Split extension vs seed eval threshold: max for extension, median for eval

Using median for both thresholds caused 41 gene regressions — graphs
exhausted the 50K node budget before connecting primer sites. Extension
thresholds need the max primer kmer count to start high and keep the
graph focused. Seed eval still uses median to avoid false abandonment
from degenerate primer off-target inflation.

Validated with full 1M benchmark: all regressions recovered, plus net
new gene recoveries (Drosophila CO1, Heliconius CO1, Gryllus 16S-v2/
NADH/ITS, bacteria gains). Documents the split rationale in
DESIGN_DECISIONS.md.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: caseywdunn

benchmarks/results/2026-04-02_sharkmer_3.0.0-dev_58c9fe5.summary.md

@@ -0,0 +1,57 @@
+# Benchmark Summary
+
+- **Version**: sharkmer 3.0.0-dev (https://github.com/caseywdunn/sharkmer)
+- **Commit**: 58c9fe5
+- **Date**: 2026-04-02
+- **Source**: `2026-04-02_sharkmer_3.0.0-dev_58c9fe5.yaml`
+
+Legend: `✓` product + BLAST hit   `?` product, no BLAST hit   `·` no product
+
+## angiospermae
+
+| Sample | Reads | psbA-trnH | rpl36-infA-rps8 | trnK-rps16 | trnV-atpE | trnC-ycf6 | ycf6-psbM | psbM-trnD | atpB-rbcL | trnL-F | ITS |
+| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
+| Liriodendron_tulipifera | 1000k | ? | ? | ? | · | ? | ? | ? | ? | ? | · |
+| Acer_monspessulanum | 1000k | ? | · | · | · | ? | ? | ? | ? | · | ? |
+
+## bacteria
+
+| Sample | Reads | 16S-27F-338R | 16S-V2f-V3r | 16S-341F-785R | 16S-PRK341F-PRK806R | 16S-515F-806R | 16S-515F-806RB | 16S-515F-Y-926R | 16S-B969F-BA1406R | 16S-799F-1391R | 16S-967F-1391R | 16S-799F-1193R | 16S-68F-783Rabc | 16S-68F-518R | 16S-341F-783Rabc |
+| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
+| Covercrop_rhizosphere | 1000k | · | · | · | ? | ? | ? | · | · | · | · | · | ? | · | · |
+| Coral_metagenome | 1000k | · | · | ? | ? | ? | ? | · | · | · | · | · | · | · | ? |
+| Seawater_metagenome | 1000k | · | · | · | · | · | · | · | · | · | · | · | · | · | · |
+
+## cnidaria
+
+| Sample | Reads | 16S | CO1 | 18S | 28S | ITS | ITS-v2 | EF1A | 28S-v2 |
+| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
+| Porites_lutea | 1000k | · | · | ? | ? | ? | ? | ? | ? |
+| Xenia_sp | 1000k | ? | · | ? | ? | ? | ? | ? | ? |
+| Agalma_elegans | 1000k | · | · | ? | ? | ? | ? | · | ? |
+
+## cnidaria, bacteria
+
+| Sample | Reads | 16S | CO1 | 18S | 28S | ITS | ITS-v2 | EF1A | 28S-v2 | 16S-27F-338R | 16S-V2f-V3r | 16S-341F-785R | 16S-PRK341F-PRK806R | 16S-515F-806R | 16S-515F-806RB | 16S-515F-Y-926R | 16S-B969F-BA1406R | 16S-799F-1391R | 16S-967F-1391R | 16S-799F-1193R | 16S-68F-783Rabc | 16S-68F-518R | 16S-341F-783Rabc |
+| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
+| Rhopilema_esculentum | 1000k | · | · | ? | ? | · | ? | · | ? | · | ? | ? | ? | ? | ? | · | ? | · | ? | · | · | · | ? |
+
+## human
+
+| Sample | Reads | mt1404-3947 | mt3734-6739 | mt6511-9220 | mt8910-10648 | mt10360-12226 | mt11977-13830 | mt13477-15349 | mt14898-151 | mt16488-1677 |
+| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
+| Homo_sapiens | 1000k | ? | ? | ? | ? | ? | ? | ? | ? | ? |
+
+## insecta
+
+| Sample | Reads | 12S | 16S | CO1 | CO2 | CytB | ND1 | ND4 | ND5 | 16S-v2 | CO1-v2 | CO2-v2 | NADH | EF1g | Fz4 | Gpdh | Pgi | Yp2 | 18S | 28S | ITS | 18S-v2 | 28S-v2 | ITS-v2 | ITS-v3 |
+| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
+| Drosophila_melanogaster | 1000k | ? | · | ? | ? | ? | ? | · | ? | · | ? | ? | · | · | · | · | · | · | ? | · | · | ? | · | · | · |
+| Heliconius_pachinus | 1000k | ? | · | ? | ? | ? | ? | · | ? | · | ? | · | · | · | · | · | · | · | ? | · | · | · | · | · | · |
+| Gryllus_bimaculatus | 1000k | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | · | ? | · | · | · | · | · | ? | ? | ? | ? | · | · | · |
+
+## teleostei
+
+| Sample | Reads | 18S | 16S | CO1 | CytB | 12S |
+| --- | --- | --- | --- | --- | --- | --- |
+| Nomeus_gronovii | 1000k | ? | ? | ? | · | ? |