Merge pull request #64 from sharonsun1999/master

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aidenlab · Mar 10, 2021 · 4045991 · 4045991
2 parents 686f7db + 1921471
commit 4045991
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Showing 7 changed files with 2,281 additions and 1,998 deletions.
diff --git a/.idea/.gitignore b/.idea/.gitignore
diff --git a/C++/CMakeLists.txt b/C++/CMakeLists.txt
@@ -0,0 +1,12 @@
+cmake_minimum_required(VERSION 3.13)  # CMake version check
+project(strawC)               # Create project "simple_example"
+set(CMAKE_CXX_STANDARD 14)            # Enable c++14 standard
+
+# g++ -std=c++0x -o straw main.cpp straw.cpp -lcurl -lz
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++0x -lcurl -lz")
+
+# Add main.cpp file of project root directory as source file
+set(SOURCE_FILES main.cpp straw.cpp)
+add_executable(straw ${SOURCE_FILES})
+
+target_link_libraries(straw curl z)
diff --git a/C++/main.cpp b/C++/main.cpp
@@ -28,25 +28,29 @@ using namespace std;
 
 int main(int argc, char *argv[])
 {
-  if (argc != 8) {
-    cerr << "Not enough arguments" << endl;
-    cerr << "Usage: straw <observed/oe> <NONE/VC/VC_SQRT/KR> <hicFile(s)> <chr1>[:x1:x2] <chr2>[:y1:y2] <BP/FRAG> <binsize>" << endl;
-    exit(1);
-  }
-
-  string matrix=argv[1];
-  string norm=argv[2];
-  string fname=argv[3];
-  string chr1loc=argv[4];
-  string chr2loc=argv[5];
-  string unit=argv[6];
-  string size=argv[7];
-  int binsize=stoi(size);
-  vector<contactRecord> records;
-
-  records = straw(matrix, norm, fname, chr1loc, chr2loc, unit, binsize);
-  int length=records.size();
-  for (int i=0; i<length; i++) {
-    printf("%d\t%d\t%.14g\n", records[i].binX, records[i].binY, records[i].counts);
-  }
+    if (argc != 7 && argc != 8) {
+        cerr << "Incorrect arguments" << endl;
+        cerr << "Usage: straw <NONE/VC/VC_SQRT/KR> <hicFile(s)> <chr1>[:x1:x2] <chr2>[:y1:y2] <BP/FRAG> <binsize>" << endl;
+        cerr << "Usage: straw <oe> <NONE/VC/VC_SQRT/KR> <hicFile(s)> <chr1>[:x1:x2] <chr2>[:y1:y2] <BP/FRAG> <binsize>" << endl;
+        exit(1);
+    }
+    int offset = 0;
+    string matrix = "observed";
+    if(argc == 8){
+        offset = 1;
+        matrix = argv[1];
+    }
+    string norm = argv[1 + offset];
+    string fname = argv[2 + offset];
+    string chr1loc = argv[3 + offset];
+    string chr2loc = argv[4 + offset];
+    string unit = argv[5 + offset];
+    string size = argv[6 + offset];
+    int binsize = stoi(size);
+    vector<contactRecord> records;
+    records = straw(matrix, norm, fname, chr1loc, chr2loc, unit, binsize);
+    long length = records.size();
+    for (long i = 0; i < length; i++) {
+        printf("%d\t%d\t%.14g\n", records[i].binX, records[i].binY, records[i].counts);
+    }
 }