Was on old branch, needed to merge

CHANGELOG

@@ -1,3 +1,6 @@
+# 0.0.53 (unreleased)
+- add datastructure FNCLS which uses floating point starts and ends
+
 # 0.0.52 (20.02.20)
 - fix missing functions in headers (thanks Igor Gotlibovych)
 

ncls/__init__.py

@@ -12,4 +12,14 @@ def NCLS(starts, ends, ids):
     else:
         raise Exception("Starts/Ends not int64 or int32: " + str(starts.dtype))
 
+
+def FNCLS(starts, ends, ids):
+
+    from ncls.src.fncls import FNCLS
+
+    if starts.dtype == np.double:
+        return FNCLS(starts, ends, ids)
+    else:
+        raise Exception("Starts/Ends not double: " + str(starts.dtype))
+
 from ncls.version import __version__

ncls/src/cfncls.pxd

@@ -0,0 +1,74 @@
+from libc.stdint cimport int64_t
+
+
+cdef extern from "stdlib.h":
+    void free(void *)
+    void *malloc(size_t)
+    void *calloc(size_t,size_t)
+    void *realloc(void *,size_t)
+    int c_abs "abs" (int)
+    void qsort(void *base, size_t nmemb, size_t size,
+            int (*compar)(void *,void *))
+
+cdef extern from "stdio.h":
+    ctypedef struct FILE:
+        pass
+
+    FILE *fopen(char *,char *)
+    FILE *open_memstream(void *, size_t *)
+    FILE *fmemopen (void *, size_t, const char *)
+
+    int fclose(FILE *)
+    int fflush(FILE *)
+    int sscanf(char *str,char *fmt,...)
+    int sprintf(char *str,char *fmt,...)
+    int fprintf(FILE *ifile,char *fmt,...)
+    char *fgets(char *str,int size,FILE *ifile)
+
+
+cdef extern from "ncls/src/fintervaldb.h":
+    ctypedef struct IntervalMap:
+        double start
+        double end
+        int target_id
+        int sublist
+
+    ctypedef struct IntervalIterator:
+        pass
+
+    ctypedef struct SublistHeader:
+        int start
+        int len
+
+    int find_overlap_start(double start, double end, IntervalMap im[], int n)
+    int imstart_qsort_cmp(void *void_a,void *void_b)
+    # int target_qsort_cmp(void *void_a,void *void_b)
+    IntervalMap *read_intervals(int n,FILE *ifile)
+    SublistHeader *build_nested_list(IntervalMap im[],int n,int *p_n,int *p_nlists)
+    SublistHeader *build_nested_list_inplace(IntervalMap im[],int n,int *p_n,int *p_nlists)
+    IntervalMap *interval_map_alloc(int n)
+    IntervalIterator *interval_iterator_alloc()
+    int free_interval_iterator(IntervalIterator *it)
+    IntervalIterator *reset_interval_iterator(IntervalIterator *it)
+    int *alloc_array(int n)
+    int find_intervals_stack(int start_stack[], int end_stack[], int sp, int start,
+                             int end, IntervalMap im[], int n,
+                             SublistHeader subheader[], IntervalMap buf[],
+                             int *nfound)
+
+    int find_intervals(IntervalIterator *it0,
+                       double start,
+                       double end,
+                       IntervalMap im[],
+                       int n,
+                       SublistHeader subheader[],
+                       int nlists,
+                       IntervalMap buf[],
+                       int nbuf,
+                       int *p_nreturn,
+                       IntervalIterator **it_return)
+    void find_k_next(int start, int end,
+                    IntervalMap im[], int n,
+                    SublistHeader subheader[], int nlists,
+                    IntervalMap buf[], int ktofind,
+                    int *p_nreturn)