| 1002 |
|
int wlen=rlen; |
| 1003 |
|
GXSeqData seqdata; |
| 1004 |
|
int numruns=revCompl ? 2 : 1; |
| 1005 |
+ |
GList<GXAlnInfo> bestalns(true, true, false); |
| 1006 |
|
for (int ai=0;ai<adaptors5.Count();ai++) { |
| 1007 |
|
for (int r=0;r<numruns;r++) { |
| 1008 |
|
if (r) { |
| 1015 |
|
} |
| 1016 |
|
GXAlnInfo* aln=match_adaptor(seqdata, adaptors5[ai].trim_type, gxmem_l, 90); |
| 1017 |
|
if (aln) { |
| 1018 |
< |
trimmed=true; |
| 1018 |
> |
if (aln->strong) { |
| 1019 |
> |
trimmed=true; |
| 1020 |
> |
bestalns.Add(aln); |
| 1021 |
> |
break; //will check the rest next time |
| 1022 |
> |
} |
| 1023 |
> |
else bestalns.Add(aln); |
| 1024 |
> |
} |
| 1025 |
> |
} //forward and reverse? |
| 1026 |
> |
if (trimmed) break; //will check the rest in the next cycle |
| 1027 |
> |
}//for each 5' adaptor |
| 1028 |
> |
if (bestalns.Count()>0) { |
| 1029 |
> |
GXAlnInfo* aln=bestalns[0]; |
| 1030 |
|
if (aln->sl-1 > wlen-aln->sr) { |
| 1031 |
|
//keep left side |
| 1032 |
|
l3-=(wlen-aln->sl+1); |
| 1036 |
|
l5+=aln->sr; |
| 1037 |
|
if (l5>=rlen) l5=rlen-1; |
| 1038 |
|
} |
| 1039 |
< |
delete aln; |
| 1040 |
< |
if (l3-l5+1<min_read_len) return true; |
| 1039 |
> |
//delete aln; |
| 1040 |
> |
//if (l3-l5+1<min_read_len) return true; |
| 1041 |
|
wseq=seq.substr(l5,l3-l5+1); |
| 1042 |
|
wlen=wseq.length(); |
| 1043 |
< |
} |
| 1044 |
< |
} //forward and reverse? |
| 1045 |
< |
}//for each 5' adaptor |
| 1034 |
< |
return trimmed; |
| 1043 |
> |
return true; //break the loops here to report a good find |
| 1044 |
> |
} |
| 1045 |
> |
return false; |
| 1046 |
|
} |
| 1047 |
|
|
| 1048 |
|
//convert qvs to/from phred64 from/to phread33 |
