Move `kseq_ptr_t` to the `_utils.hpp` helper header

include/fastani/map/base_types.pxd

@@ -43,7 +43,7 @@ cdef extern from "map/include/base_types.hpp" namespace "skch" nogil:
     cdef cppclass QueryMetaData[ K, MV ]:
         K       kseq
         seqno_t seqCounter
-        int     sketchsize
+        int     sketchSize
         MV      minimizerTableQuery
 
 

include/fastani/map/compute_map.pxd

 from libc.stdint cimport uint64_t
 from libcpp.vector cimport vector
 from libcpp.functional cimport function
+from libcpp11.fstream cimport ofstream
 
 from fastani.map.base_types cimport seqno_t, offset_t, ContigInfo, MappingResult, MappingResultsVector_t
 from fastani.map.map_parameters cimport Parameters
@@ -12,12 +13,12 @@ cdef extern from "map/include/computeMap.hpp" namespace "skch" nogil:
 
     cdef cppclass Map:
 
-        cppclass L1_candidateLocus_t:
+        struct L1_candidateLocus_t:
             seqno_t  seqId
             offset_t rangeStartPos
             offset_t rangeEndPos
 
-        cppclass L2_mapLocus_t:
+        struct L2_mapLocus_t:
             seqno_t         seqId
             offset_t        meanOptimalPos
             Sketch.MIIter_t optimalStart
@@ -37,10 +38,4 @@ cdef extern from "map/include/computeMap.hpp" namespace "skch" nogil:
             function[void(MappingResult&)] f = nullptr
         )
 
-        Map(
-            const Parameters &p,
-            const Sketch &refsketch,
-            uint64_t &totalQueryFragments,
-            int queryno,
-            MappingResultsVector_t &r
-        )
+        void mapSingleQuerySeq[Q](Q&, MappingResultsVector_t&, ofstream&)

include/kseq/__init__.pxd

@@ -7,6 +7,5 @@ cdef extern from "common/kseq.h":
         size_t m
         char*  s
 
-    ctypedef __kseq_t kseq_t
-    cdef struct __kseq_t:
+    cdef cppclass kseq_t:
         kstring_t seq

pyfastani/_utils.cpp

-#include <iostream>
-#include <ctime>
-#include <chrono>
-#include <functional>
-
 #include "_utils.hpp"
 
-
-skch::Map* new_map_with_result_vector(
-    const skch::Parameters &p,
-    const skch::Sketch &refsketch,
-    uint64_t &totalQueryFragments,
-    int queryno,
-    skch::MappingResultsVector_t &r
-) {
-  auto fn = std::bind(skch::Map::insertL2ResultsToVec, std::ref(r), std::placeholders::_1);
-  return new skch::Map( p, refsketch, totalQueryFragments, queryno, fn );
-}
-
 int omp_get_thread_num(void) {
     return 1; // Make the logger shut up.
 }

pyfastani/_utils.hpp

 #ifndef __UTILS_HPP
 #define __UTILS_HPP
 
-#include "map/include/computeMap.hpp"
-
 #include <stdint.h>
-#include <functional>
+#include <chrono>
+#include <limits>
+#include <iostream>
+#include <vector>
 
+#include "common/kseq.h"
 #include "map/include/base_types.hpp"
-#include "map/include/computeMap.hpp"
-
-skch::Map* new_map_with_result_vector(
-    const skch::Parameters &p,
-    const skch::Sketch &refsketch,
-    uint64_t &totalQueryFragments,
-    int queryno,
-    skch::MappingResultsVector_t &r
-);
+#include "map/include/winSketch.hpp"
 
 // not needed anywhere except in `cgi::correctRefGenomeIds`
 // so we can just patch them
 extern int omp_get_thread_num(void);
 extern int omp_get_num_threads(void);
 
+typedef kseq_t* kseq_ptr_t;
+
 #endif

pyfastani/_utils.pxd

 from libc.stdint cimport uint64_t
 
+from kseq cimport kseq_t
 from fastani.map.base_types cimport MappingResultsVector_t
 from fastani.map.compute_map cimport Map
 from fastani.map.map_parameters cimport Parameters
@@ -8,10 +9,7 @@ from fastani.map.win_sketch cimport Sketch
 
 cdef extern from "_utils.hpp" nogil:
 
-    Map* new_map_with_result_vector(
-        const Parameters &p,
-        const Sketch &refsketch,
-        uint64_t &totalQueryFragments,
-        int queryno,
-        MappingResultsVector_t &r
-    )
+    int omp_get_thread_num()
+    int omp_get_num_threads()
+
+    ctypedef kseq_t* kseq_ptr_t