From 5c3d96dba87db46c9a9e6a0de14a3d5e77b3424f Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Thu, 8 Dec 2011 15:36:27 -0500
Subject: [PATCH] Further nullBed tweaking.
---
src/intersectBed/intersectBed.cpp | 3 +--
src/utils/bedFile/bedFile.h | 13 ++++++++-----
src/utils/chromsweep/chromsweep.cpp | 28 +++++++++++++---------------
3 files changed, 22 insertions(+), 22 deletions(-)
diff --git a/src/intersectBed/intersectBed.cpp b/src/intersectBed/intersectBed.cpp
index 735fd8d7..3581bf2e 100644
--- a/src/intersectBed/intersectBed.cpp
+++ b/src/intersectBed/intersectBed.cpp
@@ -198,7 +198,7 @@ void BedIntersect::IntersectBed() {
vector<BED> hits;
hits.reserve(100);
- BED a, nullBed;
+ BED a;
// open the "A" file, process each BED entry and searh for overlaps.
_bedA->Open();
@@ -226,7 +226,6 @@ void BedIntersect::IntersectBed() {
}
}
}
- a = nullBed;
}
_bedA->Close();
}
diff --git a/src/utils/bedFile/bedFile.h b/src/utils/bedFile/bedFile.h
index 25475a32..c12066c3 100644
--- a/src/utils/bedFile/bedFile.h
+++ b/src/utils/bedFile/bedFile.h
@@ -481,6 +481,7 @@ private:
istream *_bedStream;
string _bedLine;
+ BED _nullBed;
string _header;
bool _firstLine;
vector<string> _bedFields;
@@ -509,14 +510,19 @@ private:
*/
template <typename T>
inline BedLineStatus parseLine (T &bed, const vector<string> &lineVector) {
-
+
+ // clear out the data from the last line.
+ bed = _nullBed;
unsigned int numFields = lineVector.size();
// bail out if we have a blank line
if (numFields == 0) {
return BED_BLANK;
}
-
+ // bail out if we have a comment line
+ if (lineVector[0].find("#") == 0) {
+ return BED_HEADER;
+ }
if (numFields >= 3) {
// line parsing for all lines after the first non-header line
@@ -623,7 +629,6 @@ private:
bed.name = lineVector[3];
bed.score = lineVector[4];
bed.strand = lineVector[5];
- bed.otherFields.clear();
for (unsigned int i = 6; i < lineVector.size(); ++i) {
bed.otherFields.push_back(lineVector[i]);
}
@@ -677,7 +682,6 @@ private:
}
if (this->bedType > 2) {
- bed.otherFields.clear();
for (unsigned int i = 2; i < numFields; ++i)
bed.otherFields.push_back(lineVector[i]);
}
@@ -717,7 +721,6 @@ private:
template <typename T>
inline bool parseGffLine (T &bed, const vector<string> &lineVector, int lineNum, unsigned int numFields) {
if (numFields == this->bedType) {
- bed.otherFields.clear();
if (this->bedType >= 8 && _isGff) {
bed.chrom = lineVector[0];
if (isInteger(lineVector[3]))
diff --git a/src/utils/chromsweep/chromsweep.cpp b/src/utils/chromsweep/chromsweep.cpp
index 70eac679..5027362e 100644
--- a/src/utils/chromsweep/chromsweep.cpp
+++ b/src/utils/chromsweep/chromsweep.cpp
@@ -62,19 +62,17 @@ ChromSweep::~ChromSweep(void) {
void ChromSweep::ScanCache() {
- if (_query->_status != BED_INVALID) {
- vector<BED>::iterator c = _cache.begin();
- while (c != _cache.end())
- {
- if ((_curr_qy.chrom == c->chrom) && !(after(_curr_qy, *c))) {
- if (IsValidHit(_curr_qy, *c)) {
- _hits.push_back(*c);
- }
- ++c;
- }
- else {
- c = _cache.erase(c);
+ vector<BED>::iterator c = _cache.begin();
+ while (c != _cache.end())
+ {
+ if ((_curr_qy.chrom == c->chrom) && !(after(_curr_qy, *c))) {
+ if (IsValidHit(_curr_qy, *c)) {
+ _hits.push_back(*c);
}
+ ++c;
+ }
+ else {
+ c = _cache.erase(c);
}
}
}
@@ -156,7 +154,6 @@ bool ChromSweep::Next(pair<BED, vector<BED> > &next) {
_results.push(make_pair(_curr_qy, _hits));
// reset for the next query
_hits.clear();
- _curr_qy = _nullBed;
_query->GetNextBed(_curr_qy, true);
_curr_chrom = _curr_qy.chrom;
}
@@ -167,7 +164,8 @@ bool ChromSweep::Next(pair<BED, vector<BED> > &next) {
_results.pop();
return true;
}
- // otherwise, the party is over.
- else {return false;}
+ else {
+ return false;
+ }
}
--
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