmer necessarily share the same minimizer and therefore always land in the same partition — no kmer can appear in two different partitions.
|
||||
|
||||
### Phase 1 — provisional index and spectrum
|
||||
|
||||
1. Enumerate all kmers from the dereplicated superkmers of the partition.
|
||||
2. Build a provisional MPHF over this key set; capacity is pre-allocated from the sidecar estimate (slight overestimate, harmless).
|
||||
3. Accumulate counts: for each kmer in each superkmer, `count[MPHF(kmer)] += sk.count()`.
|
||||
4. Compute the kmer frequency spectrum (histogram: occurrences → number of kmers).
|
||||
5. Apply count filter (e.g. discard singletons). After filtering, the exact number of surviving kmers is known.
|
||||
6. Discard the provisional MPHF.
|
||||
|
||||
### Phase 2 — definitive index
|
||||
|
||||
Build a new MPHF over the filtered kmer set only, with the exact key count available. This is the persistent per-partition index used for all downstream operations (queries, set operations).
|
||||
|
||||
---
|
||||
|
||||
## Candidates
|
||||
|
||||
@@ -8,31 +31,41 @@ The choice of Minimal Perfect Hash Function for phase 6 is not yet settled. Thre
|
||||
|
||||
- ~3.7 bits/key; mature crate, used in production bioinformatics (Pufferfish, Piscem)
|
||||
- Parallel construction; well-tested with DNA kmer data at scale
|
||||
- Drawback: largest space footprint of the three
|
||||
- Drawback: largest space footprint; streaming construction (no exact count needed) was its main differentiator — irrelevant here since exact count is available at phase 2
|
||||
|
||||
**ptr_hash** (PtrHash algorithm, Groot Koerkamp, SEA 2025):
|
||||
|
||||
- ~2.4 bits/key; fastest queries (≥2.1× over alternatives, 8–12 ns/key for u64 in tight loops) and fastest construction (≥3.1×)
|
||||
- Theoretical foundation solid; paper and Rust crate from the same author
|
||||
- Requires exact key count at construction — available at phase 2
|
||||
- Drawback: published February 2025 — very young, no production track record
|
||||
|
||||
**FMPHGO** (`ph` crate, Beling, ACM JEA 2023):
|
||||
|
||||
- ~2.1 bits/key — most compact of the three; good query speed; parallelisable construction
|
||||
- More established than ptr_hash; actively maintained
|
||||
- Currently preferred candidate
|
||||
- Works well with overestimated capacity → natural fit for phase 1
|
||||
|
||||
## MPHF choice per phase
|
||||
|
||||
**Phase 1** (provisional, discarded after spectrum computation): FMPHGO. Tolerates overestimated capacity, compact, no need to optimise for query speed on a temporary structure.
|
||||
|
||||
**Phase 2** (persistent, queried repeatedly): open between FMPHGO and ptr_hash. Exact key count is available, so both operate optimally. ptr_hash's query speed advantage (2.1–3.3×) is meaningful for the persistent index but carries the risk of a very young crate. FMPHGO is the conservative default; ptr_hash is worth revisiting once it has broader production use.
|
||||
|
||||
boomphf is effectively eliminated: its space overhead is the largest and its streaming-construction advantage does not apply here.
|
||||
|
||||
---
|
||||
|
||||
## Space at scale
|
||||
|
||||
For 1 024 partitions × 100 M kmers/partition:
|
||||
For 1 024 partitions × 100 M kmers/partition (phase 2 index, after filtering):
|
||||
|
||||
| MPHF | bits/key | Total MPHF size |
|
||||
|---------|----------|-----------------|
|
||||
| boomphf | 3.7 | ~47 GB |
|
||||
| ptr_hash | 2.4 | ~31 GB |
|
||||
| FMPHGO | 2.1 | ~27 GB |
|
||||
| MPHF | bits/key | Total MPHF size |
|
||||
|----------|----------|-----------------|
|
||||
| boomphf | 3.7 | ~47 GB |
|
||||
| ptr_hash | 2.4 | ~31 GB |
|
||||
| FMPHGO | 2.1 | ~27 GB |
|
||||
|
||||
In practice, partition sizes depend on the dataset. For a human genome at 30× coverage with p=10 (1 024 partitions), realistic partition sizes are 3–30 M kmers → 1–8 MB per MPHF, well within RAM.
