From 821bb784fd58b41a267cca36864a5f61bb974b81 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Tue, 30 Oct 2012 13:00:24 -0400
Subject: [PATCH] 80 char width
---
src/utils/bedFile/bedFile.h | 402 ++++++++++++++++++++++++------------
1 file changed, 273 insertions(+), 129 deletions(-)
diff --git a/src/utils/bedFile/bedFile.h b/src/utils/bedFile/bedFile.h
index d2b323fd..ac65eaab 100644
--- a/src/utils/bedFile/bedFile.h
+++ b/src/utils/bedFile/bedFile.h
@@ -150,7 +150,8 @@ public:
// BEDALL
BED(string chrom, CHRPOS start, CHRPOS end, string name,
- string score, string strand, vector<string> fields, vector<uint16_t> other_idxs)
+ string score, string strand, vector<string> fields,
+ vector<uint16_t> other_idxs)
: chrom(chrom),
start(start),
end(end),
@@ -323,7 +324,9 @@ BIN getBin(CHRPOS start, CHRPOS end) {
start >>= _binNextShift;
end >>= _binNextShift;
}
- cerr << "start " << start << ", end " << end << " out of range in findBin (max is 512M)" << endl;
+ cerr << "start " << start << ", end " << end
+ << " out of range in findBin (max is 512M)"
+ << endl;
return 0;
}
@@ -406,17 +409,21 @@ public:
// Get the next BED entry in an opened BED file.
bool GetNextBed (BED &bed, bool forceSorted = false);
- // Returns the next MERGED (i.e., non-overlapping) interval in an opened BED file
+ // Returns the next MERGED (i.e., non-overlapping) interval in
+ // an opened BED file
// NOTE: assumes input file is sorted by chrom then start
bool GetNextMergedBed(BED &merged_bed);
- // load a BED file into a map keyed by chrom, then bin. value is vector of BEDs
+ // load a BED file into a map keyed by chrom, then bin. value is
+ // vector of BEDs
void loadBedFileIntoMap();
- // load a BED file into a map keyed by chrom, then bin. value is vector of BEDCOVs
+ // load a BED file into a map keyed by chrom, then bin. value is
+ // vector of BEDCOVs
void loadBedCovFileIntoMap();
- // load a BED file into a map keyed by chrom, then bin. value is vector of BEDCOVLISTs
+ // load a BED file into a map keyed by chrom, then bin. value is
+ // vector of BEDCOVLISTs
void loadBedCovListFileIntoMap();
// load a BED file into a map keyed by chrom. value is vector of BEDs
@@ -438,19 +445,22 @@ public:
// Given a chrom, start, end and strand for a single feature,
// increment a the number of hits for each feature in B file
// that the feature overlaps
- void countHits(const BED &a, bool sameStrand = false, bool diffStrand = false, bool countsOnly = false);
+ void countHits(const BED &a, bool sameStrand = false,
+ bool diffStrand = false, bool countsOnly = false);
// same as above, but has special logic that processes a set of
// BED "blocks" from a single entry so as to avoid over-counting
// each "block" of a single BAM/BED12 as distinct coverage. That is,
// if one read has four block, we only want to count the coverage as
// coming from one read, not four.
