From 1c50a05f5525e95ec79f45d6cf2e74eee302491d Mon Sep 17 00:00:00 2001
From: usama <usama@compbio.fmph.uniba.sk>
Date: Wed, 10 Jun 2015 12:38:08 +0200
Subject: [PATCH] small changes

---
 README.md   |  1 +
 example.cfg |  4 ++--
 gaml.cc     | 11 ++++++-----
 graph.cc    |  4 ++--
 4 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/README.md b/README.md
index d07783f..124827b 100644
--- a/README.md
+++ b/README.md
@@ -54,6 +54,7 @@ LastGraph in your Velvet output directory.
 Defaults to 50000.
 - t0=number             Optional. Initial temperature. Defaults to 0.008.
 - do_proprocess=whatever If set, we do only postprocessing.
+- blasr_path=path        Optional. Path to BLASR (used with pacbio reads). Default "blasr/alignment/bin".
 
 Moves configuration
 -------------------
diff --git a/example.cfg b/example.cfg
index 5110aae..bc9cf36 100644
--- a/example.cfg
+++ b/example.cfg
@@ -1,7 +1,7 @@
-graph=../aureus/workDir/LastGraph
+graph=../qual/aureus/workDir/LastGraph
 t0=0.02
 max_iterations=10000
-starting_assembly=../aureus/Assemblies/Allpaths-LG/genome.scf.fasta
+starting_assembly=../qual/aureus/Assemblies/Allpaths-LG/genome.scf.fasta
 
 [rs1]
 cache_prefix=/scratch/GAML/rs1y
diff --git a/gaml.cc b/gaml.cc
index 3a7ee8c..f9701c7 100644
--- a/gaml.cc
+++ b/gaml.cc
@@ -26,8 +26,8 @@
 using namespace std;
 using namespace boost;
 
-string gBowtiePath = "../programs/bowtie2";
-string gBlasrPath = "../programs/blasr/alignment/bin";
+string gBowtiePath;
+string gBlasrPath;
 
 double ExtractDouble(const string& key, unordered_map<string, string>& cfg, double def) {
   if (cfg.count(key)) {
@@ -81,6 +81,8 @@ struct AssemblySettings {
     localp = ExtractInt("local_p", configs, 60);
     fixlenp = ExtractInt("fixlen_p", configs, 1);
     t0 = ExtractDouble("t0", configs, 0.008);
+    gBlasrPath = ExtractString("blasr_path", configs, "blasr/alignment/bin");
+    gBowtiePath = ExtractString("bowtie_path", configs, "bowtie2");
   }
 };
 
@@ -91,8 +93,8 @@ void Optimize(Graph& gr, ProbCalculator& prob_calc, vector<vector<int>> paths,
     int longest_read, AssemblySettings& settings) {
   int threshold = settings.threshold;
   gr.CalcReachability();
-/*  gr.CalcReachabilityBig(threshold);
-  gr.CalcReachabilityLimit(2*longest_read);*/
+  gr.CalcReachabilityBig(threshold);
+  gr.CalcReachabilityLimit(2*longest_read);
   gr.reach_limit_.resize(gr.nodes.size());
 
   int total_len;
@@ -105,7 +107,6 @@ void Optimize(Graph& gr, ProbCalculator& prob_calc, vector<vector<int>> paths,
     printf("%d/%d ", e.first, e.second);
   }
   printf("\n");
-  exit(0);
   OutputPathsToFile(paths, gr, kmer, threshold, settings.output_prefix);
   printf("\n");
 
diff --git a/graph.cc b/graph.cc
index 74e39d0..26efa1f 100644
--- a/graph.cc
+++ b/graph.cc
@@ -146,7 +146,7 @@ void Graph::CalcReachabilityLimit(int max_dist) {
         }
       }
     }
-    printf("r %d %d\n", i, reach_limit_[i].size());
+//    printf("r %d %d\n", i, reach_limit_[i].size());
   }
   printf("reach limit end\n");
 }
@@ -159,7 +159,7 @@ void Graph::CalcReachabilityBig(int threshold) {
   for (int i = 0; i < nodes.size(); i++) {
     if (nodes[i]->s.length() <= threshold) continue;
     big++;
-    printf("r %d/%d %d\n", i, nodes.size(), big);
+//    printf("r %d/%d %d\n", i, nodes.size(), big);
     queue<int> fr;
     // TODO: usama je chudak a alokuje velke veci casto
 //    vector<bool> visited(nodes.size());