diff --git a/bin/coverageBed b/bin/coverageBed
index 3f9086fe300f9409f985f2c0b89f7e01561c096d..6ee16e6ef711715bda3a8f81732120d8247f5115 100755
Binary files a/bin/coverageBed and b/bin/coverageBed differ
diff --git a/bin/windowBed b/bin/windowBed
index a8047ab1f7133f2136476956490a683761d65767..0432862f09d5d3e93a0b871ce8045ca2455eb016 100755
Binary files a/bin/windowBed and b/bin/windowBed differ
diff --git a/obj/bedFile.o b/obj/bedFile.o
index 677732840635a3d2c8010733f735c461e5dc04d0..63bdc5d40ec60ccd1463a783a9481ed25c825b7a 100644
Binary files a/obj/bedFile.o and b/obj/bedFile.o differ
diff --git a/obj/coverageBed.o b/obj/coverageBed.o
index d06f390598f3a5fd967228e9d62dcf704b6c9c67..795a5a9733910bcdedb9665c3dc359c73b829fb4 100644
Binary files a/obj/coverageBed.o and b/obj/coverageBed.o differ
diff --git a/obj/coverageMain.o b/obj/coverageMain.o
index 3abada83c36e08187f4d1bc9676e90c36284872e..3c9d29313fecb8571879892c04cee1fa6d346348 100644
Binary files a/obj/coverageMain.o and b/obj/coverageMain.o differ
diff --git a/obj/lineFileUtilities.o b/obj/lineFileUtilities.o
index 64bf51a50e59e402409a9245a6cf4d74a08f53dc..631ef944a81a79b8ab415f90d1734efd8c94ee78 100644
Binary files a/obj/lineFileUtilities.o and b/obj/lineFileUtilities.o differ
diff --git a/obj/windowBed.o b/obj/windowBed.o
index 035265a30a33f863bc4bc1e1507e2ddd27cabbad..facaff63abac2a58b946a155fa13dc8b45e463f3 100644
Binary files a/obj/windowBed.o and b/obj/windowBed.o differ
diff --git a/obj/windowMain.o b/obj/windowMain.o
index f170f6166eda2ca3cac4ac3aae49aafa5bada8ca..b9a16ed7294b69b4758ea933f2250ab8ead4d30a 100644
Binary files a/obj/windowMain.o and b/obj/windowMain.o differ
diff --git a/src/closestBed/b.bed b/src/closestBed/b.bed
index 807c0cd01f2c9c9841060c2adca918f19ab7c102..9b0e3730019c266cdf3a5f07ae54d772d289598b 100644
--- a/src/closestBed/b.bed
+++ b/src/closestBed/b.bed
@@ -1,3 +1,5 @@
chr1 20000 30000 geneA 100 +
chr1 20000 30000 geneB 100 -
-
+chr1 19999 30000 geneC 100 +
+chr1 80 90 geneD 100 +
+chr1 112 1000 geneE 100 +
diff --git a/src/closestBed/closestBed.cpp b/src/closestBed/closestBed.cpp
index e3d0bb6997f109aa5300aebb30a61a0f1bd8ff13..07aeaa87cabb700b1c8f150718d71439c6c48758 100755
--- a/src/closestBed/closestBed.cpp
+++ b/src/closestBed/closestBed.cpp
@@ -83,51 +83,39 @@ void BedClosest::FindWindowOverlaps(BED &a, vector<BED> &hits) {
while ((numOverlaps == 0) && (slop <= MAXSLOP)) {
- if ((a.start - slop) > 0) {
- aFudgeStart = a.start - slop;
- }
- else {
- aFudgeStart = 0;
- }
- if ((a.start + slop) < 2 * MAXSLOP) {
- aFudgeEnd = a.end + slop;
- }
- else {
- aFudgeEnd = 2 * MAXSLOP;
- }
+ // add some slop (starting at 0 bases) to a in hopes
+ // of finding a hit in B
+ if ((a.start - slop) > 0) aFudgeStart = a.start - slop;
+ else aFudgeStart = 0;
+
+ if ((a.start + slop) < 2 * MAXSLOP) aFudgeEnd = a.end + slop;
+ else aFudgeEnd = 2 * MAXSLOP;
- bedB->binKeeperFind(bedB->bedMap[a.chrom], aFudgeStart, aFudgeEnd, hits);
+ bedB->FindOverlapsPerBin(a.chrom, aFudgeStart, aFudgeEnd, a.strand, hits, this->forceStrand);
- for (vector<BED>::iterator h = hits.begin(); h != hits.end(); ++h) {
-
- // if forcing strandedness, move on if the hit
- // is not on the same strand as A.
