Merge pull request #2 from Lilian92/master

adding the seed option for the simulate mode

Author: brianwalenz

src/seqrequester/seqrequester.C

@@ -274,6 +274,12 @@ main(int argc, char **argv) {
       simPar.rcProb = strtodouble(argv[++arg]);
     }
 
+    else if ((mode == modeSimulate) && (strcmp(argv[arg], "-seed") == 0)) {
+      simPar.randomSeedValid = true;
+      simPar.randomSeed      = strtouint32(argv[++arg]);
+    }
+
+
     //else if ((mode == modeSimulate) && (strcmp(argv[arg], "-name") == 0)) {
     //  strncpy(simPar.sequenceName, argv[++arg], FILENAME_MAX);
     //}

src/seqrequester/simulate.C

@@ -446,6 +446,9 @@ doSimulate(vector<char *>     &inputs,
   if (simPar.desiredNumBases > 0)
     nBasesMax = simPar.desiredNumBases;
 
+  if (simPar.randomSeedValid)
+    simPar.mt.mtSetSeed(simPar.randomSeed);
+
   //  Fail?
 
   if ((nBasesMax == uint64max) &&
@@ -466,6 +469,11 @@ doSimulate(vector<char *>     &inputs,
   uint64            seqsLen = 0;
 
   doSimulate_loadSequences(simPar, seqs, seqsLen);
+  // Reset nBaseMax when the coverage is given while the genomeSize is not
+  if ( (simPar.desiredCoverage > 0) && (simPar.genomeSize == 0) ) {
+      simPar.genomeSize = seqsLen;
+      nBasesMax = simPar.desiredCoverage * simPar.genomeSize;
+  }
 
   //  Make reads!
 

src/seqrequester/simulate.H

@@ -55,6 +55,9 @@ public:
 
   double  rcProb             = 0.5;
 
+  bool    randomSeedValid    = false;
+  uint32  randomSeed         = 0;
+
   mtRandom             mt;
   sampledDistribution  dist;