|
||||
For a human genome at 30× coverage with 1 024 partitions, realistic partition sizes are 3–30 M unique kmers → 1–8 MB per phase-2 MPHF, well within RAM.
|
||||
|
||||
## On-disk and mmap considerations
|
||||
|
||||
@@ -42,7 +75,7 @@ No established Rust crate provides a natively on-disk MPHF. **SSHash** (Sparse a
|
||||
|
||||
## Open questions
|
||||
|
||||
- Confirm actual partition sizes on representative metagenomic datasets before fixing the choice.
|
||||
- Evaluate whether ptr_hash's query speed advantage (2.1–3.3×) justifies adopting a crate that is less than a year old.
|
||||
- Assess rkyv integration cost for FMPHGO if true zero-copy mmap becomes necessary.
|
||||
- Confirm actual partition sizes and overestimation factor on representative metagenomic datasets.
|
||||
- Revisit ptr_hash for phase 2 once the crate has broader production track record.
|
||||
- Assess rkyv integration cost for FMPHGO if true zero-copy mmap becomes necessary for the persistent index.
|
||||
- Keep SSHash in mind if the indexing architecture is reconsidered at a higher level.
|
||||
|
||||
@@ -0,0 +1,64 @@
|
||||
#!/usr/bin/env python3
|
||||
"""Plot kmer frequency spectrum from kmer_spectrum_raw.json (log-log scale)."""
|
||||
|
||||
import json
|
||||
import sys
|
||||
import argparse
|
||||
import matplotlib.pyplot as plt
|
||||
|
||||
|
||||
def load_spectrum(path: str):
|
||||
with open(path) as f:
|
||||
data = json.load(f)
|
||||
spectrum = data["spectrum"]
|
||||
pairs = sorted((int(k), v) for k, v in spectrum.items() if v > 0)
|
||||
counts = [x for x, _ in pairs]
|
||||
freqs = [y for _, y in pairs]
|
||||
return counts, freqs, data.get("f0"), data.get("f1")
|
||||
|
||||
|
||||
def main():
|
||||
parser = argparse.ArgumentParser(description="Log-log kmer spectrum plot")
|
||||
parser.add_argument("spectrum", nargs="?", default="kmer_spectrum_raw.json",
|
||||
help="Path to kmer_spectrum_raw.json")
|
||||
parser.add_argument("-o", "--output", default=None,
|
||||
help="Save figure to file (PNG/SVG/PDF). Omit to display interactively.")
|
||||
parser.add_argument("--max-count", type=int, default=None,
|
||||
help="Truncate x-axis at this count value")
|
||||
args = parser.parse_args()
|
||||
|
||||
counts, freqs, f0, f1 = load_spectrum(args.spectrum)
|
||||
|
||||
if args.max_count:
|
||||
pairs = [(c, f) for c, f in zip(counts, freqs) if c <= args.max_count]
|
||||
counts, freqs = zip(*pairs) if pairs else ([], [])
|
||||
|
||||
fig, ax = plt.subplots(figsize=(9, 5))
|
||||
ax.plot(counts, freqs, ".", markersize=2, linewidth=0.6, color="steelblue")
|
||||
ax.set_xscale("log")
|
||||
ax.set_yscale("log")
|
||||
ax.set_xlabel("Repetition degree (count)", fontsize=12)
|
||||
ax.set_ylabel("Number of distinct k-mers", fontsize=12)
|
||||
ax.set_title("K-mer frequency spectrum", fontsize=13)
|
||||
|
||||
info = []
|
||||
if f0 is not None:
|
||||
info.append(f"F₀ = {f0:,}")
|
||||
if f1 is not None:
|
||||
info.append(f"F₁ = {f1:,}")
|
||||
if info:
|
||||
ax.text(0.98, 0.97, " ".join(info), transform=ax.transAxes,
|
||||
ha="right", va="top", fontsize=9, color="gray")
|
||||
|
||||
ax.grid(True, which="both", linestyle="--", linewidth=0.4, alpha=0.6)
