From 2c71be5e5740cdebe856d0838a0028af80ddb2dc Mon Sep 17 00:00:00 2001
From: niyarin <inoanet@gmail.com>
Date: Fri, 10 Apr 2020 16:42:16 +0900
Subject: [PATCH] Fix wrong usage of util->bin.

---
 src/cljam/io/bam_index/writer.clj |  4 ++--
 src/cljam/io/sam/util.clj         |  2 +-
 src/cljam/io/util/bin.clj         |  4 ++--
 test/cljam/io/util/bin_test.clj   | 40 +++++++++++++++++++++++++++----
 4 files changed, 40 insertions(+), 10 deletions(-)

diff --git a/src/cljam/io/bam_index/writer.clj b/src/cljam/io/bam_index/writer.clj
index 6b2c639b..b1239c1b 100644
--- a/src/cljam/io/bam_index/writer.clj
+++ b/src/cljam/io/bam_index/writer.clj
@@ -73,8 +73,8 @@
 
 (defn- update-bin-index
   [bin-index ^BAMPointerBlock aln]
-  (let [bin (util-bin/reg->bin (.pos aln) (inc (.end aln))
-                               linear-index-shift linear-index-depth)
+  (let [bin (util-bin/reg->bin
+             (.pos aln) (.end aln) linear-index-shift linear-index-depth)
         beg (.pointer-beg aln)
         end (.pointer-end aln)]
     (assoc bin-index bin
diff --git a/src/cljam/io/sam/util.clj b/src/cljam/io/sam/util.clj
index 52879339..533b08a9 100644
--- a/src/cljam/io/sam/util.clj
+++ b/src/cljam/io/sam/util.clj
@@ -46,6 +46,6 @@
 (defn compute-bin
   "Returns indexing bin based on alignment start and end."
   [aln]
-  (let [beg (dec (:pos aln))
+  (let [beg (:pos aln)
         end (get-end aln)]
     (util-bin/reg->bin beg end linear-index-shift linear-index-depth)))
diff --git a/src/cljam/io/util/bin.clj b/src/cljam/io/util/bin.clj
index cbc4b66d..a76d4b0f 100644
--- a/src/cljam/io/util/bin.clj
+++ b/src/cljam/io/util/bin.clj
@@ -71,8 +71,8 @@
   "Calculates bin given an alignment covering [beg, end]"
   ^long [^long beg ^long end ^long min-shift ^long depth]
   (let [max-pos (max-pos min-shift depth)
-        beg (Math/min max-pos (Math/max 0 (dec beg)))
-        end (Math/min max-pos (Math/max 0 (dec end)))]
+        beg (dec (Math/min max-pos (Math/max 1  beg)))
+        end (dec (Math/min max-pos (Math/max 1  end)))]
     (loop [level depth]
       (if-not (neg? level)
         (let [beg-bins (leading-bins-at-level beg level min-shift depth)]
diff --git a/test/cljam/io/util/bin_test.clj b/test/cljam/io/util/bin_test.clj
index 5f1c2077..ce53e699 100644
--- a/test/cljam/io/util/bin_test.clj
+++ b/test/cljam/io/util/bin_test.clj
@@ -59,8 +59,38 @@
     5 37448))
 
 (deftest reg->bin-test
-  (is (= (util-bin/reg->bin 1 1 14 6) 37449))
-  (is (= (util-bin/reg->bin 1 1 14 7) 299593))
-  (is (= (util-bin/reg->bin 1 32769 15 6) 4681))
-  (is (= (util-bin/reg->bin 1 2 0 2) 1))
-  (is (= (util-bin/reg->bin 240877561 240877568 14 6) 52150)))
+  (testing "BAI-compatible"
+    (are [?start ?end ?bin]
+         (= ?bin (util-bin/reg->bin ?start ?end 14 5))
+      0 0 4681
+      0 1 4681
+      1 1 4681
+      1 16384 4681
+      16384 16384 4681
+      16384 16385 585
+      16385 16385 4682
+      131072 131072 4688
+      131072 131073 73
+      8388608 8388609 1
+      67108864 67108865 0
+      536870912 536870912 37448
+      536870912 536870913 37448))
+  (testing "1-by-1"
+    (are [?start ?end ?bin]
+         (= ?bin (util-bin/reg->bin ?start ?end 0 2))
+      0 1 9
+      1 1 9
+      2 2 10
+      1 2 1
+      1 8 1
+      1 9 0
+      8 9 0
+      9 9 17
+      63 64 8
+      64 64 72
+      64 64 72))
+  (testing "various min-shfits and depths"
+    (is (= (util-bin/reg->bin 1 1 14 6) 37449))
+    (is (= (util-bin/reg->bin 1 1 14 7) 299593))
+    (is (= (util-bin/reg->bin 1 32769 15 6) 4681))
+    (is (= (util-bin/reg->bin 240877561 240877568 14 6) 52150))))