| 99 |
|
bool final_report = false) |
| 100 |
|
{ |
| 101 |
|
const vector<BowtieHit>& hits = hits_for_read.hits; |
| 102 |
+ |
|
| 103 |
+ |
if (hits.size() >= max_multihits * 5) |
| 104 |
+ |
return; |
| 105 |
+ |
|
| 106 |
|
for (size_t i = 0; i < hits.size(); ++i) |
| 107 |
|
{ |
| 108 |
|
if (hits[i].edit_dist() > max_read_mismatches) |
| 221 |
|
{ |
| 222 |
|
const vector<BowtieHit>& left = left_hits.hits; |
| 223 |
|
const vector<BowtieHit>& right = right_hits.hits; |
| 224 |
< |
|
| 224 |
> |
|
| 225 |
> |
if (left.size() >= max_multihits * 5 || right.size() >= max_multihits * 5) |
| 226 |
> |
return; |
| 227 |
> |
|
| 228 |
|
for (size_t i = 0; i < left.size(); ++i) |
| 229 |
|
{ |
| 230 |
|
if (left[i].edit_dist() > max_read_mismatches) continue; |
| 231 |
< |
|
| 231 |
> |
|
| 232 |
|
BowtieHit lh = left[i]; |
| 233 |
|
AlignStatus align_status(lh, gtf_junctions, |
| 234 |
|
junctions, insertions, deletions, fusions, coverage); |
| 268 |
|
} |
| 269 |
|
} |
| 270 |
|
} |
| 271 |
< |
|
| 271 |
> |
|
| 272 |
|
if ((report_secondary_alignments || !final_report) && best_hits.size() > 0) |
| 273 |
|
{ |
| 274 |
|
cmp_pair_alignment cmp(gtf_junctions); |
| 830 |
|
FusionSet& fusions, |
| 831 |
|
const FusionSet& fusions_ref = empty_fusions) |
| 832 |
|
{ |
| 833 |
+ |
if (!fusion_search) |
| 834 |
+ |
return; |
| 835 |
+ |
|
| 836 |
|
if (hits.hits.size() > fusion_multireads) |
| 837 |
|
return; |
| 838 |
|
|
| 942 |
|
update_junctions(best_hits, *junctions); |
| 943 |
|
update_insertions_and_deletions(best_hits, *insertions, *deletions); |
| 944 |
|
update_fusions(best_hits, *rt, *fusions); |
| 945 |
< |
|
| 945 |
> |
|
| 946 |
|
// Get next hit group |
| 947 |
|
l_hs.next_read_hits(curr_left_hit_group); |
| 948 |
|
curr_left_obs_order = it.observation_order(curr_left_hit_group.insert_id); |
| 1058 |
|
//if (!zpacker.empty()) left_um_fname+=".z"; |
| 1059 |
|
GBamWriter* left_um_out=new GBamWriter(left_um_fname.c_str(), sam_header.c_str()); |
| 1060 |
|
GBamWriter* right_um_out=NULL; |
| 1061 |
< |
|
| 1061 |
> |
|
| 1062 |
|
//if (left_um_out.openWrite(left_um_fname.c_str(), zpacker)==NULL) |
| 1063 |
|
// err_die("Error: cannot open file %s for writing!\n",left_um_fname.c_str()); |
| 1064 |
|
ReadStream right_reads_file(right_reads_fname); |
| 1333 |
|
right_um_out, false); |
| 1334 |
|
|
| 1335 |
|
|
| 1336 |
< |
// pclose (pipe close), which waits for a process to end, seems to conflict with boost::thread::join somehow, |
| 1337 |
< |
// resulting in deadlock like behavior. |
| 1336 |
> |
// pclose (pipe close), which waits for a process to end, seems to conflict with boost::thread::join somehow, |
| 1337 |
> |
// resulting in deadlock like behavior. |
| 1338 |
|
delete left_um_out; |
| 1339 |
|
delete right_um_out; |
| 1340 |
|
|