|
||||
fig.tight_layout()
|
||||
|
||||
if args.output:
|
||||
fig.savefig(args.output, dpi=150)
|
||||
print(f"Saved to {args.output}", file=sys.stderr)
|
||||
else:
|
||||
plt.show()
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
main()
|
||||
Generated
+1137
-41
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,24 @@
|
||||
use clap::Args;
|
||||
use obikpartitionner::KmerPartition;
|
||||
use std::path::PathBuf;
|
||||
use tracing::info;
|
||||
|
||||
#[derive(Args)]
|
||||
pub struct CountArgs {
|
||||
/// Partition directory produced by the `partition` command
|
||||
#[arg(short, long)]
|
||||
pub partition: PathBuf,
|
||||
}
|
||||
|
||||
pub fn run(args: CountArgs) {
|
||||
let kp = KmerPartition::open(&args.partition).unwrap_or_else(|e| {
|
||||
eprintln!("error: {e}");
|
||||
std::process::exit(1)
|
||||
});
|
||||
|
||||
info!("counting kmers in {}", args.partition.display());
|
||||
kp.count_kmer().unwrap_or_else(|e| {
|
||||
eprintln!("error: {e}");
|
||||
std::process::exit(1)
|
||||
});
|
||||
}
|
||||
@@ -1,2 +1,3 @@
|
||||
pub mod count;
|
||||
pub mod partition;
|
||||
pub mod superkmer;
|
||||
|
||||
@@ -136,4 +136,5 @@ pub fn run(args: PartitionArgs) {
|
||||
|
||||
info!("dereplicating...");
|
||||
kp.lock().unwrap().dereplicate().expect("dereplicate error");
|
||||
kp.lock().unwrap().count_kmer().expect("count kmer error");
|
||||
}
|
||||
|
||||
@@ -16,6 +16,8 @@ enum Commands {
|
||||
Superkmer(cmd::superkmer::SuperkmerArgs),
|
||||
/// Partition super-kmers on disk by minimizer
|
||||
Partition(cmd::partition::PartitionArgs),
|
||||
/// Count kmers from an existing dereplicated partition directory
|
||||
Count(cmd::count::CountArgs),
|
||||
}
|
||||
|
||||
fn main() {
|
||||
@@ -37,6 +39,7 @@ fn main() {
|
||||
match cli.command {
|
||||
Commands::Superkmer(args) => cmd::superkmer::run(args),
|
||||
Commands::Partition(args) => cmd::partition::run(args),
|
||||
Commands::Count(args) => cmd::count::run(args),
|
||||
}
|
||||
|
||||
#[cfg(feature = "profiling")]
|
||||
|
||||
@@ -13,3 +13,5 @@ sysinfo = "0.33"
|
||||
serde = { version = "1", features = ["derive"] }
|
||||
serde_json = "1"
|
||||
tracing = "0.1.44"
|
||||
ph = "0.11"
|
||||
memmap2 = "0.9.10"
|
||||
|
||||
@@ -1,8 +1,12 @@
|
||||
use std::collections::HashMap;
|
||||
use std::collections::{BTreeMap, HashMap, HashSet};
|
||||
use std::fs;
|
||||
use std::io;
|
||||
use std::path::{Path, PathBuf};
|
||||
use tracing::debug;
|
||||
use tracing::{debug, info};
|
||||
|
||||
use memmap2::MmapMut;
|
||||
use obikseq::kmer::Kmer;
|
||||
use ph::fmph::GOFunction;
|
||||
|
||||
use sysinfo::System;
|
||||
|
||||
@@ -99,6 +103,42 @@ impl KmerPartition {
|
||||
Ok(partition)
|
||||
}
|
||||
|
||||
pub fn open<P: AsRef<Path>>(path: P) -> SKResult<Self> {
|
||||
let root_path = path.as_ref().to_owned();
|
||||
if !root_path.exists() {
|
||||
return Err(io::Error::new(
|
||||
io::ErrorKind::NotFound,
|
||||
format!("{}: partition directory not found", root_path.display()),
|
||||
)
|
||||
.into());
|
||||
}
|
||||
let meta_path = root_path.join(META_FILENAME);
|
||||
let meta: PartitionMeta = serde_json::from_reader(fs::File::open(&meta_path)?)