- void countSplitHits(const vector<BED> &bedBlock, bool sameStrand = false, bool diffStrand = false, bool countsOnly = false);
+ void countSplitHits(const vector<BED> &bedBlock, bool sameStrand = false,
+ bool diffStrand = false, bool countsOnly = false);
// Given a chrom, start, end and strand for a single feature,
// increment a the number of hits for each feature in B file
// that the feature overlaps
- void countListHits(const BED &a, int index, bool sameStrand, bool diffStrand);
+ void countListHits(const BED &a, int index,
+ bool sameStrand, bool diffStrand);
// the bedfile with which this instance is associated
string bedFile;
@@ -467,6 +477,7 @@ public:
BedLineStatus _status;
int _lineNum;
+
private:
// data
@@ -530,11 +541,18 @@ private:
if (_typeIsKnown == true) {
switch(_fileType) {
case BED_FILETYPE:
- if (parseBedLine(bed, lineVector, _lineNum, numFields) == true) return BED_VALID;
+ if (parseBedLine(bed, lineVector,
+ _lineNum, numFields) == true)
+ {return BED_VALID;}
+
case VCF_FILETYPE:
- if (parseVcfLine(bed, lineVector, _lineNum, numFields) == true) return BED_VALID;
+ if (parseVcfLine(bed, lineVector,
+ _lineNum, numFields) == true)
+ {return BED_VALID;}
case GFF_FILETYPE:
- if (parseGffLine(bed, lineVector, _lineNum, numFields) == true) return BED_VALID;
+ if (parseGffLine(bed, lineVector,
+ _lineNum, numFields) == true)
+ {return BED_VALID;}
default:
printf("ERROR: file type encountered. Exiting\n");
exit(1);
@@ -547,7 +565,8 @@ private:
setGff(false);
setZeroBased(true);
setFileType(BED_FILETYPE);
- setBedType(numFields); // we now expect numFields columns in each line
+ // we now expect numFields columns in each line
+ setBedType(numFields);
// test to see if the file has true blocked BED12 records
if (numFields == 12) {
@@ -563,34 +582,61 @@ private:
}
else setBed12(false);
}
- if (parseBedLine(bed, lineVector, _lineNum, numFields) == true) return BED_VALID;
+ if (parseBedLine(bed, lineVector,
+ _lineNum, numFields) == true)
+ {
+ return BED_VALID;
+ }
}
- // it's VCF, assuming the second column is numeric and there are at least 8 fields.
+ // it's VCF, assuming the second column is numeric and
+ // there are at least 8 fields.
else if (isInteger(lineVector[1]) && numFields >= 8) {
setGff(false);
setVcf(true);
setZeroBased(false);
setFileType(VCF_FILETYPE);
- setBedType(numFields); // we now expect numFields columns in each line
- if (parseVcfLine(bed, lineVector, _lineNum, numFields) == true) return BED_VALID;
+ // we now expect numFields columns in each line
+ setBedType(numFields);
+ 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 >= 8) && isInteger(lineVector[3]) && isInteger(lineVector[4])) {
+ // it's GFF, assuming columns columns 4 and 5 are numeric
+ // and we have 9 fields total.
+ else if ((numFields >= 8) &&
+ isInteger(lineVector[3]) &&
+ isInteger(lineVector[4]))
+ {
setGff(true);
setZeroBased(false);
setFileType(GFF_FILETYPE);
- setBedType(numFields); // we now expect numFields columns in each line
- if (parseGffLine(bed, lineVector, _lineNum, numFields) == true) return BED_VALID;
+ // we now expect numFields columns in each line
+ setBedType(numFields);
+ if (parseGffLine(bed, lineVector,
+ _lineNum, numFields) == true)
+ {
+ return BED_VALID;
+ }
}
else {
- cerr << "Unexpected file format. Please use tab-delimited BED, GFF, or VCF. " <<
- "Perhaps you have non-integer starts or ends at line " << _lineNum << "?" << endl;
+ cerr << "Unexpected file format. "
+ << "Please use tab-delimited BED, GFF, or VCF. "
+ << "Perhaps you have non-integer starts or ends "
+ << "at line "
+ << _lineNum
+ << "?"
+ << endl;
exit(1);
}
}
}
else {
- cerr << "It looks as though you have less than 3 columns at line: " << _lineNum << ". Are you sure your files are tab-delimited?" << endl;
+ cerr << "It looks as though you have less than 3 columns at line: "
+ << _lineNum
+ << ". Are you sure your files are tab-delimited?"
+ << endl;
exit(1);
}
// default
@@ -602,8 +648,9 @@ private:
parseBedLine: converts a lineVector into either BED or BEDCOV (templated, hence in header to avoid linker issues.)
*/
template <typename T>
- inline bool parseBedLine (T &bed, const vector<string> &lineVector, int _lineNum, unsigned int numFields) {
-
+ inline bool parseBedLine (T &bed, const vector<string> &lineVector,
+ int _lineNum, unsigned int numFields)
+ {
// process as long as the number of fields in this
// line matches what we expect for this file.
if (numFields == this->bedType) {
@@ -612,13 +659,19 @@ private:
int i;
i = atoi(lineVector[1].c_str());
if (i<0) {
- cerr << "Error: malformed BED entry at line " << _lineNum << ". Start Coordinate detected that is < 0. Exiting." << endl;
+ cerr << "Error: malformed BED entry at line "
+ << _lineNum
+ << ". Start Coordinate detected that is < 0. Exiting."
