From 0df75e5e40b2b9ad9c44b113e1422b065b92d330 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Wed, 26 Oct 2011 09:39:02 -0400
Subject: [PATCH] reserve space up front for chromsweep
---
src/intersectBed/intersectBed.cpp | 1 +
src/utils/chromsweep/chromsweep.cpp | 53 ++++++++++++++---------------
src/utils/chromsweep/chromsweep.h | 1 +
3 files changed, 27 insertions(+), 28 deletions(-)
diff --git a/src/intersectBed/intersectBed.cpp b/src/intersectBed/intersectBed.cpp
index 83f402d9..de7bd74b 100644
--- a/src/intersectBed/intersectBed.cpp
+++ b/src/intersectBed/intersectBed.cpp
@@ -232,6 +232,7 @@ void BedIntersect::IntersectBed() {
ChromSweep sweep = ChromSweep(_bedA, _bedB, _sameStrand, _diffStrand);
pair<BED, vector<BED> > hit_set;
+ hit_set.second.reserve(10000);
while (sweep.Next(hit_set)) {
processHits(hit_set.first, hit_set.second);
}
diff --git a/src/utils/chromsweep/chromsweep.cpp b/src/utils/chromsweep/chromsweep.cpp
index d13c3e2f..e4dcf560 100644
--- a/src/utils/chromsweep/chromsweep.cpp
+++ b/src/utils/chromsweep/chromsweep.cpp
@@ -49,8 +49,8 @@ ChromSweep::ChromSweep(string &bedAFile, string &bedBFile)
_qy_lineNum = 0;
_db_lineNum = 0;
- _hits.reserve(1000);
- _cache.reserve(1000);
+ _hits.reserve(100000);
+ _cache.reserve(100000);
_bedA = new BedFile(bedAFile);
_bedB = new BedFile(bedBFile);
@@ -76,18 +76,8 @@ void ChromSweep::ScanCache() {
while (c != _cache.end())
{
if ((_curr_qy.chrom == c->chrom) && !(after(_curr_qy, *c))) {
- if (overlaps(_curr_qy.start, _curr_qy.end, c->start, c->end) > 0) {
- bool strands_are_same = (_curr_qy.strand == c->strand);
- // test for necessary strandedness
- if ( (_sameStrand == false && _diffStrand == false)
- ||
- (_sameStrand == true && strands_are_same == true)
- ||
- (_diffStrand == true && strands_are_same == false)
- )
- {
- _hits.push_back(*c);
- }
+ if (IsValidHit(_curr_qy, *c)) {
+ _hits.push_back(*c);
}
++c;
}
@@ -99,7 +89,7 @@ void ChromSweep::ScanCache() {
}
-bool ChromSweep::ChromChange()
+bool ChromSweep::ChromChange()
{
// the files are on the same chrom
if ((_curr_qy.chrom == _curr_db.chrom) || (_db_status == BED_INVALID) || (_qy_status == BED_INVALID)) {
@@ -135,6 +125,24 @@ bool ChromSweep::ChromChange()
}
}
+bool ChromSweep::IsValidHit(const BED &query, const BED &db) {
+ // do we have an overlap in the DB?
+ if (overlaps(query.start, query.end, db.start, db.end) > 0) {
+ // Now test for necessary strandedness.
+ bool strands_are_same = (query.strand == db.strand);
+ if ( (_sameStrand == false && _diffStrand == false)
+ ||
+ (_sameStrand == true && strands_are_same == true)
+ ||
+ (_diffStrand == true && strands_are_same == false)
+ )
+ {
+ return true;
+ }
+ }
+ return false;
+}
+
bool ChromSweep::Next(pair<BED, vector<BED> > &next) {
if (!_bedA->Empty()) {
@@ -145,19 +153,8 @@ bool ChromSweep::Next(pair<BED, vector<BED> > &next) {
// advance the db until we are ahead of the query. update hits and cache as necessary
while (!_bedB->Empty() && _curr_qy.chrom == _curr_db.chrom && !(after(_curr_db, _curr_qy)))
{
- // do we have an overlap in the DB?
- if (overlaps(_curr_qy.start, _curr_qy.end, _curr_db.start, _curr_db.end) > 0) {
- // Now test for necessary strandedness.
- bool strands_are_same = (_curr_qy.strand == _curr_db.strand);
- if ( (_sameStrand == false && _diffStrand == false)
- ||
- (_sameStrand == true && strands_are_same == true)
- ||
- (_diffStrand == true && strands_are_same == false)
- )
- {
- _hits.push_back(_curr_db);
- }
+ if (IsValidHit(_curr_qy, _curr_db)) {
+ _hits.push_back(_curr_db);
}
_cache.push_back(_curr_db);
_db_status = _bedB->GetNextBed(_curr_db, _db_lineNum);
diff --git a/src/utils/chromsweep/chromsweep.h b/src/utils/chromsweep/chromsweep.h
index c3246116..af5f6798 100644
--- a/src/utils/chromsweep/chromsweep.h
+++ b/src/utils/chromsweep/chromsweep.h
@@ -83,6 +83,7 @@ private:
void ScanCache();
bool ChromChange();
+ bool IsValidHit(const BED &query, const BED &db);
};
#endif /* CHROMSWEEP_H */
--
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