CommonHeader header;
readCommonHeader(in, header);
-
+
int count = 0;
+ mycount = 0;
//check magic number and version
if (header.magicNumber != 779314790) { m->mothurOut("Magic Number is not correct, not a valid .sff file"); m->mothurOutEndLine(); return count; }
}
count++;
+ mycount++;
//report progress
if((count+1) % 10000 == 0){ m->mothurOut(toString(count+1)); m->mothurOutEndLine(); }
int SffInfoCommand::decodeName(string& timestamp, string& region, string& xy, string name) {
try {
- string time = name.substr(0, 6);
- unsigned int timeNum = m->fromBase36(time);
-
- int q1 = timeNum / 60;
- int sec = timeNum - 60 * q1;
- int q2 = q1 / 60;
- int minute = q1 - 60 * q2;
- int q3 = q2 / 24;
- int hr = q2 - 24 * q3;
- int q4 = q3 / 32;
- int day = q3 - 32 * q4;
- int q5 = q4 / 13;
- int mon = q4 - 13 * q5;
- int year = 2000 + q5;
-
- timestamp = toString(year) + "_" + toString(mon) + "_" + toString(day) + "_" + toString(hr) + "_" + toString(minute) + "_" + toString(sec);
-
- region = name.substr(7, 2);
-
- string xyNum = name.substr(9);
- unsigned int myXy = m->fromBase36(xyNum);
- int x = myXy >> 12;
- int y = myXy & 4095;
-
- xy = toString(x) + "_" + toString(y);
+ if (name.length() >= 6) {
+ string time = name.substr(0, 6);
+ unsigned int timeNum = m->fromBase36(time);
+ int q1 = timeNum / 60;
+ int sec = timeNum - 60 * q1;
+ int q2 = q1 / 60;
+ int minute = q1 - 60 * q2;
+ int q3 = q2 / 24;
+ int hr = q2 - 24 * q3;
+ int q4 = q3 / 32;
+ int day = q3 - 32 * q4;
+ int q5 = q4 / 13;
+ int mon = q4 - 13 * q5;
+ int year = 2000 + q5;
+
+ timestamp = toString(year) + "_" + toString(mon) + "_" + toString(day) + "_" + toString(hr) + "_" + toString(minute) + "_" + toString(sec);
+ }
+
+ if (name.length() >= 9) {
+ region = name.substr(7, 2);
+
+ string xyNum = name.substr(9);
+ unsigned int myXy = m->fromBase36(xyNum);
+ int x = myXy >> 12;
+ int y = myXy & 4095;
+
+ xy = toString(x) + "_" + toString(y);
+ }
+
return 0;
}
catch(exception& e) {
if (trim) {
if(header.clipQualRight < header.clipQualLeft){
+ out << ">" << header.name << " xy=" << header.xy << endl;
out << "0\t0\t0\t0";
}
else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){