From 6078f7bba7b6d7d6055967e3970cf5cfd3a4a5c1 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Wed, 5 Jan 2011 22:10:28 -0500
Subject: [PATCH] Allowed 8 or 9 column GFF/GTF files. Many thanks to Michael
Hoffman.
---
src/utils/bedFile/bedFile.h | 106 +++++++++++++++++++++++++++---------
1 file changed, 79 insertions(+), 27 deletions(-)
diff --git a/src/utils/bedFile/bedFile.h b/src/utils/bedFile/bedFile.h
index ddf29d3d..8f26a024 100644
--- a/src/utils/bedFile/bedFile.h
+++ b/src/utils/bedFile/bedFile.h
@@ -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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