- if ((this->forceStrand) && (a.strand != h->strand)) {
- continue; // continue force the next iteration of the for loop.
- }
-
+ vector<BED>::const_iterator h = hits.begin();
+ vector<BED>::const_iterator hitsEnd = hits.end();
+ for (; h != hitsEnd; ++h) {
+
numOverlaps++;
// do the actual features overlap?
int s = max(a.start, h->start);
int e = min(a.end, h->end);
-
+ int overlapBases = (e - s); // the number of overlapping bases b/w a and b
+ int aLength = (a.end - a.start); // the length of a in b.p.
+
if (s < e) {
-
// is there enough overlap (default ~ 1bp)
- float overlap = (float)(e-s) / (float)(a.end - a.start);
-
- if ( overlap > 0 ) {
-
+ float overlap = (float) overlapBases / (float) aLength;
+ if ( overlap > 0 ) {
// is this hit the closest?
if (overlap > maxOverlap) {
closestB.clear();
closestB.push_back(*h);
maxOverlap = overlap;
}
- else if (overlap == maxOverlap) {
- closestB.push_back(*h);
- }
+ else if (overlap == maxOverlap) closestB.push_back(*h);
}
}
else if (h->end < a.start){
@@ -136,9 +124,7 @@ void BedClosest::FindWindowOverlaps(BED &a, vector<BED> &hits) {
closestB.push_back(*h);
minDistance = a.start - h->end;
}
- else if ((a.start - h->end) == minDistance) {
- closestB.push_back(*h);
- }
+ else if ((a.start - h->end) == minDistance) closestB.push_back(*h);
}
else {
if ((h->start - a.end) < minDistance) {
@@ -146,16 +132,11 @@ void BedClosest::FindWindowOverlaps(BED &a, vector<BED> &hits) {
closestB.push_back(*h);
minDistance = h->start - a.end;
}
- else if ((h->start - a.end) == minDistance) {
- closestB.push_back(*h);
- }
+ else if ((h->start - a.end) == minDistance) closestB.push_back(*h);
}
-
}
- /* if no overlaps were found, we'll
- widen the range by SLOPGROWTH in each direction
- and search again.
- */
+ // if no overlaps were found, we'll widen the range
+ // by SLOPGROWTH in each direction and search again.
slop += SLOPGROWTH;
}
}
diff --git a/src/coverageBed/a.bed b/src/coverageBed/a.bed
index 85f3053569196656a50374b959849c6fa916139b..0f5d644c0ea294599ab8dd2c494404ea8243b36d 100644
--- a/src/coverageBed/a.bed
+++ b/src/coverageBed/a.bed
@@ -1,5 +1,5 @@
-chr1 10 20
-chr1 20 30
-chr1 30 40
-chr1 100 200
+chr1 10 20 a1 1 -
+chr1 20 30 a2 1 -
+chr1 30 40 a3 1 -
+chr1 100 200 a4 1 +
diff --git a/src/coverageBed/b.bed b/src/coverageBed/b.bed
index 771446e580ea023462e0dd0c72efb1a06aef6b64..d881601d94bd1bca15c0760d353537965c164cf7 100644
--- a/src/coverageBed/b.bed
+++ b/src/coverageBed/b.bed
@@ -1,3 +1,3 @@
-chr1 0 100
-chr1 100 200
-chr2 0 100
+chr1 0 100 b1 1 +
+chr1 100 200 b2 1 -
+chr2 0 100 b3 1 +
diff --git a/src/coverageBed/coverageBed.cpp b/src/coverageBed/coverageBed.cpp
index 388122e49c7601b11bc06496858e4648a6ebaef8..d7d6f94954faf74fbe595f986e7c45aa3329bc80 100755
--- a/src/coverageBed/coverageBed.cpp
+++ b/src/coverageBed/coverageBed.cpp
@@ -40,7 +40,6 @@ void BedCoverage::GetCoverage(istream &bedInput) {
string bedLine;
int lineNum = 0; // current input line number
vector<string> bedFields; // vector for a BED entry
-
bedFields.reserve(12);
// process each entry in A
@@ -49,55 +48,76 @@ void BedCoverage::GetCoverage(istream &bedInput) {
lineNum++;
Tokenize(bedLine,bedFields);
BED a;
-
- // find the overlaps with B if it's a valid BED entry.
