10 using namespace shogun;
35 memcpy(
m_all_pos, all_pos, len*
sizeof(int32_t));
39 SG_ERROR(
"IntronList: Out of mem 1");
61 if (end_pos[k]<end_pos[k-1])
62 SG_ERROR(
"end pos array is not sorted: end_pos[k-1]:%i end_pos[k]:%i\n", end_pos[k-1], end_pos[k]);
72 ASSERT(start_pos[k]<end_pos[k]);
79 SG_ERROR(
"IntronList: Out of mem 4");
80 new_list[from_list_len]= start_pos[k];
87 ASSERT(q_list_len==from_list_len);
90 SG_ERROR(
"IntronList: Out of mem 5");
91 new_list[q_list_len]= quality[k];
114 int32_t coverage = 0;
116 for (
int i=1;i<from_list[0]; i++)
122 coverage = coverage+1;
126 values[0] = coverage;