| 370 |
|
} |
| 371 |
|
#ifdef GDEBUG |
| 372 |
|
GMessage(" After trimming:\n"); |
| 373 |
< |
GMessage("<==%s\n",rseq.chars()); |
| 373 |
> |
GMessage("%s\n",rseq.chars()); |
| 374 |
|
#endif |
| 375 |
|
writeRead(f_out, seqid, seqinfo, rseq, rqv, outcounter); |
| 376 |
|
} |
| 834 |
|
maxloc=loc; |
| 835 |
|
} |
| 836 |
|
} |
| 837 |
+ |
li=maxloc.pos; |
| 838 |
|
if ((maxloc.score>poly_minScore && ri>=rlen-3) || |
| 839 |
|
(maxloc.score==poly_minScore && ri==rlen-1) || |
| 840 |
|
(maxloc.score>(poly_minScore<<1) && ri>=rlen-6)) { |
| 841 |
< |
l5=li; |
| 842 |
< |
l3=ri; |
| 841 |
> |
//trimming this li-ri match at 3' end |
| 842 |
> |
l3=li-1; |
| 843 |
> |
if (l3<0) l3=0; |
| 844 |
|
return true; |
| 845 |
|
} |
| 846 |
|
return false; |
| 908 |
|
maxloc=loc; |
| 909 |
|
} |
| 910 |
|
} |
| 911 |
< |
|
| 911 |
> |
ri=maxloc.pos; |
| 912 |
|
if ((maxloc.score==poly_minScore && li==0) || |
| 913 |
|
(maxloc.score>poly_minScore && li<2) |
| 914 |
|
|| (maxloc.score>(poly_minScore<<1) && li<6)) { |
| 915 |
< |
l5=li; |
| 916 |
< |
l3=ri; |
| 915 |
> |
//adjust l5 to reflect this trimming of 5' end |
| 916 |
> |
l5=ri+1; |
| 917 |
> |
if (l5>rlen-1) l5=rlen-1; |
| 918 |
|
return true; |
| 919 |
|
} |
| 920 |
|
return false; |
| 1039 |
|
return true; |
| 1040 |
|
} |
| 1041 |
|
|
| 1042 |
+ |
#ifdef GDEBUG |
| 1043 |
+ |
void showTrim(GStr& s, int l5, int l3) { |
| 1044 |
+ |
if (l5>0) { |
| 1045 |
+ |
color_bg(c_red); |
| 1046 |
+ |
} |
| 1047 |
+ |
for (int i=0;i<s.length()-1;i++) { |
| 1048 |
+ |
if (i && i==l5) color_resetbg(); |
| 1049 |
+ |
fprintf(stderr, "%c", s[i]); |
| 1050 |
+ |
if (i==l3) color_bg(c_red); |
| 1051 |
+ |
} |
| 1052 |
+ |
fprintf(stderr, "%c", s[s.length()-1]); |
| 1053 |
+ |
color_reset(); |
| 1054 |
+ |
fprintf(stderr, "\n"); |
| 1055 |
+ |
} |
| 1056 |
+ |
#endif |
| 1057 |
+ |
|
| 1058 |
|
char process_read(GStr& rname, GStr& rseq, GStr& rqv, int &l5, int &l3) { |
| 1059 |
|
//returns 0 if the read was untouched, 1 if it was just trimmed |
| 1060 |
|
// and a trash code if it was trashed |
| 1062 |
|
l3=rseq.length()-1; |
| 1063 |
|
#ifdef GDEBUG |
| 1064 |
|
GMessage(">%s\n", rname.chars()); |
| 1065 |
< |
GMessage("==>%s\n",rseq.chars()); |
| 1065 |
> |
GMessage("%s\n",rseq.chars()); |
| 1066 |
|
#endif |
| 1067 |
|
if (l3-l5+1<min_read_len) { |
| 1068 |
|
return 's'; |
| 1104 |
|
trim_code=0; |
| 1105 |
|
if (trim_poly5(wseq, w5, w3, polyA_seed)) { |
| 1106 |
|
trim_code='A'; |
| 1088 |
– |
#ifdef GDEBUG |
| 1089 |
– |
GMessage("\t-trimmed poly-A at 5' end\n"); |
| 1090 |
– |
#endif |
| 1107 |
|
} |
| 1108 |
|
else if (trim_poly5(wseq, w5, w3, polyT_seed)) { |
| 1109 |
|
trim_code='T'; |
| 1094 |
– |
#ifdef GDEBUG |
| 1095 |
– |
GMessage("\t-trimmed poly-T at 5' end\n"); |
| 1096 |
– |
#endif |
| 1110 |
|
} |
| 1111 |
|
else if (trim_adapter5(wseq, w5, w3)) { |
| 1112 |
|
trim_code='5'; |
| 1100 |
– |
#ifdef GDEBUG |
| 1101 |
– |
GMessage("\t-trimmed adapter at 5' end\n"); |
| 1102 |
– |
#endif |
| 1113 |
|
} |
| 1114 |
|
if (trim_code) { |
| 1115 |
+ |
#ifdef GDEBUG |
| 1116 |
+ |
GMessage("#### TRIM by '%c' code ( w5-w3 = %d-%d ):\n",trim_code, w5,w3); |
| 1117 |
+ |
showTrim(wseq, w5, w3); |
| 1118 |
+ |
#endif |
| 1119 |
|
int trimlen=wseq.length()-(w3-w5+1); |
| 1120 |
|
num_trimmed5++; |
| 1121 |
|
if (trimlen<min_trimmed5) |
| 1144 |
|
trim_code='3'; |
| 1145 |
|
} |
| 1146 |
|
if (trim_code) { |
| 1147 |
+ |
#ifdef GDEBUG |
| 1148 |
+ |
GMessage("#### TRIM by '%c' code ( w5-w3 = %d-%d ):\n",trim_code, w5,w3); |
| 1149 |
+ |
showTrim(wseq, w5, w3); |
| 1150 |
+ |
#endif |
| 1151 |
|
int trimlen=wseq.length()-(w3-w5+1); |
| 1152 |
|
num_trimmed3++; |
| 1153 |
|
if (trimlen<min_trimmed3) |