+ << endl;
exit(1);
}
bed.start = (CHRPOS)i;
i = atoi(lineVector[2].c_str());
if (i<0) {
- cerr << "Error: malformed BED entry at line " << _lineNum << ". End Coordinate detected that is < 0. Exiting." << endl;
+ cerr << "Error: malformed BED entry at line "
+ << _lineNum
+ << ". End Coordinate detected that is < 0. Exiting."
+ << endl;
exit(1);
}
bed.end = (CHRPOS)i;
@@ -651,8 +704,11 @@ private:
}
}
else if (this->bedType != 3) {
- cerr << "Error: unexpected number of fields at line: " << _lineNum
- << ". Verify that your files are TAB-delimited. Exiting..." << endl;
+ cerr << "Error: unexpected number of fields at line: "
+ << _lineNum
+ << ". Verify that your files are TAB-delimited. "
+ << "Exiting..."
+ << endl;
exit(1);
}
@@ -661,20 +717,33 @@ private:
return true;
}
else {
- cerr << "Error: malformed BED entry at line " << _lineNum << ". Start was greater than end. Exiting." << endl;
+ cerr << "Error: malformed BED entry at line "
+ << _lineNum
+ << ". Start was greater than end. Exiting."
+ << endl;
exit(1);
}
}
else if (numFields == 1) {
- cerr << "Only one BED field detected: " << _lineNum << ". Verify that your files are TAB-delimited. Exiting..." << endl;
+ cerr << "Only one BED field detected: "
+ << _lineNum
+ << ". Verify that your files are TAB-delimited. Exiting..."
+ << endl;
exit(1);
}
else if ((numFields != this->bedType) && (numFields != 0)) {
- cerr << "Differing number of BED fields encountered at line: " << _lineNum << ". Exiting..." << endl;
+ cerr << "Differing number of BED fields encountered at line: "
+ << _lineNum
+ << ". Exiting..."
+ << endl;
exit(1);
}
else if ((numFields < 3) && (numFields != 0)) {
- cerr << "TAB delimited BED file with at least 3 fields (chrom, start, end) is required at line: "<< _lineNum << ". Exiting..." << endl;
+ cerr << "TAB delimited BED file with at least 3 fields"
+ << " (chrom, start, end) is required at line: "
+ << _lineNum
+ << ". Exiting..."
+ << endl;
exit(1);
}
return false;
@@ -685,12 +754,16 @@ private:
parseVcfLine: converts a lineVector into either BED or BEDCOV (templated, hence in header to avoid linker issues.)
*/
template <typename T>
- inline bool parseVcfLine (T &bed, const vector<string> &lineVector, int _lineNum, unsigned int numFields) {
+ inline bool parseVcfLine (T &bed, const vector<string> &lineVector,
+ int _lineNum, unsigned int numFields)
+ {
if (numFields == this->bedType) {
bed.fields = lineVector;
bed.chrom = lineVector[0];
- bed.start = atoi(lineVector[1].c_str()) - 1; // VCF is one-based
- bed.end = bed.start + lineVector[3].size(); // VCF 4.0 stores the size of the affected REF allele.
+ // VCF is one-based
+ bed.start = atoi(lineVector[1].c_str()) - 1;
+ // VCF 4.0 stores the size of the affected REF allele.
+ bed.end = bed.start + lineVector[3].size();
bed.strand = "+";
// construct the name from the ref and alt alleles.
// if it's an annotated variant, add the rsId as well.
@@ -708,24 +781,41 @@ private:
return true;
}
else if (bed.start > bed.end) {
- cerr << "Error: malformed VCF entry at line " << _lineNum << ". Start was greater than end. Exiting." << endl;
+ cerr << "Error: malformed VCF entry at line "
+ << _lineNum
+ << ". Start was greater than end. Exiting."
+ << endl;
exit(1);
}
else if ( (bed.start < 0) || (bed.end < 0) ) {
- cerr << "Error: malformed VCF entry at line " << _lineNum << ". Coordinate detected that is < 0. Exiting." << endl;
+ cerr << "Error: malformed VCF entry at line "
+ << _lineNum << ". Coordinate detected that is < 0. "
+ << "Exiting."
+ << endl;
exit(1);
}
}
else if (numFields == 1) {
- cerr << "Only one VCF field detected: " << _lineNum << ". Verify that your files are TAB-delimited. Exiting..." << endl;
+ cerr << "Only one VCF field detected: "
+ << _lineNum
+ << ". Verify that your files are TAB-delimited. "
+ << "Exiting..."
