From 611f1c86892ab3a856a52b1e23190750bae4580c Mon Sep 17 00:00:00 2001
From: Mike Lin <dna@mlin.net>
Date: Sat, 7 Dec 2019 12:33:52 -1000
Subject: [PATCH] unifier: with preference=small, also require all alleles at a
 site to mutually overlap

---
 src/unifier.cc  | 22 +++++++++++++++++-----
 test/unifier.cc | 47 +++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 64 insertions(+), 5 deletions(-)

diff --git a/src/unifier.cc b/src/unifier.cc
index 6db20590..fc72a27d 100644
--- a/src/unifier.cc
+++ b/src/unifier.cc
@@ -289,18 +289,30 @@ auto prune_alleles(const unifier_config& cfg, const minimized_alleles& alleles,
     for (const minimized_allele& mal : valleles) {
         // find existing site(s) overlapping this allele
         auto related_site = sites.end();
-        bool multiple_sites = false;
-        for (auto site = sites.begin(); site != sites.end(); site++) {
+        bool reject = false;
+        for (auto site = sites.begin(); site != sites.end() && !reject; site++) {
             if (mal.first.pos.overlaps(site->first)) {
                 if (related_site == sites.end()) {
-                    related_site = site;
+                    if (cfg.preference == UnifierPreference::Small) {
+                        // for preference=small, also require overlap with all
+                        // alleles currently at the site
+                        for (const auto& site_allele : site->second) {
+                            if (!mal.first.pos.overlaps(site_allele.first.pos)) {
+                                reject = true;
+                                break;
+                            }
+                        }
+                    }
+                    if (!reject) {
+                        related_site = site;
+                    }
                 } else {
-                    multiple_sites = true;
+                    reject = true;
                     break;
                 }
             }
         }
-        if (multiple_sites) {
+        if (reject) {
             // reject since this allele overlaps multiple existing sites
             pruned.insert(mal);
             continue;
diff --git a/test/unifier.cc b/test/unifier.cc
index 9ded85b0..7f91eb01 100644
--- a/test/unifier.cc
+++ b/test/unifier.cc
@@ -78,3 +78,50 @@ TEST_CASE("unifier max_alleles_per_site") {
         REQUIRE(sites[0].alleles[1].dna == "G");
     }
 }
+
+TEST_CASE("unifier small preference") {
+    discovered_alleles dal;
+    discovered_allele_info dai;
+
+    dai.is_ref = true; dai.topAQ = top_AQ(99); dai.zGQ = zygosity_by_GQ(1,0,100);
+    dal[allele(range(0, 100, 101), "A")] = dai;
+    dal[allele(range(0, 104, 105), "A")] = dai;
+    dai.is_ref = false; dai.topAQ = top_AQ(99); dai.zGQ = zygosity_by_GQ(1,0,101);
+    dal[allele(range(0, 100, 101), "G")] = dai;
+    dal[allele(range(0, 104, 105), "T")] = dai;
+    dai.is_ref = true; dai.topAQ = top_AQ(99); dai.zGQ = zygosity_by_GQ(1,0,100);
+    dal[allele(range(0, 100, 102), "AC")] = dai;
+    dai.is_ref = false; dai.topAQ = top_AQ(99); dai.zGQ = zygosity_by_GQ(1,0,101);
+    dal[allele(range(0, 100, 102), "A")] = dai;
+    dai.is_ref = true; dai.topAQ = top_AQ(99); dai.zGQ = zygosity_by_GQ(1,0,100);
+    dal[allele(range(0, 101, 104), "CTG")] = dai;
+    dai.is_ref = false; dai.topAQ = top_AQ(99); dai.zGQ = zygosity_by_GQ(1,0,110);
+    dal[allele(range(0, 101, 104), "C")] = dai;
+    dai.is_ref = true; dai.topAQ = top_AQ(99); dai.zGQ = zygosity_by_GQ(1,0,100);
+    dal[allele(range(0, 99, 105), "GACTGA")] = dai;
+    dai.is_ref = false; dai.topAQ = top_AQ(99); dai.zGQ = zygosity_by_GQ(1,0,120);
+    dal[allele(range(0, 99, 105), "G")] = dai;
+
+    unifier_config cfg;
+    cfg.preference = UnifierPreference::Small;
+    cfg.monoallelic_sites_for_lost_alleles = true;
+
+    vector<unified_site> sites;
+    unifier_stats stats;
+    Status s = unified_sites(cfg, 200, dal, sites, stats);
+
+    cout << s.str() << endl;
+    REQUIRE(s.ok());
+    REQUIRE(sites.size() == 4);
+    REQUIRE(sites[0].pos == range(0, 99, 105));
+    REQUIRE(sites[0].alleles.size() == 2);
+    REQUIRE(sites[0].monoallelic);
+    REQUIRE(sites[1].pos == range(0, 100, 102));
+    REQUIRE(sites[1].alleles.size() == 3);
+    REQUIRE(sites[2].pos == range(0, 101, 104));
+    REQUIRE(sites[2].alleles.size() == 2);
+    REQUIRE(sites[2].monoallelic);
+    REQUIRE(sites[3].pos == range(0, 104, 105));
+    REQUIRE(sites[3].alleles.size() == 2);
+    REQUIRE(!sites[3].monoallelic);
+}