Small change to handle the odd case when no alignment is performed.

diff --git a/htswanalysis/src/complexity_count.cpp b/htswanalysis/src/complexity_count.cpp
index 28e42953c6a8490e3cfdc3166002953fe7805830..22975ee6eecdec9f7e3284d23c74a2143eea49e9 100644 (file)
--- a/htswanalysis/src/complexity_count.cpp
+++ b/htswanalysis/src/complexity_count.cpp
@@ -59,10 +59,11 @@ void read_align_file(char* filename, Hits& features) {
     string line_str(line);
     vector<string> fields;
     split(line_str, delim, fields);
-    if(fields.size() <= 3) { continue; }
+    if(fields.size() <= 4) { continue; }
     vector<string> location; split(fields[3], location_delim, location);
+    if(location.size() != 2) { continue; }
     int chr = chromstr_to_int(location[0]);
-    if(chr == -1) { continue; }
+    if(chr < 0) { continue; }
     int pos = atoi(location[1].c_str());
     bool strand = ((fields[4].c_str())[0] == 'F')?0:1;
 
@@ -90,12 +91,13 @@ void print_features(Hits& hits, string filename, unsigned int size_1, unsigned i
 }
 
 unsigned int count_complexity(Hits& data) {
-  int chrom = -1; 
+  unsigned int num_hits = data.size();
 
   unsigned int n_island = 0;
   unsigned int island_size = 0;
+  int chrom = data.begin()->chr;
   for(Hits::iterator i = data.begin()+1; i != data.end()-1 && i != data.end(); ++i) {
-    if(chrom == -1 || i->chr != chrom) {
+    if(i->chr != chrom) {
       chrom = i->chr;
     } else if( (i+1)->chr != chrom ) { continue; }
     int prev = (i-1)->start;
@@ -117,8 +119,9 @@ int main(int argc, char** argv) {
   char label1[128]; strcpy(label1,argv[1]);
   Hits align1; read_align_file(argv[2], align1); 
 
-  int complexity;
-  if(align1.size() == 0) complexity = 0; else complexity = count_complexity(align1);
+  if(align1.size() <= 1) { cerr << "No alignment\n"; exit(0); }
+
+  int complexity = count_complexity(align1);
 
   cout << label1 << "\t" << complexity << "\t" << align1.size()/1000000 << "M\t" << (double)complexity/(double)align1.size() << endl;
 }