- if (bedA->parseLine(a, bedFields, lineNum)) {
-
- // increment the count of overlaps for each feature in B that
- // overlaps the current A interval
- bedB->countHits(bedB->bedMap[a.chrom], a, this->forceStrand);
+
+ if (bedA->parseLine(a, bedFields, lineNum)) {
+ // count a as a hit with all the relevant features in B
+ bedB->countHits(a, this->forceStrand);
}
// reset for the next input line
bedFields.clear();
}
- // now, report the count of hist for each feature in B.
- for (masterBedMap::iterator c = bedB->bedMap.begin(); c != bedB->bedMap.end(); ++c) {
- map<int, vector<BED> > bin2Beds = c->second;
-
- for (map<int, vector<BED> >::iterator b = bin2Beds.begin(); b != bin2Beds.end(); ++b) {
-
- vector<BED> beds = b->second;
- for (unsigned int i = 0; i < beds.size(); i++) {
-
+ //vector<int> depths; // track the discrete depths for each base in B
+ // used to calculate, min, max, median, etc.
+
+ // now, report the count of hits for each feature in B.
+ masterBedMap::const_iterator chromItr = bedB->bedMap.begin();
+ masterBedMap::const_iterator chromEnd = bedB->bedMap.end();
+ for (; chromItr != chromEnd; ++chromItr) {
+
+ binsToBeds::const_iterator binItr = chromItr->second.begin();
+ binsToBeds::const_iterator binEnd = chromItr->second.end();
+ for (; binItr != binEnd; ++binItr) {
+
+ vector<BED>::const_iterator bedItr = binItr->second.begin();
+ vector<BED>::const_iterator bedEnd = binItr->second.end();
+ for (; bedItr != bedEnd; ++bedItr) {
+
int zeroDepthCount = 0;
int depth = 0;
+ int start = min(bedItr->minOverlapStart, bedItr->start);
- int start = min(beds[i].minOverlapStart, beds[i].start);
-
- for (int pos = start+1; pos <= beds[i].end; pos++) {
-
- if (beds[i].depthMap.find(pos) != beds[i].depthMap.end()) {
- depth += beds[i].depthMap[pos].starts;
+ for (int pos = start+1; pos <= bedItr->end; pos++) {
+
+ if (bedItr->depthMap.find(pos) != bedItr->depthMap.end()) {
+
+ map<unsigned int, DEPTH> dMap = bedItr->depthMap;
+ depth += dMap[pos].starts;
+ //depths.push_back(depth);
- if ((depth == 0) && (pos > beds[i].start) && (pos <= beds[i].end)) {
+ if ((depth == 0) && (pos > bedItr->start) && (pos <= bedItr->end)) {
zeroDepthCount++;
}
- depth = depth - beds[i].depthMap[pos].ends;
+ depth = depth - dMap[pos].ends;
}
else {
- if ((depth == 0) && (pos > beds[i].start) && (pos <= beds[i].end)) {
+ if ((depth == 0) && (pos > bedItr->start) && (pos <= bedItr->end)) {
zeroDepthCount++;
}
+ //depths.push_back(depth);
}
}
// Report the coverage for the current interval.