|
||||
.map_err(io::Error::other)?;
|
||||
|
||||
let format = match meta.format.as_str() {
|
||||
"gzip" => Format::Gzip,
|
||||
"bzip2" => Format::Bzip,
|
||||
"lzma" => Format::Lzma,
|
||||
"zstd" => Format::Zstd,
|
||||
_ => Format::No,
|
||||
};
|
||||
let level = level_from_u32(meta.level);
|
||||
let n_partitions = 1usize << meta.n_bits;
|
||||
let writers = (0..n_partitions).map(|_| None).collect();
|
||||
Ok(Self {
|
||||
root_path,
|
||||
n_partitions,
|
||||
partitions_mask: (1u64 << meta.n_bits) - 1,
|
||||
kmer_size: meta.kmer_size,
|
||||
minimizer_size: meta.minimizer_size,
|
||||
writers,
|
||||
format,
|
||||
level,
|
||||
closed: true, // read-only: writing is not allowed on an opened partition
|
||||
})
|
||||
}
|
||||
|
||||
pub fn write(&mut self, sk: &mut SuperKmer) -> SKResult<()> {
|
||||
self.check_not_closed()?;
|
||||
let partition = self.partition_of(sk)?;
|
||||
@@ -190,6 +230,73 @@ impl KmerPartition {
|
||||
Ok(())
|
||||
}
|
||||
|
||||
/// For each partition that has a `dereplicated.{ext}` file:
|
||||
/// 1. Enumerates all unique canonical kmers (two passes over the file).
|
||||
/// 2. Builds a provisional MPHF (FMPHGO) over those kmers.
|
||||
/// 3. Writes a flat binary count file (`counts1.bin`, one `u32` per slot,
|
||||
/// memory-mapped) accumulating kmer abundances from the superkmer counts.
|
||||
/// 4. Persists the MPHF to `mphf1.bin` for downstream use.
|
||||
/// 5. Writes a global `kmer_spectrum_raw.json` at the partition root.
|
||||
///
|
||||
/// Partitions are processed in parallel via Rayon (one task per thread).
|
||||
/// Peak memory per partition is ~80 MB, so n_threads partitions run simultaneously.
|
||||
pub fn count_kmer(&self) -> SKResult<()> {
|
||||
let ext = format_ext(self.format);
|
||||
let root = &self.root_path;
|
||||
let k = self.kmer_size;
|
||||
|
||||
let results: Vec<SKResult<()>> = (0..self.n_partitions)
|
||||
.into_par_iter()
|
||||
.map(|i| {
|
||||
let dir = root.join(format!("part_{:05}", i));
|
||||
let dedup_path = dir.join(format!("dereplicated.{ext}"));
|
||||
if !dedup_path.exists() {
|
||||
return Ok(());
|
||||
}
|
||||
info!("counting kmers in partition {}/{}", i, self.n_partitions);
|
||||
count_partition(&dir, &dedup_path, k)
|
||||
})
|
||||
.collect();
|
||||
for r in results {
|
||||
r?;
|
||||
}
|
||||
|
||||
// Aggregate per-partition spectra into a global one at the root.
