| 154 |
|
|
| 155 |
|
void writePrepBam(GBamWriter* wbam, Read& read, uint32_t rid, char trashcode=0) { |
| 156 |
|
if (wbam==NULL) return; |
| 157 |
< |
string rname; |
| 158 |
< |
str_appendInt(rname,rid); |
| 159 |
< |
GBamRecord bamrec(rname.c_str(), -1, 0, false, read.seq.c_str(), NULL, read.qual.c_str()); |
| 160 |
< |
bamrec.add_aux("ZN", 'Z',read.name.length(),(uint8_t*)read.name.c_str()); |
| 157 |
> |
string rnum; |
| 158 |
> |
str_appendInt(rnum,rid); |
| 159 |
> |
string rname(read.name); |
| 160 |
> |
size_t pl=rname.length()-1; |
| 161 |
> |
GBamRecord bamrec(rnum.c_str(), -1, 0, false, read.seq.c_str(), NULL, read.qual.c_str()); |
| 162 |
> |
int matenum=0; |
| 163 |
> |
if (rname[pl-1]=='/') { |
| 164 |
> |
if (rname[pl]=='1') { |
| 165 |
> |
bamrec.set_flag(BAM_FREAD1); |
| 166 |
> |
matenum=1; |
| 167 |
> |
} |
| 168 |
> |
else if (rname[pl]=='2') { |
| 169 |
> |
bamrec.set_flag(BAM_FREAD2); |
| 170 |
> |
matenum=2; |
| 171 |
> |
} |
| 172 |
> |
if (matenum) rname.resize(pl-1); |
| 173 |
> |
} |
| 174 |
> |
|
| 175 |
> |
bamrec.add_aux("ZN", 'Z',read.name.length(),(uint8_t*)rname.c_str()); |
| 176 |
|
if (trashcode) { |
| 177 |
|
bamrec.set_flag(BAM_FQCFAIL); |
| 178 |
|
bamrec.add_aux("ZT", 'A', 1, (uint8_t*)&trashcode); |
| 281 |
|
// Chuck the read if there are at least 5 'N's or if it's mostly |
| 282 |
|
// (>90%) 'N's and 'A's |
| 283 |
|
char trash_code=0; |
| 284 |
< |
if (percent_A > 0.9 || |
| 285 |
< |
percent_C > 0.9 || |
| 286 |
< |
percent_G > 0.9 || |
| 287 |
< |
percent_T > 0.9) |
| 284 |
> |
if (percent_A > 0.8 || |
| 285 |
> |
percent_C > 0.8 || |
| 286 |
> |
percent_G > 0.8 || |
| 287 |
> |
percent_T > 0.8) |
| 288 |
|
trash_code='L'; |
| 289 |
|
else if (percent_N >= 0.1 || percent_4 >=0.1) |
| 290 |
|
trash_code='N'; |