- int length = beds[i].end - beds[i].start;
-
- bedB->reportBedTab(beds[i]);
- printf("%d\t%d\t%d\t%0.7f\n", beds[i].count, (length-zeroDepthCount), length, (float) (length-zeroDepthCount)/length);
+ int length = bedItr->end - bedItr->start;
+ int nonZeroBases = (length-zeroDepthCount);
+ float fractCovered = (float) nonZeroBases /length;
+ //sort(depths.begin(), depths.end());
+
+ bedB->reportBedTab(*bedItr);
+ printf("%d\t%d\t%d\t%0.7f\n", bedItr->count, nonZeroBases, length, fractCovered);
+ /*
+ cout << bedItr->count << "\t";
+ cout << (length-zeroDepthCount) << "\t";
+ cout << length << "\t";
+ cout << setw (10);
+ cout << fractCovered << "\t";
+ cout << *min_element(depths.begin(), depths.end()) << "\t";
+ cout << *max_element(depths.begin(), depths.end()) << "\t";
+ cout << *(depths.begin()+depths.size()/2) << "\n";
+ depths.clear();
+ */
}
}
}
diff --git a/src/coverageBed/coverageBed.h b/src/coverageBed/coverageBed.h
index e4654e646e2b0936b8f8922f356243b58e77c8e5..25d340a0a033e643344272701aa419d788b69604 100755
--- a/src/coverageBed/coverageBed.h
+++ b/src/coverageBed/coverageBed.h
@@ -14,7 +14,9 @@
#include "bedFile.h"
#include <vector>
+#include <algorithm>
#include <iostream>
+#include <iomanip>
#include <fstream>
#include <stdlib.h>
diff --git a/src/coverageBed/coverageMain.cpp b/src/coverageBed/coverageMain.cpp
index 7fb04ef2b886ac1768960a573f4135342366c278..81b6f230a10acadeaae4d59483a22ed510509355 100755
--- a/src/coverageBed/coverageMain.cpp
+++ b/src/coverageBed/coverageMain.cpp
@@ -103,6 +103,11 @@ void ShowHelp(void) {
cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
+ cerr << "Options: " << endl;
+ cerr << "\t-s\t" << "Force strandedness. That is, only include hits in A that" << endl;
+ cerr << "\t\toverlap B on the same strand." << endl;
+ cerr << "\t\t- By default, hits are included without respect to strand." << endl << endl;
+
cerr << "Output: " << endl;
cerr << "\t" << " After each entry in B, reports: " << endl;
cerr << "\t 1) The number of features in A that overlapped the B interval." << endl;
diff --git a/src/coverageBed/new b/src/coverageBed/new
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/src/intersectBed/chr21.genes.bed b/src/intersectBed/chr21.genes.bed
new file mode 100644
index 0000000000000000000000000000000000000000..73d1706a4f45c164f05860a00d5edecaffe4fdaf
--- /dev/null
+++ b/src/intersectBed/chr21.genes.bed
@@ -0,0 +1,828 @@
+chr21 9928613 10012791 uc002yip.1 24 -
+chr21 9928613 10012791 uc002yiq.1 23 -
+chr21 9928613 10012791 uc002yir.1 22 -
+chr21 9928613 10012791 uc010gkv.1 19 -
+chr21 9928613 10061300 uc002yis.1 33 -
+chr21 10042683 10120808 uc002yiu.1 9 -
+chr21 10042683 10120796 uc002yit.1 10 -
+chr21 10079666 10120808 uc002yiv.1 4 -
+chr21 10080031 10081687 uc002yiw.1 2 -
+chr21 10081660 10120796 uc002yix.2 3 -
+chr21 13332351 13346202 uc002yiy.2 5 +
+chr21 13336975 13346202 uc002yiz.2 4 +
+chr21 13361138 13412440 uc002yja.2 3 +
+chr21 13904368 13935777 uc002yjb.1 11 +
+chr21 13944438 13944477 uc002yjc.1 1 +
+chr21 13945076 13945106 uc002yjd.1 1 +
+chr21 13973491 13975330 uc002yje.1 1 -
+chr21 14137333 14142556 uc002yjf.1 6 -
+chr21 14200023 14200052 uc002yjg.1 1 +
+chr21 14202070 14202096 uc002yjh.1 1 -
+chr21 14237966 14274631 uc002yji.1 6 -
+chr21 14270940 14274631 uc002yjj.2 2 -
+chr21 14321612 14438647 uc002yjk.2 3 +
+chr21 14321612 14438730 uc002yjl.2 3 +
+chr21 14403005 14501125 uc002yjm.1 10 -
