Consolidate compare_sparse as example and clean up project artifacts

Restructure the project by moving the standalone compare_sparse utility into an example directory, removing Sankoff parameter configurations and benchmark scripts, updating version control ignores, and expanding the test suite with diagnostic checks and performance benchmarks.

benchmark/test_transition_sankoff_params.yaml

@@ -1,167 +0,0 @@
-ratio_ceiling: 0.5
-cardinality_transitions:
-- from: 0
-  to: 0
-  count: 115955295
-  probability: 0.8297007290571883
-- from: 0
-  to: 1
-  count: 12901663
-  probability: 0.0923159153460836
-- from: 0
-  to: 2
-  count: 10519367
-  probability: 0.07526975347801175
-- from: 0
-  to: 3
-  count: 339782
-  probability: 0.0024312591600108434
-- from: 0
-  to: 4
-  count: 39459
-  probability: 0.00028234295870548727
-- from: 1
-  to: 0
-  count: 12901663
-  probability: 0.9007741539906029
-- from: 1
-  to: 1
-  count: 973491
-  probability: 0.0679676357956696
-- from: 1
-  to: 2
-  count: 444884
-  probability: 0.031061112720426456
-- from: 1
-  to: 3
-  count: 2739
-  probability: 0.00019123274323474897
-- from: 1
-  to: 4
-  count: 84
-  probability: 5.864750066344985e-6
-- from: 2
-  to: 0
-  count: 10519367
-  probability: 0.9590597257562327
-- from: 2
-  to: 1
-  count: 444884
-  probability: 0.04056045644508228
-- from: 2
-  to: 2
-  count: 3796
-  probability: 0.00034608458084699006
-- from: 2
-  to: 3
-  count: 327
-  probability: 0.000029812870900149037
-- from: 2
-  to: 4
-  count: 43
-  probability: 3.920346937940087e-6
-- from: 3
-  to: 0
-  count: 339782
-  probability: 0.9908029486551426
-- from: 3
-  to: 1
-  count: 2739
-  probability: 0.007986913010007698
-- from: 3
-  to: 2
-  count: 327
-  probability: 0.0009535306879417734
-- from: 3
-  to: 3
-  count: 58
-  probability: 0.00016912776728019222
-- from: 3
-  to: 4
-  count: 30
-  probability: 0.00008747987962768563
-- from: 4
-  to: 0
-  count: 39459
-  probability: 0.9957604663487016
-- from: 4
-  to: 1
-  count: 84
-  probability: 0.0021197668256491787
-- from: 4
-  to: 2
-  count: 43
-  probability: 0.0010851187321775557
-- from: 4
-  to: 3
-  count: 30
-  probability: 0.0007570595805889924
-- from: 4
-  to: 4
-  count: 11
-  probability: 0.0002775885128826305
-composition_transitions:
-- from: 'A'
-  to: 'A'
-  count: 169043
-  probability: 0.49442957633191476
-- from: 'A'
-  to: 'C'
-  count: 27672
-  probability: 0.08093712982055894
-- from: 'A'
-  to: 'G'
-  count: 124160
-  probability: 0.36315242983957063
-- from: 'A'
-  to: 'T'
-  count: 21020
-  probability: 0.06148086400795566
-- from: 'C'
-  to: 'A'
-  count: 27672
-  probability: 0.08651690662664728
-- from: 'C'
-  to: 'C'
-  count: 145183
-  probability: 0.4539167409213838
-- from: 'C'
-  to: 'G'
-  count: 23425
-  probability: 0.07323859994684925
-- from: 'C'
-  to: 'T'
-  count: 123565
-  probability: 0.3863277525051197
-- from: 'G'
-  to: 'A'
-  count: 124160
-  probability: 0.3846082361177367
-- from: 'G'
-  to: 'C'
-  count: 23425
-  probability: 0.07256320820761906
-- from: 'G'
-  to: 'G'
-  count: 148125
-  probability: 0.4588441927749658
-- from: 'G'
-  to: 'T'
-  count: 27112
-  probability: 0.08398436289967846
-- from: 'T'
-  to: 'A'
-  count: 21020
-  probability: 0.06258131551760583
-- from: 'T'
-  to: 'C'
-  count: 123565
-  probability: 0.3678810776371534
-- from: 'T'
-  to: 'G'
-  count: 27112
-  probability: 0.08071858355439246
-- from: 'T'
-  to: 'T'
-  count: 164186
-  probability: 0.4888190232908483

benchmark/transition.awk

@@ -1,18 +0,0 @@
-#!/usr/bin/awk -f
-
-/^>/ {
-    print
-    next
-}
-
-{
-    gsub(/[Aa]/, "a")
-    gsub(/[Gg]/, "A")
-    gsub(/a/, "G")
-
-    gsub(/[Cc]/, "c")
-    gsub(/[Tt]/, "C")
-    gsub(/c/, "T")
-
-    print
-}