Fix Linux build

vgteam · Jul 19, 2024 · b55be13 · b55be13 · adamnovak · Jul 19, 2024
1 parent 011e1fe
commit b55be13
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Showing 4 changed files with 8 additions and 6 deletions.
diff --git a/src/algorithms/pad_band.cpp b/src/algorithms/pad_band.cpp
@@ -6,6 +6,8 @@
 
 #include "pad_band.hpp"
 
+#include <cmath>
+
 namespace vg {
 namespace algorithms {
 

diff --git a/src/multipath_mapper.cpp b/src/multipath_mapper.cpp
@@ -61,11 +61,11 @@ namespace vg {
                                      haplo::ScoreProvider* haplo_score_provider, SnarlManager* snarl_manager,
                                      SnarlDistanceIndex* distance_index) :
         BaseMapper(graph, gcsa_index, lcp_array, haplo_score_provider),
+        choose_band_padding(algorithms::pad_band_random_walk(1.0, 0)),
         snarl_manager(snarl_manager),
         distance_index(distance_index),
         path_component_index(distance_index ? nullptr : new PathComponentIndex(graph)),
-        splice_stats(*get_regular_aligner()),
-        choose_band_padding(algorithms::pad_band_random_walk(1.0, 0))
+        splice_stats(*get_regular_aligner())
     {
         set_max_merge_supression_length();
     }

diff --git a/src/multipath_mapper.hpp b/src/multipath_mapper.hpp
@@ -198,6 +198,9 @@ namespace vg {
         // the maximum number of pairs of each motif that we will consider during spliced alignment
         size_t max_motif_pairs = 1024;
         unordered_set<path_handle_t> ref_path_handles;
+
+        // A function for computing band padding
+        std::function<size_t(const Alignment&, const HandleGraph&)> choose_band_padding;
 
         //static size_t PRUNE_COUNTER;
         //static size_t SUBGRAPH_TOTAL;
@@ -683,9 +686,6 @@ namespace vg {
         static thread_local unordered_map<double, vector<int64_t>> pessimistic_gap_memo;
         static const size_t gap_memo_max_size;
 
-        // A function for computing band padding
-        std::function<size_t(const Alignment&, const HandleGraph&)> choose_band_padding;
-
 #ifdef mpmap_instrument_mem_statistics
     public:
         ofstream _mem_stats;

diff --git a/src/subcommand/mpmap_main.cpp b/src/subcommand/mpmap_main.cpp
@@ -1901,7 +1901,7 @@ int main_mpmap(int argc, char** argv) {
     }
     multipath_mapper.adjust_alignments_for_base_quality = qual_adjusted;
     multipath_mapper.strip_bonuses = strip_full_length_bonus;
-    multipath_mapper.choose_band_padding = algorithms::pad_band_random_walk(band_padding_multiplier);
+    multipath_mapper.choose_band_padding = vg::algorithms::pad_band_random_walk(band_padding_multiplier);
 
     // set mem finding parameters
     multipath_mapper.hit_max = hit_max;