+chr21 14459414 14483611 uc010gkw.1 4 -
+chr21 14510336 14522564 uc002yjp.2 4 +
+chr21 14510336 14522564 uc002yjn.2 5 +
+chr21 14510336 14522564 uc002yjo.2 5 +
+chr21 14567990 14585577 uc002yjq.1 5 +
+chr21 14567990 14595563 uc002yjr.1 6 +
+chr21 14567990 14595563 uc010gkx.1 5 +
+chr21 14567990 14632206 uc002yjs.2 14 +
+chr21 14665307 14677380 uc002yjt.1 5 -
+chr21 14779419 14877594 uc002yjv.1 9 -
+chr21 14779419 14840535 uc010gky.1 4 -
+chr21 14779419 14840535 uc002yju.1 8 -
+chr21 15117160 15151900 uc002yjw.1 3 -
+chr21 15255426 15262718 uc002yjx.1 1 -
+chr21 15258731 15358997 uc010gkz.1 4 -
+chr21 16024366 16174248 uc010gla.1 11 +
+chr21 16024366 16174248 uc002yjz.1 25 +
+chr21 16024366 16174248 uc002yjy.1 24 +
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+chr21 16488569 16901413 uc002ykc.1 6 +
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+chr21 17807200 17861137 uc002yki.1 7 +
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+chr21 21036784 21097287 uc002yky.2 8 -
+chr21 21292503 21833085 uc002yld.1 18 +
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+chr21 22303349 22392649 uc002ylf.2 6 -
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+chr21 29318808 29348678 uc002ymx.1 18 +
+chr21 29350518 29367881 uc010glm.1 14 -
+chr21 29350518 29367881 uc002ync.1 15 -
+chr21 29350518 29367881 uc002ynb.1 15 -
+chr21 29350518 29367827 uc002yna.1 15 -
+chr21 29350518 29357059 uc002ymz.1 5 -
+chr21 29371824 29470073 uc002ynd.1 10 +
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+chr21 29593090 29640340 uc002ynj.1 5 +
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+chr21 29599430 29656086 uc002ynl.1 8 +
+chr21 29831124 30234153 uc002ynn.1 16 -
+chr21 29847736 30234153 uc002yno.1 17 -
+chr21 29875615 30234153 uc010glq.1 10 -
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+chr21 30613320 30614478 uc002ynw.1 1 -
+chr21 30631201 30631883 uc002ynx.1 1 -
+chr21 30642587 30642795 uc002yny.1 1 -
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+chr21 42946930 43068687 uc002zbx.1 19 +
+chr21 42946930 43068687 uc002zby.1 14 +
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+chr21 42946930 43068687 uc002zca.1 19 +
+chr21 42946930 43068687 uc002zcb.1 19 +
+chr21 42946930 43068687 uc002zcc.1 18 +
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+chr21 42946930 43068687 uc002zcf.1 18 +
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+chr21 42946930 43068687 uc002zbm.1 20 +
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+chr21 43136869 43139149 uc002zcj.1 1 -
+chr21 43142404 43172747 uc002zcl.1 11 -
+chr21 43142404 43172747 uc010gpg.1 11 -
+chr21 43142404 43172747 uc002zck.1 11 -
+chr21 43143219 43172747 uc010gph.1 11 -
+chr21 43186446 43202842 uc002zcm.1 4 +
+chr21 43186446 43202842 uc002zcn.1 3 +
+chr21 43209994 43218800 uc002zco.1 2 -
+chr21 43267711 43326757 uc002zcq.1 11 +
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+chr21 43346369 43361583 uc002zcs.1 14 -
+chr21 43346369 43369020 uc002zct.1 17 -
+chr21 43346369 43369020 uc002zcu.1 17 -
+chr21 43346369 43369493 uc002zcv.1 17 -
+chr21 43346371 43369493 uc002zcw.2 18 -
+chr21 43348252 43353725 uc002zcx.1 6 -
+chr21 43386134 43398431 uc002zcy.1 7 -
+chr21 43386134 43400757 uc002zcz.1 9 -
+chr21 43386134 43400757 uc002zda.1 8 -
+chr21 43386134 43400757 uc002zdb.1 8 -
+chr21 43386141 43400757 uc010gpi.1 7 -
+chr21 43390818 43400757 uc002zdc.1 3 -
+chr21 43462209 43465982 uc002zdd.1 3 +