|
||||
let mut global_spectrum: BTreeMap<u32, u64> = BTreeMap::new();
|
||||
let mut global_f0: u64 = 0;
|
||||
let mut global_f1: u64 = 0;
|
||||
|
||||
for i in 0..self.n_partitions {
|
||||
let path = root
|
||||
.join(format!("part_{:05}", i))
|
||||
.join("kmer_spectrum_raw.json");
|
||||
if !path.exists() {
|
||||
continue;
|
||||
}
|
||||
let v: serde_json::Value =
|
||||
serde_json::from_str(&fs::read_to_string(&path)?).map_err(io::Error::other)?;
|
||||
global_f0 += v["f0"].as_u64().unwrap_or(0);
|
||||
global_f1 += v["f1"].as_u64().unwrap_or(0);
|
||||
if let Some(obj) = v["spectrum"].as_object() {
|
||||
for (c_str, freq) in obj {
|
||||
if let (Ok(c), Some(f)) = (c_str.parse::<u32>(), freq.as_u64()) {
|
||||
*global_spectrum.entry(c).or_insert(0) += f;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
let global_spectrum_map: BTreeMap<String, u64> =
|
||||
global_spectrum.iter().map(|(&c, &f)| (format!("{c:010}"), f)).collect();
|
||||
serde_json::to_writer_pretty(
|
||||
fs::File::create(root.join("kmer_spectrum_raw.json"))?,
|
||||
&serde_json::json!({ "f0": global_f0, "f1": global_f1, "spectrum": &global_spectrum_map }),
|
||||
)
|
||||
.map_err(io::Error::other)?;
|
||||
|
||||
Ok(())
|
||||
}
|
||||
|
||||
// ── private ───────────────────────────────────────────────────────────────
|
||||
|
||||
fn check_not_closed(&self) -> SKResult<()> {
|
||||
@@ -289,6 +396,18 @@ fn optimal_buckets(raw_path: &Path, available_bytes: u64) -> usize {
|
||||
n.next_power_of_two() as usize
|
||||
}
|
||||
|
||||
fn level_from_u32(n: u32) -> Level {
|
||||
match n {
|
||||
0 => Level::Zero, 1 => Level::One, 2 => Level::Two, 3 => Level::Three,
|
||||
4 => Level::Four, 5 => Level::Five, 6 => Level::Six, 7 => Level::Seven,
|
||||
8 => Level::Eight, 9 => Level::Nine, 10 => Level::Ten, 11 => Level::Eleven,
|
||||
12 => Level::Twelve, 13 => Level::Thirteen, 14 => Level::Fourteen,
|
||||
15 => Level::Fifteen, 16 => Level::Sixteen, 17 => Level::Seventeen,
|
||||
18 => Level::Eighteen, 19 => Level::Nineteen, 20 => Level::Twenty,
|
||||
_ => Level::TwentyOne,
|
||||
}
|
||||
}
|
||||
|
||||
fn format_ext(format: Format) -> &'static str {
|
||||
match format {
|
||||
Format::Gzip => "skmer.gz",
|
||||
@@ -391,6 +510,122 @@ fn flush_map(map: HashMap<SuperKmer, u64>, writer: &mut SKFileWriter) -> SKResul
|
||||
Ok(())
|
||||
}
|
||||
|
||||
/// Build the provisional MPHF and count file for one partition directory.
|
||||
fn count_partition(dir: &Path, dedup_path: &Path, k: usize) -> SKResult<()> {
|
||||
// Estimate number of kmers from sidecar to pre-allocate the HashSet.
|
||||
let capacity = SKFileMeta::read(dedup_path)
|
||||
.ok()
|
||||
.flatten()
|
||||
.map(|m| {
|
||||
let km1 = (k as u64).saturating_sub(1);
|
||||
m.length_sum.saturating_sub(m.instances.saturating_mul(km1)) as usize
|
||||
})
|
||||
.unwrap_or(0);
|
||||
debug!("{}: sidecar capacity estimate={capacity}", dir.display());
|
||||
|
||||
// Pass 1: collect all unique canonical kmers.
