From 2ebf8e7d395a38ca806e8652b2ed73f9a50539b2 Mon Sep 17 00:00:00 2001
From: Tim Sterne-Weiler <tim.sterne.weiler@utoronto.ca>
Date: Sun, 4 Jun 2017 22:46:01 -0700
Subject: [PATCH 1/3] initial fix to deprecated warnings in runtests.jl

---
 src/sais.jl      |  2 +-
 test/runtests.jl | 12 ++++++------
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/sais.jl b/src/sais.jl
index a972901..8d7fbff 100644
--- a/src/sais.jl
+++ b/src/sais.jl
@@ -361,7 +361,7 @@ function induceSA(T,SA,C,B,n,k)
     for i = n:-1:1
         if 0 < (j = SA[i])
             j -= 1
-            if (c0 = T[j+1]) != c1
+            if Int(c0 = T[j+1]) != Int(c1)
                 B[Int(c1)+1] = b
                 c1 = c0
                 b = B[Int(c1)+1]
diff --git a/test/runtests.jl b/test/runtests.jl
index 4e78854..d9b6295 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -3,7 +3,7 @@ using Base.Test
 
 function test_suffix(args)
     for file in args
-        T = open(readall,file)
+        T = open(readstring,file)
         tic()
         SA = suffixsort(T)
         t = toq()
@@ -33,7 +33,7 @@ function sufcheck(T,SA)
         end
     end
     for i = 1:n
-        C[T[i]+1] += 1
+       C[Int(T[i])+1] += 1
     end
     p = 0
     for i = 1:256
@@ -41,8 +41,8 @@ function sufcheck(T,SA)
         C[i] = p
         p += t
     end
-    q = C[T[n]+1]
-    C[T[n]+1] += 1
+    q = C[Int(T[n])+1]
+    C[Int(T[n])+1] += 1
     for i = 1:n
         p = SA[i]
         if 0 < p
@@ -83,5 +83,5 @@ function walkdir(dir,files)
     return unique(files)
 end
 
-files = walkdir(Pkg.dir("SuffixArrays"),{})
-test_suffix(files)
\ No newline at end of file
+files = walkdir(Pkg.dir("SuffixArrays"),[])
+test_suffix(files)

From e7ba249a622819f44cf5edef1bfbb6f7aec8a187 Mon Sep 17 00:00:00 2001
From: Tim Sterne-Weiler <tim.sterne.weiler@utoronto.ca>
Date: Sun, 4 Jun 2017 23:13:04 -0700
Subject: [PATCH 2/3] fix assignment error in cast

---
 src/sais.jl | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/sais.jl b/src/sais.jl
index 8d7fbff..14dcffc 100644
--- a/src/sais.jl
+++ b/src/sais.jl
@@ -361,7 +361,8 @@ function induceSA(T,SA,C,B,n,k)
     for i = n:-1:1
         if 0 < (j = SA[i])
             j -= 1
-            if Int(c0 = T[j+1]) != Int(c1)
+            c0 = T[j+1]
+            if Int(c0) != Int(c1)
                 B[Int(c1)+1] = b
                 c1 = c0
                 b = B[Int(c1)+1]

From 5526d9f3d1c6652a297ab621f1cc89266f38fdcf Mon Sep 17 00:00:00 2001
From: Tim Sterne-Weiler <tim.sterne.weiler@utoronto.ca>
Date: Sun, 4 Jun 2017 23:16:29 -0700
Subject: [PATCH 3/3] char to int casts for getindex, runtests.jl passes

---
 test/runtests.jl | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/test/runtests.jl b/test/runtests.jl
index d9b6295..c3d8970 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -48,7 +48,7 @@ function sufcheck(T,SA)
         if 0 < p
             p -= 1
             c = T[p+1]
-            t = C[c+1]
+            t = C[Int(c)+1]
         else
             p = n-1
             c = T[p+1]
@@ -59,9 +59,9 @@ function sufcheck(T,SA)
             return -4
         end
         if t != q
-            C[c+1] += 1
-            if n <= C[c+1] || T[SA[C[c+1]+1]+1] != c
-                C[c+1] = -1
+           C[Int(c)+1] += 1
+           if n <= C[Int(c)+1] || T[SA[C[Int(c)+1]+1]+1] != c
+              C[Int(c)+1] = -1
             end
         end
     end