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Commit 6078f7bb authored by Aaron's avatar Aaron
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Allowed 8 or 9 column GFF/GTF files. Many thanks to Michael Hoffman.

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src/utils/bedFile/bedFile.h
+ 79
− 27
View file @ 6078f7bb
......@@ -460,7 +460,7 @@ private:
if (parseVcfLine(bed, lineVector, lineNum, numFields) == true) return BED_VALID;
}
// it's GFF, assuming columns columns 4 and 5 are numeric and we have 9 fields total.
else if ((numFields == 9) && isInteger(lineVector[3]) && isInteger(lineVector[4])) {
else if ((numFields >= 8) && isInteger(lineVector[3]) && isInteger(lineVector[4])) {
setGff(true);
setFileType(GFF_FILETYPE);
setBedType(numFields); // we now expect numFields columns in each line
......@@ -612,7 +612,7 @@ private:
template <typename T>
inline bool parseGffLine (T &bed, const vector<string> &lineVector, int lineNum, unsigned int numFields) {
if (numFields == this->bedType) {
if (this->bedType == 9 && _isGff) {
if (this->bedType >= 8 && _isGff) {
bed.chrom = lineVector[0];
// substract 1 to force the start to be BED-style
bed.start = atoi(lineVector[3].c_str()) - 1;
......@@ -622,11 +622,13 @@ private:
bed.strand = lineVector[6].c_str();
bed.otherFields.push_back(lineVector[1]); // add GFF "source". unused in BED
bed.otherFields.push_back(lineVector[7]); // add GFF "fname". unused in BED
bed.otherFields.push_back(lineVector[8]); // add GFF "group". unused in BED
// handle the optional 9th field.
if (this->bedType == 9)
bed.otherFields.push_back(lineVector[8]); // add GFF "group". unused in BED
}
else {
cerr << "Error: unexpected number of fields at line: " << lineNum <<
". Verify that your files are TAB-delimited and that your GFF file has 9 fields. Exiting..." << endl;
". Verify that your files are TAB-delimited and that your GFF file has 8 or 9 fields. Exiting..." << endl;
exit(1);
}
if (bed.start > bed.end) {
......@@ -647,8 +649,8 @@ private:
cerr << "Differing number of GFF fields encountered at line: " << lineNum << ". Exiting..." << endl;
exit(1);
}
else if ((numFields < 9) && (numFields != 0)) {
cerr << "TAB delimited GFF file with 9 fields is required at line: "<< lineNum << ". Exiting..." << endl;
else if ((numFields < 8) && (numFields != 0)) {
cerr << "TAB delimited GFF file with 8 or 9 fields is required at line: "<< lineNum << ". Exiting..." << endl;
exit(1);
}
return false;
......@@ -704,11 +706,21 @@ public:
}
}
// GFF
else if (this->bedType == 9) {
printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t%s\t", bed.chrom.c_str(), bed.otherFields[0].c_str(),
bed.name.c_str(), bed.start+1, bed.end,
bed.score.c_str(), bed.strand.c_str(),
bed.otherFields[1].c_str(), bed.otherFields[2].c_str());
else if (_isGff == true) {
// "GFF-8"
if (this->bedType == 8) {
printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t", bed.chrom.c_str(), bed.otherFields[0].c_str(),
bed.name.c_str(), bed.start+1, bed.end,
bed.score.c_str(), bed.strand.c_str(),
bed.otherFields[1].c_str());
}
// "GFF-9"
else if (this->bedType == 9) {
printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t%s\t", bed.chrom.c_str(), bed.otherFields[0].c_str(),
bed.name.c_str(), bed.start+1, bed.end,
bed.score.c_str(), bed.strand.c_str(),
bed.otherFields[1].c_str(), bed.otherFields[2].c_str());
}
}
}
......@@ -762,12 +774,22 @@ public:
}
printf("\n");
}
//GFF
else if (this->bedType == 9) {
printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t%s\n", bed.chrom.c_str(), bed.otherFields[0].c_str(),
bed.name.c_str(), bed.start+1, bed.end,
bed.score.c_str(), bed.strand.c_str(),
bed.otherFields[1].c_str(), bed.otherFields[2].c_str());
// GFF
else if (_isGff == true) {
// "GFF-8"
if (this->bedType == 8) {
printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\n", bed.chrom.c_str(), bed.otherFields[0].c_str(),
bed.name.c_str(), bed.start+1, bed.end,
bed.score.c_str(), bed.strand.c_str(),
bed.otherFields[1].c_str());
}
// "GFF-9"
else if (this->bedType == 9) {
printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t%s\n", bed.chrom.c_str(), bed.otherFields[0].c_str(),
bed.name.c_str(), bed.start+1, bed.end,
bed.score.c_str(), bed.strand.c_str(),
bed.otherFields[1].c_str(), bed.otherFields[2].c_str());
}
}
}
......@@ -821,11 +843,21 @@ public:
}
}
// GFF
else if (this->bedType == 9) {
printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t%s\t", bed.chrom.c_str(), bed.otherFields[0].c_str(),
else if (_isGff == true) {
// "GFF-8"
if (this->bedType == 8) {
printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t", bed.chrom.c_str(), bed.otherFields[0].c_str(),
bed.name.c_str(), start+1, end,
bed.score.c_str(), bed.strand.c_str(),
bed.otherFields[1].c_str());
}
// "GFF-9"
else if (this->bedType == 9) {
printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t%s\t", bed.chrom.c_str(), bed.otherFields[0].c_str(),
bed.name.c_str(), start+1, end,
bed.score.c_str(), bed.strand.c_str(),
bed.otherFields[1].c_str(), bed.otherFields[2].c_str());
}
}
}
......@@ -881,11 +913,21 @@ public:
printf("\n");
}
// GFF
else if (this->bedType == 9) { // add 1 to the start for GFF
printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t%s\n", bed.chrom.c_str(), bed.otherFields[0].c_str(),
else if (_isGff == true) {
// "GFF-9"
if (this->bedType == 8) {
printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\n", bed.chrom.c_str(), bed.otherFields[0].c_str(),
bed.name.c_str(), start+1, end,
bed.score.c_str(), bed.strand.c_str(),
bed.otherFields[1].c_str());
}
// "GFF-8"
else if (this->bedType == 9) {
printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t%s\n", bed.chrom.c_str(), bed.otherFields[0].c_str(),
bed.name.c_str(), start+1, end,
bed.score.c_str(), bed.strand.c_str(),
bed.otherFields[1].c_str(), bed.otherFields[2].c_str());
}
}
}
......@@ -895,7 +937,7 @@ public:
*/
void reportNullBedTab() {
if (_isGff == false) {
if (_isGff == false && _isVcf == false) {
if (this->bedType == 3) {
printf (".\t-1\t-1\t");
}
......@@ -915,8 +957,13 @@ public:
}
}
}
else if (this->bedType == 9) {
printf (".\t.\t.\t-1\t-1\t-1\t.\t.\t.\t");
else if (_isGff == true && _isVcf == false) {
if (this->bedType == 8) {
printf (".\t.\t.\t-1\t-1\t-1\t.\t.\t");
}
else if (this->bedType == 9) {
printf (".\t.\t.\t-1\t-1\t-1\t.\t.\t.\t");
}
}
}
......@@ -926,7 +973,7 @@ public:
*/
void reportNullBedNewLine() {
if (_isGff == false) {
if (_isGff == false && _isVcf == false) {
if (this->bedType == 3) {
printf (".\t-1\t-1\n");
}
......@@ -947,8 +994,13 @@ public:
printf("\n");
}
}
else if (this->bedType == 9) {
printf (".\t.\t.\t-1\t-1\t-1\t.\t.\t.\n");
else if (_isGff == true && _isVcf == false) {
if (this->bedType == 8) {
printf (".\t.\t.\t-1\t-1\t-1\t.\t.\n");
}
else if (this->bedType == 9) {
printf (".\t.\t.\t-1\t-1\t-1\t.\t.\t.\n");
}
}
}
......
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