Fix a bug with Clipper.

Author: Parsoa

caller.cpp

@@ -1,6 +1,12 @@
+#include <ctime>
+
 #include "caller.hpp"
 
+using namespace std ;
+
 void Caller::run() {
+    time_t t ;
+    time(&t) ;
     config = Configuration::getInstance();
     lprint({"PingPong SV Caller running on", to_string(config->threads), "threads.."}) ;
     // load reference genome and SFS
@@ -60,7 +66,9 @@ void Caller::run() {
         ovcf << sv << endl ;
     }
     ovcf.close() ;
-    lprint({"Complete. Exiting.."}) ;
+    time_t e ;
+    time(&e) ;
+    lprint({"Complete. Runtime:", to_string(e - t) + " seconds."}) ;
 }
 
 void Caller::load_input_sfs() {
@@ -103,7 +111,7 @@ void Caller::load_input_sfs() {
             c += read.second.size() ;
         }
     }
-    lprint({"Loaded", to_string(c), "SFS strings on", to_string(r), " reads."}) ;
+    lprint({"Loaded", to_string(c), "SFS strings on", to_string(r), "reads."}) ;
 }
 
 void Caller::print_vcf_header() {

caller.hpp

@@ -13,8 +13,6 @@
 #include "extender.hpp"
 #include "chromosomes.hpp"
 
-using namespace std;
-
 class Caller {
 
 public:

clipper.cpp

@@ -21,7 +21,7 @@ vector<Clip> Clipper::remove_duplicates(const vector<Clip> &clips) {
     return unique_clips;
 }
 
-vector<Clip> Clipper::combine(const vector<Clip> &clips) {
+vector<Clip> Clipper::combine(const vector<Clip>& clips) {
     int threads = 4 ;
     vector<vector<Clip>> _p_combined_clips ;
     _p_combined_clips.resize(threads) ;
@@ -47,7 +47,7 @@ vector<Clip> Clipper::combine(const vector<Clip> &clips) {
         }
     }
     vector<Clip> combined_clips ;
-    for (int i = 0; i < chromosomes.size(); i++) {
+    for (int i = 0; i < threads; i++) {
         combined_clips.insert(combined_clips.begin(), _p_combined_clips[i].begin(), _p_combined_clips[i].end()) ;
     }
     return combined_clips ;

extender.cpp

@@ -121,7 +121,7 @@ pair<int, int> Extender::get_unique_kmers(const vector<pair<int, int>> &alpairs,
 
 // Parallelize within each chromosome
 void Extender::extend_parallel() {
-    lprint({"Extending superstrings on.."}) ; 
+    lprint({"Extending superstrings on", to_string(threads), "threads.."}) ; 
     int p = 0 ;
     int b = 0 ;
     for (int i = 0; i < 2; i++) {
@@ -174,7 +174,7 @@ void Extender::extend_parallel() {
         if (s - t == 0) {
             s += 1 ;
         }
-        cerr << "[I] Processed batch " << std::left << std::setw(7) << b << ". Reads so far " << std::right << std::setw(12) << u << ". Reads per second: " <<  u / (s - t) << ". Time: " << std::setw(8) << std::fixed << s - t << "\r" ;
+        cerr << "[I] Processed batch " << std::left << std::setw(7) << b << ". Reads so far: " << std::right << std::setw(12) << u << ". Reads per second: " <<  u / (s - t) << ". Time: " << std::setw(8) << std::fixed << s - t << "\r" ;
         printed = true ;
     }
     if (printed) {
@@ -399,9 +399,8 @@ void Extender::cluster_no_interval_tree() {
         [] (const ExtSFS& lhs, const ExtSFS&  rhs) {
                 return lhs.e - lhs.s < rhs.e - rhs.s ;
         }) ;
-    // TODO: is this good?
     int dist = (r->e - r->s) * 1.1 ;
-    lprint({"Maximum extended-SFS length:", to_string(dist), "bp."}) ;
+    lprint({"Maximum extended-SFS length:", to_string(dist), "bp. Using separation distance", to_string(dist) + "."}) ;
     // find large gaps
     int prev_i = 0 ;
     int prev_e = extended_sfs[0].e ;