xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-10-03 18:58:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

smaller memory requirement

Browse Source
This commit is contained in:
chhylp123
2022-05-12 16:15:58 -04:00
parent dd8888aa90
commit a2198891e7
8 changed files with 1345 additions and 2581 deletions
Download Patch File Download Diff File Expand all files Collapse all files
POA.cpp
+25 -38
View File
@@ -307,66 +307,53 @@ void addUnmatchedSeqToGraph(Graph* g, char* g_read_seq, long long g_read_length,
}
void addmatchedSeqToGraph(Graph* backbone, long long currentNodeID, char* x_string, long long x_length,
char* y_string, long long y_length, CIGAR* cigar, long long backbone_start, long long backbone_end)
char* y_string, long long y_length, window_list *cigar_idx, window_list_alloc *cigar_s, long long backbone_start, long long backbone_end)
{
int x_i, y_i, cigar_i;
x_i = 0;
y_i = 0;
cigar_i = 0;
int operation;
int operationLen;
int i;
int last_operation = -1;
int64_t x_i = 0, y_i = 0, c_i = 0, c_n = cigar_idx->clen;
uint32_t i, operLen; uint8_t oper; int8_t last_oper = -1;
// if(currentNodeID == 366 && x_length == 9 && y_length == 9) {
// fprintf(stderr, "[M::%s] currentNodeID::%lld, x_length::%lld, c_n::%ld, cidx::%u, cigar_s_n::%lld\n", __func__,
// currentNodeID, x_length, c_n, cigar_idx->cidx, (long long)cigar_s->c.n);
// }
///note that node 0 is the start node
///0 is match, 1 is mismatch, 2 is up, 3 is left
///2 mean y has more bases, while 3 means x has more bases
while (cigar_i < cigar->length)
{
operation = cigar->C_C[cigar_i];
operationLen = cigar->C_L[cigar_i];
for (c_i = 0; c_i < c_n; c_i++) {
get_cigar_cell(cigar_idx, cigar_s, c_i, &oper, &operLen);
///match/mismatch
if (operation == 0 || operation == 1)
{
for (i = 0; i < operationLen; i++)
{
// if(currentNodeID == 366 && x_length == 9 && y_length == 9) {
// fprintf(stderr, "[M::%s] c_i::%ld, oper::%u, operLen::%u, last_oper::%d\n", __func__, c_i, oper, operLen, last_oper);
// }
if (oper == 0 || oper == 1) { ///match/mismatch
for (i = 0; i < operLen; i++) {
///if the previous node is insertion, this node might be mismatch/match
add_mismatchEdge_weight(backbone, currentNodeID, y_string[y_i], last_operation);
x_i++;
y_i++;
currentNodeID++;
add_mismatchEdge_weight(backbone, currentNodeID, y_string[y_i], last_oper);
x_i++; y_i++; currentNodeID++;
}
}///insertion
else if (operation == 2)
{
} else if (oper == 2) { ///insertion
///the begin and end of cigar cannot be 2, so -1 is right here
///if (operationLen <= CORRECT_INDEL_LENGTH)
{
add_insertionEdge_weight(backbone, currentNodeID, y_string + y_i, operationLen);
add_insertionEdge_weight(backbone, currentNodeID, y_string + y_i, operLen);
backbone->g_nodes.list[currentNodeID].num_insertions++;
}
y_i += operationLen;
}
else if (operation == 3)
{
y_i += operLen;
} else if (oper == 3) {
///3 means x has more bases, that means backbone has more bases
///like a mismatch (-)
///if (operationLen <= CORRECT_INDEL_LENGTH)
{
add_deletionEdge_weight(backbone, currentNodeID, operationLen);
add_deletionEdge_weight(backbone, currentNodeID, operLen);
}
currentNodeID += operationLen;
x_i += operationLen;
currentNodeID += operLen;
x_i += operLen;
}
last_operation = operation;
cigar_i++;
last_oper = oper;
}
}