bump fqfeeder and phmap

include/FastxParser.hpp

@@ -10,9 +10,7 @@
 #include <thread>
 #include <vector>
 
-extern "C" {
-#include "kseq.h"
-}
+#include "kseq++.hpp"
 
 #include "concurrentqueue.h"
 
@@ -59,27 +57,24 @@ typename _Unique_if<T>::_Known_bound make_unique(Args&&...) = delete;
 #endif //__FASTX_PARSER_PRECXX14_MAKE_UNIQUE__
 
 namespace fastx_parser {
-struct ReadSeq {
-    std::string seq;
-    std::string name;
-    ~ReadSeq() {}
-};
 
-struct ReadQual {
-  std::string seq;
-  std::string name;
-  std::string qual;
-  ~ReadQual() {}
-};
+using ReadSeq = klibpp::KSeq;
+using ReadQual = klibpp::KSeq;
 
+// The ReadPair and ReadQualPair are obviously
+// redundant. But, having them as separate types
+// here would allow us to say something at compile
+// time about if we expect to be able to look
+// at qualities etc.  Think more about if we
+// really want to keep both of these.
 struct ReadPair {
-  ReadSeq first;
-  ReadSeq second;
+  klibpp::KSeq first;
+  klibpp::KSeq second;
 };
 
 struct ReadQualPair {
-  ReadQual first;
-  ReadQual second;
+  klibpp::KSeq first;
+  klibpp::KSeq second;
 };
 
 template <typename T> class ReadChunk {

include/FastxParserThreadUtils.hpp

@@ -6,8 +6,13 @@
 #include <pthread.h>
 #include <random>
 #include <thread>
+
 #if defined(__SSE2__)
-#include "simde/x86/sse2.h"
+ #if defined(HAVE_SIMDE)
+  #include "simde/x86/sse2.h"
+ #else
+  #include <emmintrin.h>
+ #endif
 #endif
 
 // Most of this code is taken directly from
@@ -23,7 +28,11 @@ static const size_t MAX_BACKOFF_ITERS = 1024;
 
 ALWAYS_INLINE static void cpuRelax() {
 #if defined(__SSE2__)  // AMD and Intel
-  simde_mm_pause();
+  #if defined(HAVE_SIMDE)
+    simde_mm_pause();
+  #else
+    _mm_pause();
+  #endif
 #elif defined(__i386__) || defined(__x86_64__)
   asm volatile("pause");
 #elif defined(__aarch64__)

include/SalmonUtils.hpp

@@ -189,6 +189,14 @@ inline void incLoop(std::atomic<double>& val, double inc) {
 
 std::string getCurrentTimeAsString();
 
+// encodes the heuristic for guessing how threads should
+// be allocated based on the available reads
+// returns true if input was modified and false otherwise.
+bool configure_parsing(size_t nfiles,            // input param
+                       size_t& worker_threads,   // input/output param
+                       uint32_t& parse_threads    // input/output param
+);
+
 bool validateOptionsAlignment_(SalmonOpts& sopt);
 bool validateOptionsMapping_(SalmonOpts& sopt);