updating many of the magic numbers in the code. These numbers are fur…

…ther explained in a separate markdown file

src/AbismalAlign.hpp

@@ -51,7 +51,7 @@ struct AbismalAlign {
   const size_t q_sz_max;
   const size_t bw;
 
-  static const uint16_t max_off_diag = 2;
+  static const uint16_t max_off_diag = 4;
 };
 
 template <score_t (*scr_fun)(const uint8_t, const uint8_t),
@@ -239,8 +239,8 @@ namespace simple_aln {
   static const score_t match = 1;
   static const score_t mismatch = -1;
   static const score_t indel = -1;
+  static const score_t min_diffs_to_align = 1;
   static const std::array<score_t, 2> score_lookup = {match, mismatch};
-  static const score_t min_diffs_to_align = 4;
 
   inline score_t default_score(const uint32_t len, const score_t diffs) {
     return match*(len - diffs) + mismatch*diffs;

src/AbismalIndex.hpp

@@ -36,19 +36,17 @@ namespace seed {
   static const uint32_t key_weight = 26;
 
   // window in which we select the best k-mer
-  static const uint32_t w_index = 20;
-
-  // GS: must be >= w_index to guarantee the minimizer was indexed
-  static const uint32_t w_map = 30;
-
-  // max k-mers used for comparison
-  static const size_t max_seeds = 5;
+  static const uint32_t window_size = 30;
 
   // number of positions to sort within buckets
   static const uint32_t n_sorting_positions = 128;
 
   // seed size during mapping, or size of a two-letter exact match
-  static const uint32_t n_seed_positions = 32;
+  static const uint32_t n_seed_positions = 26;
+
+  // maximum number of candidates per seed as function of
+  // overrepresented k-mers
+  static const double overrep_kmer_quantile = 1e-6;
 
   static const size_t hash_mask = (1ull << seed::key_weight) - 1;
 

src/abismal.cpp

@@ -256,7 +256,7 @@ struct se_candidates {
   static const uint32_t max_size;
 };
 
-const uint32_t se_candidates::max_size = 200;
+const uint32_t se_candidates::max_size = 20;
 
 inline bool
 chrom_and_posn(const ChromLookup &cl, const string &cig, const uint32_t p,
@@ -443,7 +443,7 @@ struct pe_candidates {
   static const uint32_t max_size;
 };
 
-const uint32_t pe_candidates::max_size = 400;
+const uint32_t pe_candidates::max_size = 100;
 
 inline double pct(const double a, const double b) {return 100.0*a/b;}