+ << endl;
exit(1);
}
else if ((numFields != this->bedType) && (numFields != 0)) {
- cerr << "Differing number of VCF fields encountered at line: " << _lineNum << ". Exiting..." << endl;
+ cerr << "Differing number of VCF fields encountered at line: "
+ << _lineNum
+ << ". Exiting..."
+ << endl;
exit(1);
}
else if ((numFields < 2) && (numFields != 0)) {
- cerr << "TAB delimited VCF file with at least 2 fields (chrom, pos) is required at line: "<< _lineNum << ". Exiting..." << endl;
+ cerr << "TAB delimited VCF file with at least 2 fields "
+ << "(chrom, pos) is required at line: "
+ << _lineNum
+ << ". Exiting..."
+ << endl;
exit(1);
}
return false;
@@ -737,7 +827,9 @@ private:
parseGffLine: converts a lineVector into either BED or BEDCOV (templated, hence in header to avoid linker issues.)
*/
template <typename T>
- inline bool parseGffLine (T &bed, const vector<string> &lineVector, int lineNum, unsigned int numFields) {
+ inline bool parseGffLine (T &bed, const vector<string> &lineVector,
+ int lineNum, unsigned int numFields)
+ {
if (numFields == this->bedType) {
bed.fields = lineVector;
if (this->bedType >= 8 && _isGff) {
@@ -749,38 +841,60 @@ private:
bed.name = lineVector[2];
bed.score = lineVector[5];
bed.strand = lineVector[6].c_str();
- bed.other_idxs.push_back(1); // add GFF "source". unused in BED
- bed.other_idxs.push_back(7); // add GFF "fname". unused in BED
+ // add GFF "source". unused in BED
+ bed.other_idxs.push_back(1);
+ // add GFF "fname". unused in BED
+ bed.other_idxs.push_back(7);
// handle the optional 9th field.
if (this->bedType == 9)
- bed.other_idxs.push_back(8); // add GFF "group". unused in BED
+ // add GFF "group". unused in BED
+ bed.other_idxs.push_back(8);
bed.start--;
}
else {
- cerr << "Error: unexpected number of fields at line: " << lineNum <<
- ". Verify that your files are TAB-delimited and that your GFF file has 8 or 9 fields. Exiting..." << endl;
+ cerr << "Error: unexpected number of fields at line: "
+ << lineNum
+ << ". 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) {
- cerr << "Error: malformed GFF entry at line " << lineNum << ". Start was greater than end. Exiting." << endl;
+ cerr << "Error: malformed GFF entry at line "
+ << lineNum
+ << ". Start was greater than end. Exiting."
+ << endl;
exit(1);
}
if ( (bed.start < 0) || (bed.end < 0) ) {
- cerr << "Error: malformed GFF entry at line " << lineNum << ". Coordinate detected that is < 1. Exiting." << endl;
+ cerr << "Error: malformed GFF entry at line "
+ << lineNum
+ << ". Coordinate detected that is < 1. Exiting."
+ << endl;
exit(1);
}
return true;
}
else if (numFields == 1) {
- cerr << "Only one GFF field detected: " << lineNum << ". Verify that your files are TAB-delimited. Exiting..." << endl;
+ cerr << "Only one GFF field detected: "
+ << lineNum
+ << ". Verify that your files are TAB-delimited. Exiting..."
+ << endl;
exit(1);
}
else if ((numFields != this->bedType) && (numFields != 0)) {
- cerr << "Differing number of GFF fields encountered at line: " << lineNum << ". Exiting..." << endl;
+ cerr << "Differing number of GFF fields encountered at line: "
+ << lineNum
+ << ". Exiting..."
+ << endl;
exit(1);
}
else if ((numFields < 8) && (numFields != 0)) {
- cerr << "TAB delimited GFF file with 8 or 9 fields is required at line: "<< lineNum << ". Exiting..." << endl;
+ cerr << "TAB delimited GFF file with 8 or 9 fields is required"
+ << " at line: "
+ << lineNum
+ << ". Exiting..."
