test -A

src/pairwise.rs

@@ -137,7 +137,7 @@ pub fn pairwise(
                 eprintln!("Processed {} comparisons", i);
             }
         }
-        if write_all {
+        if write_all || output_all_comparisons {
             let mut query_containment_ani = None;
             let mut match_containment_ani = None;
             let mut average_containment_ani = None;

src/python/tests/test_manysearch.py

@@ -113,6 +113,108 @@ def test_simple(runtmp, zip_query, zip_against):
                 assert max_ani == 0.9772
 
 
+def test_simple_output_all(runtmp, zip_query, zip_against):
+    # test basic execution!
+    query_list = runtmp.output("query.txt")
+    against_list = runtmp.output("against.txt")
+
+    sig2 = get_test_data("2.fa.sig.gz")
+    sig47 = get_test_data("47.fa.sig.gz")
+    sig63 = get_test_data("63.fa.sig.gz")
+
+    make_file_list(query_list, [sig2, sig47, sig63])
+    make_file_list(against_list, [sig2, sig47, sig63])
+
+    output = runtmp.output("out.csv")
+
+    if zip_query:
+        query_list = zip_siglist(runtmp, query_list, runtmp.output("query.zip"))
+    if zip_against:
+        against_list = zip_siglist(runtmp, against_list, runtmp.output("against.zip"))
+
+    runtmp.sourmash(
+        "scripts", "manysearch", query_list, against_list, "-o", output, "-t", "0.01", "-A"
+    )
+    assert os.path.exists(output)
+
+    df = pandas.read_csv(output)
+    assert len(df) == 9
+
+    dd = df.to_dict(orient="index")
+    print(dd)
+
+    for idx, row in dd.items():
+        # identical?
+        if row["match_name"] == row["query_name"]:
+            assert row["query_md5"] == row["match_md5"], row
+            assert float(row["containment"] == 1.0)
+            assert float(row["jaccard"] == 1.0)
+            assert float(row["max_containment"] == 1.0)
+            assert float(row["query_containment_ani"] == 1.0)
+            assert float(row["match_containment_ani"] == 1.0)
+            assert float(row["average_containment_ani"] == 1.0)
+            assert float(row["max_containment_ani"] == 1.0)
+
+        else:
+            # confirm hand-checked numbers
+            q = row["query_name"].split()[0]
+            m = row["match_name"].split()[0]
+            cont = float(row["containment"])
+            jaccard = float(row["jaccard"])
+            maxcont = float(row["max_containment"])
+            intersect_hashes = int(row["intersect_hashes"])
+            query_ani = float(row["query_containment_ani"])
+            match_ani = float(row["match_containment_ani"])
+            average_ani = float(row["average_containment_ani"])
+            max_ani = float(row["max_containment_ani"])
+            jaccard = round(jaccard, 4)
+            cont = round(cont, 4)
+            maxcont = round(maxcont, 4)
+            query_ani = round(query_ani, 4)
+            match_ani = round(match_ani, 4)
+            average_ani = round(average_ani, 4)
+            max_ani = round(max_ani, 4)
+            print(
+                q,
+                m,
+                f"{jaccard:.04}",
+                f"{cont:.04}",
+                f"{maxcont:.04}",
+                f"{query_ani:.04}",
+                f"{match_ani:.04}",
+                f"{average_ani:.04}",
+                f"{max_ani:.04}",
+            )
+
+            if q == "NC_011665.1" and m == "NC_009661.1":
+                assert jaccard == 0.3207
+                assert cont == 0.4828
+                assert maxcont == 0.4885
+                assert intersect_hashes == 2529
+                assert query_ani == 0.9768
+                assert match_ani == 0.9772
+                assert average_ani == 0.977
+                assert max_ani == 0.9772
+            elif q == "NC_009661.1" and m == "NC_011665.1":
+                assert jaccard == 0.3207
+                assert cont == 0.4885
+                assert maxcont == 0.4885
+                assert intersect_hashes == 2529
+                assert query_ani == 0.9772
+                assert match_ani == 0.9768
+                assert average_ani == 0.977
+                assert max_ani == 0.9772
+            else:
+                assert jaccard == 0
+                assert cont == 0
+                assert maxcont == 0
+                assert intersect_hashes == 0
+                assert query_ani == 0
+                assert match_ani == 0
+                assert average_ani == 0
+                assert max_ani == 0
+
+
 def test_simple_abund(runtmp):
     # test with abund sig
     sig2 = get_test_data("2.fa.sig.gz")

src/python/tests/test_multisearch.py

@@ -91,6 +91,78 @@ def test_simple_no_ani(runtmp, zip_query, zip_db):
                 assert intersect_hashes == 2529
 