|
||||
let mut seen: HashSet<Kmer> = HashSet::with_capacity(capacity);
|
||||
let mut pass1_superkmers: u64 = 0;
|
||||
{
|
||||
let mut reader = SKFileReader::open(dedup_path)?;
|
||||
while let Some(sk) = reader.read()? {
|
||||
pass1_superkmers += 1;
|
||||
let seql = sk.seql();
|
||||
if seql < k {
|
||||
continue;
|
||||
}
|
||||
for pos in 0..=(seql - k) {
|
||||
seen.insert(sk.kmer(pos, k).map_err(io::Error::other)?.canonical(k));
|
||||
}
|
||||
}
|
||||
}
|
||||
let kmers: Vec<Kmer> = seen.into_iter().collect();
|
||||
let n_kmers = kmers.len();
|
||||
debug!("{}: pass1 superkmers={pass1_superkmers} unique_kmers={n_kmers}", dir.display());
|
||||
|
||||
if n_kmers == 0 {
|
||||
return Ok(());
|
||||
}
|
||||
|
||||
// Build provisional MPHF.
|
||||
let mphf = GOFunction::from(kmers);
|
||||
debug!("{}: MPHF built len={}", dir.display(), mphf.len());
|
||||
|
||||
// Create memory-mapped count file (u32 per slot, zero-initialised).
|
||||
let counts_path = dir.join("counts1.bin");
|
||||
let counts_file = fs::OpenOptions::new()
|
||||
.read(true)
|
||||
.write(true)
|
||||
.create(true)
|
||||
.truncate(true)
|
||||
.open(&counts_path)?;
|
||||
counts_file.set_len((n_kmers * std::mem::size_of::<u32>()) as u64)?;
|
||||
let mut mmap = unsafe { MmapMut::map_mut(&counts_file)? };
|
||||
mmap.fill(0);
|
||||
|
||||
// Pass 2: accumulate superkmer counts into the mmap'd array.
|
||||
let mut pass2_superkmers: u64 = 0;
|
||||
let mut pass2_kmer_hits: u64 = 0;
|
||||
let mut pass2_kmer_misses: u64 = 0;
|
||||
let mut pass2_count_sum: u64 = 0;
|
||||
{
|
||||
let counts =
|
||||
unsafe { std::slice::from_raw_parts_mut(mmap.as_mut_ptr() as *mut u32, n_kmers) };
|
||||
let mut reader = SKFileReader::open(dedup_path)?;
|
||||
while let Some(sk) = reader.read()? {
|
||||
pass2_superkmers += 1;
|
||||
let seql = sk.seql();
|
||||
let sk_count = sk.count();
|
||||
if pass2_superkmers <= 3 {
|
||||
debug!("{}: sk#{pass2_superkmers} seql={seql} count={sk_count}", dir.display());
|
||||
}
|
||||
if seql < k {
|
||||
continue;
|
||||
}
|
||||
pass2_count_sum += sk_count as u64;
|
||||
for pos in 0..=(seql - k) {
|
||||
let kmer = sk.kmer(pos, k).map_err(io::Error::other)?.canonical(k);
|
||||
if let Some(idx) = mphf.get(&kmer) {
|
||||
counts[idx as usize] = counts[idx as usize].saturating_add(sk_count);
|
||||
pass2_kmer_hits += 1;
|
||||
} else {
|
||||
pass2_kmer_misses += 1;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
debug!(
|
||||
"{}: pass2 superkmers={pass2_superkmers} hits={pass2_kmer_hits} misses={pass2_kmer_misses} count_sum={pass2_count_sum}",
|
||||
dir.display()
|
||||
);
|
||||
mmap.flush()?;
|
||||
|
||||
// Build kmer frequency spectrum from the count array.
|
||||
let counts = unsafe { std::slice::from_raw_parts(mmap.as_ptr() as *const u32, n_kmers) };
|
||||
let mut spectrum: BTreeMap<u32, u64> = BTreeMap::new();
|
||||
for &c in counts {
|
||||
if c > 0 {
|
||||
*spectrum.entry(c).or_insert(0) += 1;
|
||||
}
|
||||
}
|
||||
let f0 = n_kmers as u64;
|
||||
let f1: u64 = spectrum.iter().map(|(&c, &f)| c as u64 * f).sum();
|
||||
|
||||
let spectrum_map: BTreeMap<String, u64> =
|
||||
spectrum.iter().map(|(&c, &f)| (format!("{c:010}"), f)).collect();
|
||||
serde_json::to_writer_pretty(
|
||||
fs::File::create(dir.join("kmer_spectrum_raw.json"))?,
|
||||
&serde_json::json!({ "f0": f0, "f1": f1, "spectrum": &spectrum_map }),
|
||||
)
|
||||
.map_err(io::Error::other)?;
|
||||
|
||||
// Persist MPHF to disk.
