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Small change
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endre bakken stovner authored and endre bakken stovner committed Sep 20, 2021
1 parent 64741e1 commit c871f14
Showing 1 changed file with 23 additions and 55 deletions.
78 changes: 23 additions & 55 deletions ncls/src/ncls32.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -472,18 +472,20 @@ cdef class NCLS32:
@cython.boundscheck(False)
@cython.wraparound(False)
@cython.initializedcheck(False)
cpdef set_difference_helper(self, const int32_t [::1] starts, const int32_t [::1] ends, const int64_t [::1] indexes):
cpdef set_difference_helper(self, const int32_t [::1] starts, const int32_t [::1] ends, const int64_t [::1] indexes,
const int64_t[::1] nhits):

cdef int i = 0
cdef int nhit = 0
cdef int nfound = 0
cdef int nfound_loop = 0
cdef int32_t nstart = 0
cdef int32_t nend = 0
cdef int length = len(starts)
cdef int loop_counter = 0
cdef int overlap_type_nb = 0
cdef int na = -1

cdef int spent = 0

output_arr = np.zeros(length, dtype=np.int64)
output_arr_start = np.zeros(length, dtype=np.int32)
Expand All @@ -504,40 +506,30 @@ cdef class NCLS32:

it_alloc = cn.interval_iterator_alloc()
it = it_alloc
for loop_counter in range(length):

while it:
i = 0

nstart = starts[loop_counter]
nend = ends[loop_counter]
for loop_counter in range(length):

# print("----" * 5)
# print("loop counter", loop_counter)
# print("nstart", nstart)
# print("nend", nend)
nhit = nhits[loop_counter]
nstart = starts[loop_counter]
nend = ends[loop_counter]
nfound_loop = 0
spent = 0

cn.find_intervals(it, nstart, nend, self.im, self.ntop,
while not spent:
i = 0
cn.find_intervals(it, starts[loop_counter], ends[loop_counter], self.im, self.ntop,
self.subheader, self.nlists, im_buf, 1024,
&(nhit), &(it)) # GET NEXT BUFFER CHUNK

#print("nhits:", nhit)


&(na), &(it)) # GET NEXT BUFFER CHUNK

if nfound + nhit >= length:

length = (nfound + nhit) * 2
length = (length + nhit) * 2
output_arr = np.resize(output_arr, length)
output_arr_start = np.resize(output_arr_start, length)
output = output_arr
output_start = output_arr_start
output_arr_end = np.resize(output_arr_end, length)
output_end = output_arr_end

# print(" length is", length)
# print(" nfound is", nfound)

# B covers whole of A; ignore
if nhit == 1 and starts[loop_counter] > im_buf[i].start and ends[loop_counter] < im_buf[i].end:
# print("ignore me!")
Expand All @@ -546,64 +538,40 @@ cdef class NCLS32:
output[nfound] = indexes[loop_counter]
i = nhit
nfound += 1
nfound_loop += 1

while i < nhit:
# print(" i", i)
# print("--- i:", i)
# print("--- im_buf[i]", im_buf[i])
# print(" B start:", im_buf[i].start)
# print(" B end:", im_buf[i].end)
# print(" nfound:", nfound)
# print(" output_arr_start", output_arr_start)
# print(" output_arr_end", output_arr_end)

while i < 1024:
# in case the start contributes nothing
if i < nhit - 1:
# print(" i < nhit - 1")

if nstart < im_buf[i].start:
#print(" new_start", nstart)
#print(" new_end", im_buf[i].start)
output[nfound] = indexes[loop_counter]
output_start[nfound] = nstart
output_end[nfound] = im_buf[i].start
nfound += 1
nfound_loop += 1

nstart = im_buf[i].end
elif i == nhit - 1:

# print("i == nhit -1")
#print("im_buf[i].start", im_buf[i].start)
#print("im_buf[i].end", im_buf[i].end)
#print("nstart", nstart)
#print("ends[loop_counter]", ends[loop_counter])

elif nfound_loop == nhit - 1:
if im_buf[i].start <= nstart and im_buf[i].end >= ends[loop_counter]:
# print("im_buf[i].start <= nstart and im_buf[i].end >= ends[loop_counter]")
#print("we are here " * 10)

output_start[nfound] = -1
output_end[nfound] = -1
output[nfound] = indexes[loop_counter]
output[nfound] = <long> indexes[loop_counter]
nfound += 1
nfound_loop += 1
else:
if im_buf[i].start > nstart:
# print("im_buf[i].start > nstart", im_buf[i].start, nstart)
output[nfound] = indexes[loop_counter]
output_start[nfound] = nstart
output_end[nfound] = im_buf[i].start
nfound += 1
nfound_loop += 1

if im_buf[i].end < ends[loop_counter]:
# print("im_buf[i].end < ends[loop_counter]", im_buf[i].end, ends[loop_counter])
# print("i, loop_counter", i, loop_counter)
# print("indexes[loop_counter]", indexes[loop_counter])
# print("indexes", indexes[loop_counte rloop_counter])

output[nfound] = indexes[loop_counter]
output_start[nfound] = im_buf[i].end
output_end[nfound] = ends[loop_counter]
nfound += 1
nfound_loop += 1

i += 1

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