Adopt a default extension score threshold of 1

Author: adamnovak

src/minimizer_mapper.hpp

@@ -75,7 +75,7 @@ class MinimizerMapper : public AlignerClient {
 
     //If an extension's score is smaller than the best extension's score by
     //more than this much, don't align it
-    int extension_score_threshold = 0;
+    int extension_score_threshold = 1;
 
     size_t max_multimaps = 1;
     size_t distance_limit = 1000;

src/subcommand/gaffe_main.cpp

@@ -62,7 +62,7 @@ void help_gaffe(char** argv) {
     << "  -a, --max-alignments INT      align up to INT extensions [8]" << endl
     << "  -s, --cluster-score INT       only extend clusters if they are within cluster-score of the best score" << endl
     << "  -u, --cluster-coverage FLOAT  only extend clusters if they are within cluster-coverage of the best read coverage" << endl
-    << "  -v, --extension-score INT     only align extensions if their score is within extension-score of the best score" << endl
+    << "  -v, --extension-score INT     only align extensions if their score is within extension-score of the best score [1]" << endl
     << "  -w, --extension-set INT       only align extension sets if their score is within extension-set of the best score" << endl
     << "  -O, --no-dp                   disable all gapped alignment" << endl
     << "  --track-provenance            track how internal intermediate alignment candidates were arrived at" << endl
@@ -113,7 +113,7 @@ int main_gaffe(int argc, char** argv) {
     //Throw away extension sets with scores that are this amount below the best
     double extension_set = 0;
     //Throw away extensions with scores that are this amount below the best
-    int extension_score = 0;
+    int extension_score = 1;
     // What sample name if any should we apply?
     string sample_name;
     // What read group if any should we apply?