+ << endl;
exit(1);
}
return false;
@@ -815,21 +929,28 @@ public:
printf ("%s\t%d\t%d\t", bed.chrom.c_str(), start, end);
}
else if (this->bedType == 4) {
- printf ("%s\t%d\t%d\t%s\t", bed.chrom.c_str(), start, end, bed.name.c_str());
+ printf ("%s\t%d\t%d\t%s\t",
+ bed.chrom.c_str(), start, end, bed.name.c_str());
}
else if (this->bedType == 5) {
- printf ("%s\t%d\t%d\t%s\t%s\t", bed.chrom.c_str(), start, end, bed.name.c_str(),
- bed.score.c_str());
+ printf ("%s\t%d\t%d\t%s\t%s\t",
+ bed.chrom.c_str(), start, end,
+ bed.name.c_str(), bed.score.c_str());
}
else if (this->bedType == 6) {
- printf ("%s\t%d\t%d\t%s\t%s\t%s\t", bed.chrom.c_str(), start, end, bed.name.c_str(),
- bed.score.c_str(), bed.strand.c_str());
+ printf ("%s\t%d\t%d\t%s\t%s\t%s\t",
+ bed.chrom.c_str(), start, end,
+ bed.name.c_str(), bed.score.c_str(), bed.strand.c_str());
}
else if (this->bedType > 6) {
- printf ("%s\t%d\t%d\t%s\t%s\t%s\t", bed.chrom.c_str(), start, end, bed.name.c_str(),
- bed.score.c_str(), bed.strand.c_str());
- vector<uint16_t>::const_iterator othIt = bed.other_idxs.begin();
- vector<uint16_t>::const_iterator othEnd = bed.other_idxs.end();
+ printf ("%s\t%d\t%d\t%s\t%s\t%s\t",
+ bed.chrom.c_str(), start, end, bed.name.c_str(),
+ bed.score.c_str(), bed.strand.c_str());
+
+ vector<uint16_t>::const_iterator
+ othIt = bed.other_idxs.begin();
+ vector<uint16_t>::const_iterator
+ othEnd = bed.other_idxs.end();
for ( ; othIt != othEnd; ++othIt) {
printf("%s\t", bed.fields[*othIt].c_str());
}
@@ -849,18 +970,19 @@ public:
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.fields[bed.other_idxs[0]].c_str(),
- bed.name.c_str(), start+1, end,
- bed.score.c_str(), bed.strand.c_str(),
- bed.fields[bed.other_idxs[1]].c_str());
+ printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t",
+ bed.chrom.c_str(), bed.fields[bed.other_idxs[0]].c_str(),
+ bed.name.c_str(), start+1, end, bed.score.c_str(),
+ bed.strand.c_str(), bed.fields[bed.other_idxs[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.fields[bed.other_idxs[0]].c_str(),
- bed.name.c_str(), start+1, end,
- bed.score.c_str(), bed.strand.c_str(),
- bed.fields[bed.other_idxs[1]].c_str(),
- bed.fields[bed.other_idxs[2]].c_str());
+ printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t%s\t",
+ bed.chrom.c_str(), bed.fields[bed.other_idxs[0]].c_str(),
+ bed.name.c_str(), start+1, end,
+ bed.score.c_str(), bed.strand.c_str(),
+ bed.fields[bed.other_idxs[1]].c_str(),
+ bed.fields[bed.other_idxs[2]].c_str());
}
}
}
@@ -893,22 +1015,28 @@ public:
printf ("%s\t%d\t%d\n", bed.chrom.c_str(), start, end);
}
else if (this->bedType == 4) {
- printf ("%s\t%d\t%d\t%s\n", bed.chrom.c_str(), start, end, bed.name.c_str());
+ printf ("%s\t%d\t%d\t%s\n",
+ bed.chrom.c_str(), start, end, bed.name.c_str());
}
else if (this->bedType == 5) {
- printf ("%s\t%d\t%d\t%s\t%s\n", bed.chrom.c_str(), start, end, bed.name.c_str(),
- bed.score.c_str());
+ printf ("%s\t%d\t%d\t%s\t%s\n",
+ bed.chrom.c_str(), start, end,
+ bed.name.c_str(), bed.score.c_str());
}
else if (this->bedType == 6) {
- printf ("%s\t%d\t%d\t%s\t%s\t%s\n", bed.chrom.c_str(), start, end, bed.name.c_str(),
- bed.score.c_str(), bed.strand.c_str());
+ printf ("%s\t%d\t%d\t%s\t%s\t%s\n",
+ bed.chrom.c_str(), start, end, bed.name.c_str(),
+ bed.score.c_str(), bed.strand.c_str());
}