|
||||
let mphf_path = dir.join("mphf1.bin");
|
||||
mphf.write(&mut fs::File::create(&mphf_path)?)?;
|
||||
|
||||
Ok(())
|
||||
}
|
||||
|
||||
impl Drop for KmerPartition {
|
||||
fn drop(&mut self) {
|
||||
let _ = self.close();
|
||||
|
||||
@@ -135,6 +135,18 @@ impl SuperKmer {
|
||||
}
|
||||
}
|
||||
|
||||
/// Deserialise from a raw 32-bit header word and packed sequence bytes.
|
||||
/// Preserves the full header payload (count or minimizer_pos in bits [31:8]).
|
||||
pub fn from_header_bits(bits: u32, seq: Box<[u8]>) -> Self {
|
||||
let seql = (bits & 0xFF) as u8;
|
||||
let len = stored_to_len(seql);
|
||||
debug_assert_eq!(seq.len(), byte_len(len));
|
||||
Self {
|
||||
header: SuperKmerHeader(bits),
|
||||
seq,
|
||||
}
|
||||
}
|
||||
|
||||
/// Returns the sequence length in nucleotides (1–256).
|
||||
pub fn seql(&self) -> usize {
|
||||
stored_to_len(self.header.seql())
|
||||
|
||||
@@ -26,7 +26,7 @@ pub(crate) fn read_superkmer<R: Read>(
|
||||
let byte_len = (nt_len + 3) / 4;
|
||||
seq_buf.resize(byte_len, 0);
|
||||
r.read_exact(seq_buf)?;
|
||||
Ok(Some(SuperKmer::new(seql_byte, seq_buf.as_slice().into())))
|
||||
Ok(Some(SuperKmer::from_header_bits(bits, seq_buf.as_slice().into())))
|
||||
}
|
||||
|
||||
#[cfg(test)]
|
||||
|
||||
@@ -1 +0,0 @@
|
||||
{"rustc_fingerprint":2162534064148227772,"outputs":{"7971740275564407648":{"success":true,"status":"","code":0,"stdout":"___\nlib___.rlib\nlib___.dylib\nlib___.dylib\nlib___.a\nlib___.dylib\n/Users/coissac/.rustup/toolchains/stable-aarch64-apple-darwin\noff\npacked\nunpacked\n___\ndebug_assertions\npanic=\"unwind\"\nproc_macro\ntarget_abi=\"\"\ntarget_arch=\"aarch64\"\ntarget_endian=\"little\"\ntarget_env=\"\"\ntarget_family=\"unix\"\ntarget_feature=\"aes\"\ntarget_feature=\"crc\"\ntarget_feature=\"dit\"\ntarget_feature=\"dotprod\"\ntarget_feature=\"dpb\"\ntarget_feature=\"dpb2\"\ntarget_feature=\"fcma\"\ntarget_feature=\"fhm\"\ntarget_feature=\"flagm\"\ntarget_feature=\"fp16\"\ntarget_feature=\"frintts\"\ntarget_feature=\"jsconv\"\ntarget_feature=\"lor\"\ntarget_feature=\"lse\"\ntarget_feature=\"neon\"\ntarget_feature=\"paca\"\ntarget_feature=\"pacg\"\ntarget_feature=\"pan\"\ntarget_feature=\"pmuv3\"\ntarget_feature=\"ras\"\ntarget_feature=\"rcpc\"\ntarget_feature=\"rcpc2\"\ntarget_feature=\"rdm\"\ntarget_feature=\"sb\"\ntarget_feature=\"sha2\"\ntarget_feature=\"sha3\"\ntarget_feature=\"ssbs\"\ntarget_feature=\"vh\"\ntarget_has_atomic=\"128\"\ntarget_has_atomic=\"16\"\ntarget_has_atomic=\"32\"\ntarget_has_atomic=\"64\"\ntarget_has_atomic=\"8\"\ntarget_has_atomic=\"ptr