+chr21 43658826 43671430 uc002zdf.1 14 -
+chr21 43694331 43698210 uc002zdg.1 3 +
+chr21 43706401 43722531 uc002zdh.1 4 -
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+chr21 43809497 43809957 uc002zdj.1 1 +
+chr21 43903859 43940388 uc002zdk.1 16 +
+chr21 43930440 43940388 uc002zdl.1 5 +
+chr21 43963405 44006616 uc002zdn.2 10 +
+chr21 43963405 44006616 uc010gpj.1 10 +
+chr21 43963405 44006616 uc002zdm.2 11 +
+chr21 43973208 43983169 uc002zdp.2 4 +
+chr21 43973208 43983140 uc002zdo.1 4 +
+chr21 43985728 44006616 uc002zdq.2 10 +
+chr21 44018258 44020687 uc002zdr.1 3 -
+chr21 44033845 44048411 uc002zds.2 13 +
+chr21 44033845 44048411 uc010gpk.1 12 +
+chr21 44037239 44048411 uc010gpl.1 10 +
+chr21 44041669 44048411 uc010gpm.1 8 +
+chr21 44050068 44054670 uc002zdt.1 4 -
+chr21 44050068 44054670 uc010gpn.1 2 -
+chr21 44050068 44056876 uc002zdu.1 2 -
+chr21 44109543 44231903 uc002zdv.1 10 +
+chr21 44169706 44231903 uc002zdw.1 9 +
+chr21 44191238 44231903 uc002zdx.1 11 +
+chr21 44203942 44231903 uc002zdy.1 9 +
+chr21 44256633 44304536 uc002zdz.2 7 +
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+chr21 44351635 44375491 uc002zeb.1 21 +
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+chr21 44377921 44390033 uc002zec.2 7 +
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+chr21 44490650 44506527 uc002zeh.1 12 -
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+chr21 44530190 44542530 uc002zei.1 14 +
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+chr21 44544357 44571684 uc002zek.1 25 +
+chr21 44544357 44571684 uc002zel.1 22 +
+chr21 44563661 44571684 uc002zen.1 10 +
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+chr21 44573254 44583713 uc002zer.2 7 -
+chr21 44573254 44583713 uc002zeq.2 7 -
+chr21 44573254 44583713 uc002zep.2 7 -
+chr21 44573254 44583095 uc002zeo.1 8 -
+chr21 44573254 44578835 uc010gps.1 4 -
+chr21 44578846 44583095 uc002zes.1 3 -
+chr21 44594473 44687392 uc002zet.1 33 +
+chr21 44597566 44687392 uc002zeu.1 32 +
+chr21 44597911 44687392 uc002zew.1 32 +
+chr21 44597911 44687392 uc010gpt.1 33 +
+chr21 44613431 44687392 uc002zex.1 28 +
+chr21 44635582 44687392 uc002zey.1 21 +
+chr21 44658905 44661051 uc002zez.1 2 -
+chr21 44699820 44703167 uc002zfa.1 2 +
+chr21 44700955 44701729 uc010gpu.1 1 +
+chr21 44722649 44722699 uc002zfb.1 1 -
+chr21 44728608 44728644 uc002zfc.1 1 -
+chr21 44737584 44737655 uc002zfd.1 1 -
+chr21 44742202 44955923 uc010gpv.1 13 -
+chr21 44742202 44955923 uc002zfe.1 12 -
+chr21 44761525 44765140 uc002zfg.2 2 +
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+chr21 44783495 44784506 uc002zfh.1 1 -
+chr21 44794745 44795816 uc002zfi.1 1 -
+chr21 44802333 44803071 uc002zfj.1 1 -
+chr21 44818033 44819415 uc002zfk.1 1 +
+chr21 44823991 44824909 uc002zfl.1 1 -
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+chr21 44844924 44846519 uc002zfn.2 2 +
+chr21 44856423 44857299 uc002zfo.1 1 +
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+chr21 44881700 44882800 uc002zfq.1 1 +
+chr21 44890758 44891994 uc002zfr.2 1 +
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+chr21 44902276 44902686 uc002zft.1 1 +
+chr21 44910533 44911272 uc002zfu.1 1 -
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+chr21 45013382 45046166 uc002zfy.1 6 -
+chr21 45013382 45046166 uc002zfx.1 7 -
+chr21 45049959 45062472 uc002zfz.1 4 -
+chr21 45049959 45062472 uc002zga.1 4 -
+chr21 45093940 45118169 uc002zgb.1 6 -
+chr21 45130296 45173181 uc002zgg.1 16 -