 
+def test_simple_no_ani_output_all(runtmp, zip_query, zip_db):
+    # test basic execution!
+    query_list = runtmp.output("query.txt")
+    against_list = runtmp.output("against.txt")
+
+    sig2 = get_test_data("2.fa.sig.gz")
+    sig47 = get_test_data("47.fa.sig.gz")
+    sig63 = get_test_data("63.fa.sig.gz")
+
+    make_file_list(query_list, [sig2, sig47, sig63])
+    make_file_list(against_list, [sig2, sig47, sig63])
+
+    output = runtmp.output("out.csv")
+
+    if zip_db:
+        against_list = zip_siglist(runtmp, against_list, runtmp.output("db.zip"))
+    if zip_query:
+        query_list = zip_siglist(runtmp, query_list, runtmp.output("query.zip"))
+
+    runtmp.sourmash("scripts", "multisearch", query_list, against_list, "-o", output, "-A")
+    assert os.path.exists(output)
+
+    df = pandas.read_csv(output)
+    assert len(df) == 9
+
+    dd = df.to_dict(orient="index")
+    print(dd)
+
+    for idx, row in dd.items():
+        assert not ("prob_overlap" in row)
+
+        # identical?
+        if row["match_name"] == row["query_name"]:
+            assert row["query_md5"] == row["match_md5"], row
+            assert float(row["containment"] == 1.0)
+            assert float(row["jaccard"] == 1.0)
+            assert float(row["max_containment"] == 1.0)
+            assert "query_containment_ani" not in row
+            assert "match_containment_ani" not in row
+            assert "average_containment_ani" not in row
+            assert "max_containment_ani" not in row
+
+        else:
+            # confirm hand-checked numbers
+            q = row["query_name"].split()[0]
+            m = row["match_name"].split()[0]
+            cont = float_round(row["containment"], 4)
+            jaccard = float_round(row["jaccard"], 4)
+            maxcont = float_round(row["max_containment"], 4)
+
+            intersect_hashes = int(row["intersect_hashes"])
+
+            print(q, m, f"{jaccard:.04}", f"{cont:.04}", f"{maxcont:.04}")
+
+            if q == "NC_011665.1" and m == "NC_009661.1":
+                assert jaccard == 0.3207
+                assert cont == 0.4828
+                assert maxcont == 0.4885
+                assert intersect_hashes == 2529
+
+            elif q == "NC_009661.1" and m == "NC_011665.1":
+                assert jaccard == 0.3207
+                assert cont == 0.4885
+                assert maxcont == 0.4885
+                assert intersect_hashes == 2529
+            else:
+                assert jaccard == 0
+                assert cont == 0
+                assert maxcont == 0
+                assert intersect_hashes == 0
+
+
 def test_simple_prob_overlap(runtmp, zip_query, zip_db, indexed_query, indexed_against):
     # test basic execution!
     query_list = runtmp.output("query.txt")

src/python/tests/test_pairwise.py

@@ -91,6 +91,31 @@ def test_simple_no_ani(runtmp, capfd, zip_query, indexed):
         )
 
 
+def test_simple_no_ani_output_all(runtmp, capfd, zip_query, indexed):
+    # test basic execution!
+    query_list = runtmp.output("query.txt")
+
+    sig2 = get_test_data("2.fa.sig.gz")
+    sig47 = get_test_data("47.fa.sig.gz")
+    sig63 = get_test_data("63.fa.sig.gz")
+
+    make_file_list(query_list, [sig2, sig47, sig63])
+
+    output = runtmp.output("out.csv")
+
+    if zip_query:
+        query_list = zip_siglist(runtmp, query_list, runtmp.output("query.zip"))
+
+    if indexed:
+        query_list = index_siglist(runtmp, query_list, runtmp.output("db"))
+
+    runtmp.sourmash("scripts", "pairwise", query_list, "-o", output, "-t", "-1", "-A")
+    assert os.path.exists(output)
+
+    df = pandas.read_csv(output)
+    assert len(df) == 6
+
+
 def test_simple_ani(runtmp, zip_query):
     # test basic execution!
     query_list = runtmp.output("query.txt")
@@ -158,6 +183,17 @@ def test_simple_ani(runtmp, zip_query):
             assert q2_ani == 0.9772
             assert avg_ani == 0.977
             assert max_ani == 0.9772
+        elif q == m:
+            assert jaccard == 1
+        else:
+            assert jaccard == 0
+            assert cont == 0
+            assert maxcont == 0
+            assert intersect_hashes == 0
+            assert q1_ani == 0
+            assert q2_ani == 0
+            assert avg_ani == 0
+            assert max_ani == 0
 
 
 def test_simple_threshold(runtmp, zip_query):