\"\ntarget_os=\"macos\"\ntarget_pointer_width=\"64\"\ntarget_vendor=\"apple\"\nunix\n","stderr":""},"6432102384495711296":{"success":true,"status":"","code":0,"stdout":"___\nlib___.rlib\nlib___.dylib\nlib___.dylib\nlib___.a\nlib___.dylib\n/Users/coissac/.rustup/toolchains/stable-aarch64-apple-darwin\noff\npacked\nunpacked\n___\ndebug_assertions\npanic=\"unwind\"\nproc_macro\ntarget_abi=\"\"\ntarget_arch=\"aarch64\"\ntarget_endian=\"little\"\ntarget_env=\"\"\ntarget_family=\"unix\"\ntarget_feature=\"aes\"\ntarget_feature=\"crc\"\ntarget_feature=\"dit\"\ntarget_feature=\"dotprod\"\ntarget_feature=\"dpb\"\ntarget_feature=\"dpb2\"\ntarget_feature=\"fcma\"\ntarget_feature=\"fhm\"\ntarget_feature=\"flagm\"\ntarget_feature=\"fp16\"\ntarget_feature=\"frintts\"\ntarget_feature=\"jsconv\"\ntarget_feature=\"lor\"\ntarget_feature=\"lse\"\ntarget_feature=\"neon\"\ntarget_feature=\"paca\"\ntarget_feature=\"pacg\"\ntarget_feature=\"pan\"\ntarget_feature=\"pmuv3\"\ntarget_feature=\"ras\"\ntarget_feature=\"rcpc\"\ntarget_feature=\"rcpc2\"\ntarget_feature=\"rdm\"\ntarget_feature=\"sb\"\ntarget_feature=\"sha2\"\ntarget_feature=\"sha3\"\ntarget_feature=\"ssbs\"\ntarget_feature=\"vh\"\ntarget_has_atomic=\"128\"\ntarget_has_atomic=\"16\"\ntarget_has_atomic=\"32\"\ntarget_has_atomic=\"64\"\ntarget_has_atomic=\"8\"\ntarget_has_atomic=\"ptr\"\ntarget_os=\"macos\"\ntarget_pointer_width=\"64\"\ntarget_vendor=\"apple\"\nunix\n","stderr":""},"17747080675513052775":{"success":true,"status":"","code":0,"stdout":"rustc 1.94.1 (e408947bf 2026-03-25)\nbinary: rustc\ncommit-hash: e408947bfd200af42db322daf0fadfe7e26d3bd1\ncommit-date: 2026-03-25\nhost: aarch64-apple-darwin\nrelease: 1.94.1\nLLVM version: 21.1.8\n","stderr":""}},"successes":{}}
|
||||
@@ -1 +0,0 @@
|
||||
{"rustc":17940977064402226622,"features":"[]","declared_features":"[]","target":1865439097712885860,"profile":2330448797067240312,"path":3117914143523182133,"deps":[],"local":[{"CheckDepInfo":{"dep_info":"debug/.fingerprint/obikseq-4791c70657a715c0/dep-lib-obikseq","checksum":false}}],"rustflags":[],"config":8247474407144887393,"compile_kind":0}
|
||||
@@ -1 +0,0 @@
|
||||
{"rustc":17940977064402226622,"features":"[]","declared_features":"[]","target":1865439097712885860,"profile":619605765252926426,"path":3117914143523182133,"deps":[],"local":[{"CheckDepInfo":{"dep_info":"debug/.fingerprint/obikseq-5cc47015be91e3b1/dep-test-lib-obikseq","checksum":false}}],"rustflags":[],"config":8247474407144887393,"compile_kind":0}
|
||||
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Reference in New Issue
Block a user