Merge pull request #62 from nmmsv/master

minor change in command line options

README.md

@@ -102,7 +102,7 @@ Options for different sequencing settings
 * **`--insertmean <float>`** Fragment length mean. (default: calculate if not provided)
 * **`--insertsdev <float>`** Fragment length standard deviation. (default: calculate if not provided)
 * **`--nonuniform`** Indicates non-uniform coverage in alignment file (i.e., used for exome sequencing). Using this flag removes the likelihood term corresponding to FRR count.
-* **`--min-reads-cov <int>`** Minimum number of reads required for calculation of coverage.
+* **`--min-sample-reads <int>`** Minimum number of reads per sample.
 
 Advanced parameters for likelihood model:
 * **`--frrweight <float>`** Reset weight for FRR class in likelihood model. (default 1.0)

src/genotyper.cpp

@@ -201,6 +201,11 @@ bool Genotyper::ProcessLocus(BamCramMultiReader* bamreader, Locus* locus) {
       locus->flanking_reads[samp] = sample_likelihood_maximizers[samp]->GetFlankingDataSize();
       locus->depth[samp] = sample_likelihood_maximizers[samp]->GetReadPoolSize();
       locus->called[samp] = true;
+      if (allele1 <= 0 and allele2 <= 0){
+	PrintMessageDieOnError("\tProblem maximizing likelihood. Skipping locus", M_WARNING, options->quiet);
+	locus->called[samp] = false;
+	continue;
+      }
       if (options->include_ggl && !SetGGL(*locus, samp)) {
 	PrintMessageDieOnError("\tProblem setting genotype likelihoods", M_WARNING, options->quiet);
       }
@@ -238,7 +243,7 @@ bool Genotyper::ProcessLocus(BamCramMultiReader* bamreader, Locus* locus) {
 	catch (std::exception &exc){
 	  if (options->verbose) {
 	    stringstream msg;
-	    msg<<"\tEncountered error("<< exc.what() <<") in likelihood maximization for CI. Skipping locus";
+	    msg<<"\tEncountered error("<< exc.what() <<") in likelihood maximization for confidence interval. Skipping locus";
 	    PrintMessageDieOnError(msg.str(), M_PROGRESS, options->quiet);
 	  }
 	  locus->called[samp] = false;

src/main_gangstr.cpp

@@ -66,7 +66,7 @@ void show_help() {
 	   << "\t" << "--insertmean  <float>         " << "\t" << "Fragment length mean. Comma separated list to specify for each BAM separately." << "\n" 
 	   << "\t" << "--insertsdev  <float>         " << "\t" << "Fragment length standard deviation. Comma separated list to specify for each BAM separately. " << "\n"
 	   << "\t" << "--nonuniform                  " << "\t" << "Indicate whether data has non-uniform coverage (i.e., exome)" << "\n"
-	   << "\t" << "--min-reads-cov <int>         " << "\t" << "Minimum number of reads required for calculation of coverage." << "\n"
+	   << "\t" << "--min-sample-reads <int>      " << "\t" << "Minimum number of reads per sample." << "\n"
 	   << "\n Advanced paramters for likelihood model:\n"
 	   << "\t" << "--frrweight   <float>         " << "\t" << "Weight for FRR reads. Default: " << options.frr_weight << "\n"
 	   << "\t" << "--enclweight  <float>         " << "\t" << "Weight for enclosing reads. Default: " << options.enclosing_weight << "\n"
@@ -148,7 +148,7 @@ void parse_commandline_options(int argc, char* argv[], Options* options) {
   };
   static struct option long_options[] = {
     {"skip-qscore", no_argument, NULL, OPT_SKIPQ},
-    {"min-read-cov", required_argument, NULL, OPT_MINREAD},
+    {"min-sample-reads", required_argument, NULL, OPT_MINREAD},
     {"period",      required_argument,  NULL, OPT_PERIOD},
     {"include-ggl", no_argument, NULL, OPT_GGL},
     {"grid-threshold", required_argument, NULL, OPT_GRIDTHRESH},

src/vcf_writer.cpp

@@ -90,10 +90,10 @@ void VCFWriter::WriteRecord(Locus& locus) {
   std::set<int> alt_allele_lengths;
   for (size_t i=0; i<sample_names.size(); i++) {
     std::string samp = sample_names[i];
-    if (locus.allele1[samp] != refsize) {
+    if (locus.allele1[samp] != refsize and locus.allele1[samp] > 0) {
       alt_allele_lengths.insert(locus.allele1[samp]);
     }
-    if (locus.allele2[samp] != refsize) {
+    if (locus.allele2[samp] != refsize and locus.allele2[samp] > 0) {
       alt_allele_lengths.insert(locus.allele2[samp]);
     }
   }