Add 32-bit methods

README.md

@@ -15,6 +15,9 @@ pip install ncls
 ## Changelog
 
 ```
+# 2018.13.11 (0.0.29)
+- add 32-bit methods
+
 # 2018.01.06 (0.0.23)
 - NCLS started segfaulting in travis build for pyranges. Probably due to bad string definition files in travis.
 

ncls/__init__.py

@@ -1 +1,13 @@
-from ncls.src.ncls import NCLS
+from ncls.src.ncls import NCLS64
+from ncls.src.ncls32 import NCLS32
+
+import numpy as np
+
+def NCLS(starts, ends, ids):
+
+    if starts.dtype == np.int64:
+        return NCLS64(starts, ends, ids)
+    elif starts.dtype == np.int32:
+        return NCLS32(starts, ends, ids)
+    else:
+        raise Exception("Starts/Ends not int64 or int32: " + str(starts.dtype))

ncls/src/cncls.pxd

@@ -42,8 +42,6 @@ cdef extern from "ncls/src/intervaldb.h":
         int start
         int end
         int target_id
-        int target_start
-        int target_end
         int sublist
 
     ctypedef struct IntervalIterator:
@@ -53,6 +51,7 @@ cdef extern from "ncls/src/intervaldb.h":
         int start
         int len
 
+    int find_overlap_start(int start, int 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)

ncls/src/cncls32.pxd

@@ -0,0 +1,77 @@
+
+from libc.stdint cimport int32_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/intervaldb32.h":
+    ctypedef struct IntervalMap:
+        int32_t start
+        int32_t end
+        int32_t target_id
+        int32_t sublist
+
+    ctypedef struct IntervalIterator:
+        pass
+
+    ctypedef struct SublistHeader:
+        int start
+        int len
+
+    int find_overlap_start(int32_t start, int32_t 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 start32_t,
+                             int end32_t, IntervalMap im[], int n,
+                             SublistHeader subheader[], IntervalMap buf[],
+                             int *nfound)
+
+    int find_intervals(IntervalIterator *it0,
+                       int start,
+                       int 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)
+
+    int read_imdiv(FILE *ifile,IntervalMap imdiv[],int div,int i_div,int ntop)

ncls/src/intervaldb.c

@@ -257,12 +257,15 @@ SublistHeader *build_nested_list(IntervalMap im[],int n,
     CALLOC(imsub,nsub,IntervalMap); /* TEMPORARY ARRAY FOR REPACKING SUBLISTS */
     for (i=j=0;i<n;i++) { /* GENERATE LIST FOR SORTING; ASSIGN HEADER INDEXES*/
       parent=im[i].sublist;
+      printf("Interval %i has parent %d\n", i, parent);
       if (parent>=0)  {/* IN A SUBLIST */
         imsub[j].start=i;
         imsub[j].sublist=parent;
         j++;
-        if (im[parent].sublist<0) /* A NEW PARENT! SET HIS SUBLIST HEADER INDEX */
+        if (im[parent].sublist<0){ /* A NEW PARENT! SET HIS SUBLIST HEADER INDEX */
+          printf("Setting parent %d to sublist %d\n", parent, nlists += 1);
           im[parent].sublist=nlists++;
+        }
       }
       im[i].sublist= -1; /* RESET TO DEFAULT VALUE: NO SUBLIST */
     }
@@ -272,9 +275,11 @@ SublistHeader *build_nested_list(IntervalMap im[],int n,
     CALLOC(subheader,nlists,SublistHeader); /* SUBLIST HEADER INDEX */
     for (i=0;i<nsub;i++) { /* COPY SUBLIST ENTRIES TO imsub */
       j=imsub[i].start;
+      printf("j: %d\n", j);
       parent=imsub[i].sublist;
       memcpy(imsub+i,im+j,sizeof(IntervalMap)); /* COPY INTERVAL */
       k=im[parent].sublist;
+      printf("k is %d\n", k);
       if (subheader[k].len==0) /* START A NEW SUBLIST */
         subheader[k].start=i;
       subheader[k].len++; /* COUNT THE SUBLIST ENTRIES */

ncls/src/intervaldb.h

@@ -75,6 +75,7 @@ typedef struct {
 
 extern int *alloc_array(int n);
 
+extern int find_overlap_start(int start,int end,IntervalMap im[],int n);
 extern int imstart_qsort_cmp(const void *void_a,const void *void_b);
 extern int target_qsort_cmp(const void *void_a,const void *void_b);
 extern IntervalMap *read_intervals(int n,FILE *ifile);