else if (this->bedType > 6) {
- printf ("%s\t%d\t%d\t%s\t%s\t%s", bed.chrom.c_str(), start, end, bed.name.c_str(),
- bed.score.c_str(), bed.strand.c_str());
-
- vector<uint16_t>::const_iterator othIt = bed.other_idxs.begin();
- vector<uint16_t>::const_iterator othEnd = bed.other_idxs.end();
+ printf ("%s\t%d\t%d\t%s\t%s\t%s",
+ bed.chrom.c_str(), start, end, bed.name.c_str(),
+ bed.score.c_str(), bed.strand.c_str());
+
+ vector<uint16_t>::const_iterator
+ othIt = bed.other_idxs.begin();
+ vector<uint16_t>::const_iterator
+ othEnd = bed.other_idxs.end();
for ( ; othIt != othEnd; ++othIt) {
printf("\t%s", bed.fields[*othIt].c_str());
}
@@ -930,24 +1058,24 @@ public:
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.fields[bed.other_idxs[0]].c_str(),
- bed.name.c_str(), start+1, end,
- bed.score.c_str(), bed.strand.c_str(),
- bed.fields[bed.other_idxs[1]].c_str());
+ printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\n",
+ bed.chrom.c_str(), bed.fields[bed.other_idxs[0]].c_str(),
+ bed.name.c_str(), start+1, end,
+ bed.score.c_str(), bed.strand.c_str(),
+ bed.fields[bed.other_idxs[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.fields[bed.other_idxs[0]].c_str(),
- bed.name.c_str(), start+1, end,
- bed.score.c_str(), bed.strand.c_str(),
- bed.fields[bed.other_idxs[1]].c_str(),
- bed.fields[bed.other_idxs[2]].c_str());
+ printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t%s\n",
+ bed.chrom.c_str(), bed.fields[bed.other_idxs[0]].c_str(),
+ bed.name.c_str(), start+1, end,
+ bed.score.c_str(), bed.strand.c_str(),
+ bed.fields[bed.other_idxs[1]].c_str(),
+ bed.fields[bed.other_idxs[2]].c_str());
}
}
}
-
-
/*
reportBedRangeNewLine
@@ -971,21 +1099,28 @@ public:
printf ("%s\t%d\t%d\t", bed.chrom.c_str(), start, end);
}
else if (this->bedType == 4) {
- printf ("%s\t%d\t%d\t%s\t", bed.chrom.c_str(), start, end, bed.name.c_str());
+ printf ("%s\t%d\t%d\t%s\t",
+ bed.chrom.c_str(), start, end, bed.name.c_str());
}
else if (this->bedType == 5) {
- printf ("%s\t%d\t%d\t%s\t%s\t", bed.chrom.c_str(), start, end, bed.name.c_str(),
- bed.score.c_str());
+ printf ("%s\t%d\t%d\t%s\t%s\t",
+ bed.chrom.c_str(), start, end,
+ bed.name.c_str(), bed.score.c_str());
}
else if (this->bedType == 6) {
- printf ("%s\t%d\t%d\t%s\t%s\t%s\t", bed.chrom.c_str(), start, end, bed.name.c_str(),
- bed.score.c_str(), bed.strand.c_str());
+ printf ("%s\t%d\t%d\t%s\t%s\t%s\t",
+ bed.chrom.c_str(), start, end, bed.name.c_str(),
+ bed.score.c_str(), bed.strand.c_str());
}
else if (this->bedType > 6) {
- printf ("%s\t%d\t%d\t%s\t%s\t%s\t", bed.chrom.c_str(), start, end, bed.name.c_str(),
- bed.score.c_str(), bed.strand.c_str());
- vector<uint16_t>::const_iterator othIt = bed.other_idxs.begin();
- vector<uint16_t>::const_iterator othEnd = bed.other_idxs.end();
+ printf ("%s\t%d\t%d\t%s\t%s\t%s\t",
+ bed.chrom.c_str(), start, end, bed.name.c_str(),
+ bed.score.c_str(), bed.strand.c_str());
+
+ vector<uint16_t>::const_iterator
+ othIt = bed.other_idxs.begin();
+ vector<uint16_t>::const_iterator
+ othEnd = bed.other_idxs.end();
for ( ; othIt != othEnd; ++othIt) {
printf("%s\t", bed.fields[*othIt].c_str());
}
@@ -1004,18 +1139,20 @@ public:
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.fields[bed.other_idxs[0]].c_str(),
- bed.name.c_str(), start+1, end,
- bed.score.c_str(), bed.strand.c_str(),
