Make max tests a param

bcgsc · Mar 9, 2021 · 05f2749 · 05f2749
1 parent 1b5ae82
commit 05f2749
Show file tree

Hide file tree

Showing 3 changed files with 20 additions and 5 deletions.
diff --git a/RResolver/RAlgorithmsShort.cpp b/RResolver/RAlgorithmsShort.cpp
@@ -320,7 +320,7 @@ testCombination(
  return Support(Support::UnknownReason::POSSIBLE_TESTS_LT_PLANNED);
  }
 
- if (plannedTests > opt::minTests + MAX_TESTS_OFFSET) {
+ if (plannedTests > opt::maxTests) {
  return Support(Support::UnknownReason::OVER_MAX_TESTS);
  }
 
@@ -391,7 +391,7 @@ determinePathSupport(const ContigPath& path)
  if (requiredTests < opt::minTests) {
  requiredTests = opt::minTests;
  }
- if (requiredTests > opt::minTests + MAX_TESTS_OFFSET) {
+ if (requiredTests > opt::maxTests) {
  return Support(calculatedTests, Support::UnknownReason::OVER_MAX_TESTS);
  }
 

diff --git a/RResolver/RAlgorithmsShort.h b/RResolver/RAlgorithmsShort.h
@@ -14,7 +14,6 @@
 #include <vector>
 
 const int MIN_MARGIN = 2;
-const int MAX_TESTS_OFFSET = 16; // std::numeric_limits<int>::max();
 const int R_HEURISTIC = 45;
 const double R_HEURISTIC_A = 0.49;
 const double R_HEURISTIC_B = 63.5;
@@ -55,6 +54,9 @@ extern int extract;
 /** Minimum number of sliding window moves */
 extern int minTests;
 
+/** Maximum number of sliding window moves */
+extern int maxTests;
+
 /** Maximum number of branching paths */
 extern int branching;
 

diff --git a/RResolver/RResolverShort.cpp b/RResolver/RResolverShort.cpp
@@ -48,7 +48,8 @@ static const char USAGE_MESSAGE[] =
  " Histograms are omitted if no prefix is given."
  " -t, --threshold=N set path support threshold to N. [4]"
  " -x, --extract=N extract N rmers per read. [4]"
- " -m, --min-tests=N set minimum number of sliding window moves to N. Maximum value is 127. [20]"
+ " -m, --min-tests=N set minimum number of sliding window moves to N. Cannot be higher than 127. [20]"
+ " -M, --max-tests=N set maximum number of sliding window moves to N. Cannot be higher than 127. [36]"
  " -n, --branching=N set maximum number of branching paths to N. [75]"
  " -r, --rmer=N explicitly set r value (k value used by rresolver)."
  " The number of set r values should be equalto the number of read sizes."
@@ -97,6 +98,9 @@ int extract = 4;
 /** Minimum number of sliding window moves */
 int minTests = 20;
 
+/** Maximum number of sliding window moves */
+int maxTests = 36;
+
 /** Maximum number of branching paths */
 int branching = 75;
 
@@ -121,7 +125,7 @@ int format; // used by ContigProperties
 
 }
 
-static const char shortopts[] = "b:j:g:c:k:h:t:x:m:n:r:q:eS:U:v";
+static const char shortopts[] = "b:j:g:c:k:h:t:x:m:M:n:r:q:eS:U:v";
 
 enum
 {
@@ -139,6 +143,7 @@ static const struct option longopts[] = {
  { "threshold", required_argument, NULL, 't' },
  { "extract", required_argument, NULL, 'x' },
  { "min-tests", required_argument, NULL, 'm' },
+ { "max-tests", required_argument, NULL, 'M' },
  { "branching", required_argument, NULL, 'n' },
  { "rmer", required_argument, NULL, 'r' },
  { "quality-threshold", required_argument, NULL, 'q' },
@@ -196,6 +201,11 @@ check_options(int argc, bool& die)
  std::cerr << PROGRAM ": invalid number of threads `-j`" << std::endl;
  die = true;
  }
+
+ if (opt::minTests > opt::maxTests) {
+ std::cerr << PROGRAM ": --min-tests cannot be higher than --max-tests" << std::endl;
+ die = true;
+ }
 }
 
 void
@@ -296,6 +306,9 @@ main(int argc, char** argv)
  case 'm':
  arg >> opt::minTests;
  break;
+ case 'M':
+ arg >> opt::maxTests;
+ break;
  case 'n':
  arg >> opt::branching;
  break;