Split tarjan_scc to its own header

Tupfile

@@ -19,8 +19,3 @@ PROGS += fms2mds optimize_rem_path_len mykkeltveit_set find_longest_path
 PROGS += champarnaud_set sketch_components syncmer_set syncmer_sketch frac_set
 PROGS += create_seed sketch_histo old_champarnaud_set
 run ./rules.sh $(PROGS)
-
-# MDS ilp
-ifdef ILP_PYTHON
-: MDS-ILP.py |> echo '#!/bin/bash\nTQDM_DISABLE=1 exec "@(ILP_PYTHON)"' "`realpath %f`" @(ALPHA) @(K) "\$((2*@(K)*@(K)*@(K)))" '"$@"' > %o; chmod a+rx %o |> ilp_set
-endif

compact_utilities.py

@@ -0,0 +1,69 @@
+def transposition_table(*pairs):
+    X = ''.join(pairs)
+    Y = ''.join(pair[::-1] for pair in pairs)
+
+    return str.maketrans(X, Y)
+
+
+def kmer_formatter(b: int, k: int):
+    """
+        Returns a string formatting function for base b kmers.
+    """
+
+    def kmer(x: int):
+        d = b ** k
+
+        digits = []
+        for i in range(k):
+            d //= b
+            xi, x = divmod(x, d)
+            digits.append(str(xi))
+
+        return ''.join(digits)
+
+    return kmer
+
+
+def DBG_walk_maps(b: int, k: int):
+    """
+        Returns the In and Out maps for the base b, order k De Bruijn graph.
+    """
+
+    p = b ** (k - 1)
+    s = b **  k
+
+    def In(x):
+        base = (x // b) % p
+        return [
+            base + i * p for i in range(b)
+        ]
+
+    def Out(x):
+        base = (x * b) % s
+        return [
+            base + i for i in range(b)
+        ]
+
+    return In, Out
+
+
+def PCR(b: int, k: int):
+    """
+        Produces an iterator over the PCRs of the (b, k) De Bruijn graph.
+        The PCR follows xS --> Sx, continuing until returning to XS.
+    """
+
+    kmer = kmer_formatter(b, k)
+
+    seen = set()
+    for x in range(b ** k):
+        if x in seen:
+            continue
+
+        x = kmer(x)
+        y, cycle = x, [int(x, b)]
+        while (y := y[1:] + y[0]) != x:
+            cycle.append(int(y, b))
+
+        yield cycle
+        seen.update(cycle)