Fixes compile error for clang

Author: kcleal

dysgu/call_component.pyx

@@ -72,7 +72,7 @@ cdef base_quals_aligned_clipped(AlignedSegment a):
     cdef float clipped_base_quals = 0
     cdef int left_clip = 0
     cdef int right_clip = 0
-    clip_sizes(a, left_clip, right_clip)
+    clip_sizes(a, &left_clip, &right_clip)
     clipped_bases = left_clip + right_clip
     cdef const unsigned char[:] quals = a.query_qualities
     cdef int i
@@ -121,7 +121,7 @@ cdef count_attributes2(reads1, reads2, spanning, float insert_ppf, generic_ins,
             er.n_unmapped_mates += 1
         left_clip = 0
         right_clip = 0
-        clip_sizes_hard(a, left_clip, right_clip)
+        clip_sizes_hard(a, &left_clip, &right_clip)
         if left_clip > 0 and right_clip > 0:
             er.double_clips += 1
         has_sa = a.has_tag("SA")
@@ -164,7 +164,7 @@ cdef count_attributes2(reads1, reads2, spanning, float insert_ppf, generic_ins,
 
         left_clip = 0
         right_clip = 0
-        clip_sizes(a, left_clip, right_clip)
+        clip_sizes(a, &left_clip, &right_clip)
         if left_clip or right_clip:
             er.sc += 1
         if a.flag & 1:  # paired read
@@ -180,7 +180,7 @@ cdef count_attributes2(reads1, reads2, spanning, float insert_ppf, generic_ins,
             er.NP += 1
         left_clip = 0
         right_clip = 0
-        clip_sizes_hard(a, left_clip, right_clip)
+        clip_sizes_hard(a, &left_clip, &right_clip)
         if left_clip > 0 and right_clip > 0:
             er.double_clips += 1
         if a.has_tag("SA"):
@@ -426,7 +426,7 @@ cdef make_generic_insertion_item(aln, int insert_size, int insert_std):
         v_item.svtype = "BND"
         left_clip = 0
         right_clip = 0
-        clip_sizes(aln, left_clip, right_clip)
+        clip_sizes(aln, &left_clip, &right_clip)
         clip_s = max(left_clip, right_clip)
         rand_insert_pos = 100 if not clip_s else clip_s
     v_item.inferred_sv_len = 0 if rand_insert_pos < 0 else rand_insert_pos

dysgu/graph.pyx

@@ -251,7 +251,7 @@ cdef class ClipScoper:
                unordered_set[int]& clustered_nodes):
         cdef int clip_left = 0
         cdef int clip_right = 0
-        clip_sizes(r, clip_left, clip_right)
+        clip_sizes(r, &clip_left, &clip_right)
         if chrom != self.current_chrom:
             self.scope_left.clear()
             self.scope_right.clear()
@@ -1336,7 +1336,7 @@ cpdef tuple construct_graph(genome_scanner, infile, int max_dist, int clustering
                 pos2 = -1
                 left_clip_size = 0
                 right_clip_size = 0
-                clip_sizes_hard(r, left_clip_size, right_clip_size)  # soft and hard-clips
+                clip_sizes_hard(r, &left_clip_size, &right_clip_size)  # soft and hard-clips
                 if r.flag & 8 and clipped:  # paired by inference
                     # skip if both ends are clipped, usually means its a chunk of badly mapped sequence
                     # if not (left_clip_size and right_clip_size) and ((paired_end and good_quality_clip(r, 20)) or (not paired_end and) ):

dysgu/map_set_utils.pxd

@@ -294,9 +294,9 @@ cdef extern from "<map>" namespace "std" nogil:
 
 cdef int cigar_exists(r)
 
-cdef void clip_sizes(AlignedSegment r, int& left, int& right)
+cdef void clip_sizes(AlignedSegment r, int* left, int* right)
 
-cdef void clip_sizes_hard(AlignedSegment r, int& left, int& right)
+cdef void clip_sizes_hard(AlignedSegment r, int* left, int* right)
 
 cdef int cigar_clip(r, int clip_length)
 

dysgu/map_set_utils.pyx

@@ -246,7 +246,7 @@ cdef int cigar_exists(r):
     return 0
 
 
-cdef void clip_sizes(AlignedSegment r, int& left, int& right):
+cdef void clip_sizes(AlignedSegment r, int* left, int* right):
     cdef uint32_t cigar_value
     cdef uint32_t cigar_l
     cdef uint32_t *cigar_p
@@ -258,11 +258,11 @@ cdef void clip_sizes(AlignedSegment r, int& left, int& right):
     cigar_value = cigar_p[0]
     opp = <int> cigar_value & 15
     if opp == 4:
-        left = <int> cigar_value >> 4
+        left[0] = <int> cigar_value >> 4
     cigar_value = cigar_p[cigar_l - 1]
     opp = <int> cigar_value & 15
     if opp == 4:
-        right = <int> cigar_value >> 4
+        right[0] = <int> cigar_value >> 4
 
     # c = r.cigartuples
     # if not c:
@@ -278,7 +278,7 @@ cdef void clip_sizes(AlignedSegment r, int& left, int& right):
     # return left, right
 
 
-cdef void clip_sizes_hard(AlignedSegment r, int& left, int& right):
+cdef void clip_sizes_hard(AlignedSegment r, int* left, int* right):
     cdef uint32_t cigar_value
     cdef uint32_t cigar_l
     cdef uint32_t *cigar_p
@@ -291,11 +291,11 @@ cdef void clip_sizes_hard(AlignedSegment r, int& left, int& right):
     cigar_value = cigar_p[0]
     opp = <int> cigar_value & 15
     if opp == 4 or opp == 5:
-        left = <int> cigar_value >> 4
+        left[0] = <int> cigar_value >> 4
     cigar_value = cigar_p[cigar_l - 1]
     opp = <int> cigar_value & 15
     if opp == 4 or opp == 5:
-        right = <int> cigar_value >> 4
+        right[0] = <int> cigar_value >> 4
 
     # c = r.cigartuples
     # if not c: