Updated spoa and added missing header

isovic · Mar 1, 2018 · fa371d9 · fa371d9
1 parent fb3a059
commit fa371d9
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Showing 5 changed files with 8 additions and 7 deletions.
diff --git a/src/main.cpp b/src/main.cpp
@@ -9,7 +9,7 @@
 #include "sequence.hpp"
 #include "polisher.hpp"
 
-static const char* version = "v1.0.2";
+static const char* version = "v1.0.3";
 
 static struct option options[] = {
     {"include-unpolished", no_argument, 0, 'u'},

diff --git a/src/overlap.cpp b/src/overlap.cpp
@@ -149,7 +149,7 @@ void Overlap::transmute(const std::unordered_map<std::string, uint64_t>& name_to
     } else {
         if (!transmuteId(id_to_id, q_id_ << 1 | 0, q_id_)) {
             fprintf(stderr, "[racon::Overlap::transmute] error: "
-                "missing sequence with id %lu!\n", q_id_);
+                "missing sequence with id %zu!\n", q_id_);
             exit(1);
         }
     }
@@ -162,7 +162,7 @@ void Overlap::transmute(const std::unordered_map<std::string, uint64_t>& name_to
     } else {
         if (!transmuteId(id_to_id, t_id_ << 1 | 1, t_id_)) {
             fprintf(stderr, "[racon::Overlap::transmute] error: "
-                "missing sequence with id %lu!\n", t_id_);
+                "missing sequence with id %zu!\n", t_id_);
             exit(1);
         }
     }
@@ -210,7 +210,7 @@ void Overlap::find_breaking_points(const std::vector<std::unique_ptr<Sequence>>&
             free(cigar);
         } else {
             fprintf(stderr, "[racon::Overlap::find_breaking_points] error: "
-                "edlib unable to align pair (%lu x %lu)!\n", q_id_, t_id_);
+                "edlib unable to align pair (%zu x %zu)!\n", q_id_, t_id_);
             exit(1);
         }
 

diff --git a/src/overlap.hpp b/src/overlap.hpp
@@ -6,6 +6,7 @@
 
 #pragma once
 
+#include <stdlib.h>
 #include <stdint.h>
 #include <memory>
 #include <vector>

diff --git a/src/polisher.cpp b/src/polisher.cpp
@@ -353,7 +353,7 @@ void Polisher::initialize() {
     }
     for (uint64_t i = 0; i < thread_futures.size(); ++i) {
         thread_futures[i].wait();
-        fprintf(stderr, "[racon::Polisher::initialize] aligned overlap %lu/%lu\r",
+        fprintf(stderr, "[racon::Polisher::initialize] aligned overlap %zu/%zu\r",
             i + 1, overlaps.size());
     }
     fprintf(stderr, "\n");
@@ -490,7 +490,7 @@ void Polisher::polish(std::vector<std::unique_ptr<Sequence>>& dst,
         }
         windows_[i].reset();
 
-        fprintf(stderr, "[racon::Polisher::polish] generated consensus for window %lu/%lu\r",
+        fprintf(stderr, "[racon::Polisher::polish] generated consensus for window %zu/%zu\r",
             i + 1, thread_futures.size());
     }
     fprintf(stderr, "\n");

diff --git a/vendor/spoa b/vendor/spoa
+2 −2		CMakeLists.txt
+4 −1		README.md
+5 −2		include/spoa/graph.hpp
+1 −0		src/alignment_engine.cpp
+78 −18		src/graph.cpp
+14 −5		src/main.cpp
+0 −1		src/simd_alignment_engine.cpp
+1 −1		vendor/bioparser