- bed.fields[bed.other_idxs[1]].c_str());
+ printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t",
+ bed.chrom.c_str(), bed.fields[bed.other_idxs[0]].c_str(),
+ bed.name.c_str(), start+1, end,
+ bed.score.c_str(), bed.strand.c_str(),
+ bed.fields[bed.other_idxs[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.fields[bed.other_idxs[0]].c_str(),
- bed.name.c_str(), start+1, end,
- bed.score.c_str(), bed.strand.c_str(),
- bed.fields[bed.other_idxs[1]].c_str(),
- bed.fields[bed.other_idxs[2]].c_str());
+ printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t%s\t",
+ bed.chrom.c_str(), bed.fields[bed.other_idxs[0]].c_str(),
+ bed.name.c_str(), start+1, end,
+ bed.score.c_str(), bed.strand.c_str(),
+ bed.fields[bed.other_idxs[1]].c_str(),
+ bed.fields[bed.other_idxs[2]].c_str());
}
}
}
@@ -1046,22 +1183,28 @@ public:
printf ("%s\t%d\t%d\n", bed.chrom.c_str(), start, end);
}
else if (this->bedType == 4) {
- printf ("%s\t%d\t%d\t%s\n", bed.chrom.c_str(), start, end, bed.name.c_str());
+ printf ("%s\t%d\t%d\t%s\n",
+ bed.chrom.c_str(), start, end, bed.name.c_str());
}
else if (this->bedType == 5) {
- printf ("%s\t%d\t%d\t%s\t%s\n", bed.chrom.c_str(), start, end, bed.name.c_str(),
- bed.score.c_str());
+ printf ("%s\t%d\t%d\t%s\t%s\n",
+ bed.chrom.c_str(), start, end,
+ bed.name.c_str(), bed.score.c_str());
}
else if (this->bedType == 6) {
- printf ("%s\t%d\t%d\t%s\t%s\t%s\n", bed.chrom.c_str(), start, end, bed.name.c_str(),
- bed.score.c_str(), bed.strand.c_str());
+ printf ("%s\t%d\t%d\t%s\t%s\t%s\n",
+ bed.chrom.c_str(), start, end, bed.name.c_str(),
+ bed.score.c_str(), bed.strand.c_str());
}
else if (this->bedType > 6) {
- printf ("%s\t%d\t%d\t%s\t%s\t%s", bed.chrom.c_str(), start, end, bed.name.c_str(),
- bed.score.c_str(), bed.strand.c_str());
-
- vector<uint16_t>::const_iterator othIt = bed.other_idxs.begin();
- vector<uint16_t>::const_iterator othEnd = bed.other_idxs.end();
+ printf ("%s\t%d\t%d\t%s\t%s\t%s",
+ bed.chrom.c_str(), start, end, bed.name.c_str(),
+ bed.score.c_str(), bed.strand.c_str());
+
+ vector<uint16_t>::const_iterator
+ othIt = bed.other_idxs.begin();
+ vector<uint16_t>::const_iterator
+ othEnd = bed.other_idxs.end();
for ( ; othIt != othEnd; ++othIt) {
printf("\t%s", bed.fields[*othIt].c_str());
}
@@ -1082,18 +1225,19 @@ public:
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.fields[bed.other_idxs[0]].c_str(),
- bed.name.c_str(), start+1, end,
- bed.score.c_str(), bed.strand.c_str(),
- bed.fields[bed.other_idxs[1]].c_str());
+ printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\n",
+ bed.chrom.c_str(), bed.fields[bed.other_idxs[0]].c_str(),
+ bed.name.c_str(), start+1, end,
+ bed.score.c_str(), bed.strand.c_str(), bed.fields[bed.other_idxs[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.fields[bed.other_idxs[0]].c_str(),
- bed.name.c_str(), start+1, end,
- bed.score.c_str(), bed.strand.c_str(),
- bed.fields[bed.other_idxs[1]].c_str(),
- bed.fields[bed.other_idxs[2]].c_str());
+ printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t%s\n",
+ bed.chrom.c_str(), bed.fields[bed.other_idxs[0]].c_str(),
+ bed.name.c_str(), start+1, end,
+ bed.score.c_str(), bed.strand.c_str(),
+ bed.fields[bed.other_idxs[1]].c_str(),
+ bed.fields[bed.other_idxs[2]].c_str());
}
}
}
--
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