+chr21 45130296 45165393 uc010gpw.1 15 -
+chr21 45130296 45165393 uc002zgf.2 16 -
+chr21 45130296 45155785 uc002zge.1 16 -
+chr21 45130296 45155169 uc002zgd.1 15 -
+chr21 45165393 45174016 uc002zgh.2 4 +
+chr21 45177156 45179316 uc002zgi.1 2 -
+chr21 45179070 45184188 uc002zgk.2 3 -
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+chr21 45184382 45221316 uc002zgl.1 6 +
+chr21 45184382 45221316 uc002zgm.1 6 +
+chr21 45235614 45238429 uc002zgn.1 2 -
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+chr21 45318942 45470902 uc002zgu.1 12 +
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+chr21 45318942 45470902 uc002zgv.1 12 +
+chr21 45318942 45470902 uc002zgt.1 11 +
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+chr21 45318942 45470902 uc002zgr.1 13 +
+chr21 45318942 45470902 uc010gpx.1 11 +
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+chr21 45415952 45470902 uc002zgy.1 10 +
+chr21 45478694 45503073 uc002zgz.1 3 +
+chr21 45508270 45532239 uc002zhd.1 8 -
+chr21 45508270 45532239 uc002zhc.1 9 -
+chr21 45508270 45532239 uc002zhb.1 10 -
+chr21 45508270 45521753 uc002zha.1 6 -
+chr21 45532394 45536081 uc002zhe.1 3 +
+chr21 45539291 45541696 uc002zhf.1 1 +
+chr21 45649524 45758062 uc002zhg.1 42 +
+chr21 45664058 45669413 uc002zhh.1 3 -
+chr21 45699851 45758062 uc002zhi.1 41 +
+chr21 45742542 45788753 uc010gpy.1 6 -
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+chr21 45759056 45786779 uc002zhl.1 6 -
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+chr21 45837995 45841691 uc002zhn.1 2 +
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+chr21 45888110 46180046 uc010gqb.1 14 +
+chr21 46072302 46080761 uc002zho.1 3 -
+chr21 46092504 46186795 uc002zhp.1 14 +
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+chr21 46094302 46186795 uc002zhq.1 14 +
+chr21 46094302 46186795 uc002zhr.1 14 +
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+chr21 46140549 46186795 uc002zht.1 13 +
+chr21 46226090 46249391 uc002zhu.1 35 +
+chr21 46242041 46249391 uc010gqd.1 13 +
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+chr21 46246830 46249391 uc002zhw.1 3 +
+chr21 46281393 46283633 uc002zhx.1 2 +
+chr21 46342460 46377191 uc002zib.1 9 +
+chr21 46342460 46377191 uc002zia.1 28 +
+chr21 46342460 46374147 uc002zhz.1 28 +
+chr21 46342460 46374147 uc002zhy.1 28 +
+chr21 46370831 46377191 uc002zic.1 2 +
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+chr21 46380603 46399909 uc002zig.1 15 -
+chr21 46380603 46399909 uc002zif.1 15 -
+chr21 46380603 46387083 uc002zie.1 5 -
+chr21 46381121 46399909 uc002zih.1 14 -
+chr21 46381121 46399909 uc010gqf.1 13 -
+chr21 46381326 46399909 uc010gqg.1 14 -
+chr21 46405497 46428729 uc002zii.1 4 -
+chr21 46432787 46473119 uc002zij.1 23 -
+chr21 46433466 46473079 uc002zik.1 21 -
+chr21 46433466 46473119 uc002zil.1 22 -
+chr21 46473585 46496032 uc002zim.2 3 +
+chr21 46473585 46496032 uc002zin.2 4 +
+chr21 46479475 46529664 uc002zir.1 28 -
+chr21 46479475 46511294 uc002ziq.1 18 -
+chr21 46479475 46503607 uc002zip.1 13 -
+chr21 46479475 46491502 uc002zio.1 7 -
+chr21 46480565 46496171 uc002zis.1 3 +
+chr21 46530694 46542093 uc010gqh.1 4 +
+chr21 46530694 46542093 uc002ziy.1 4 +
+chr21 46530694 46542093 uc002zix.1 5 +
+chr21 46530694 46542093 uc002ziw.1 5 +
+chr21 46530694 46542093 uc002ziv.1 5 +
+chr21 46530694 46536539 uc002ziu.1 3 +
+chr21 46530694 46536539 uc002zit.1 3 +
+chr21 46537349 46539139 uc010gqi.1 2 +
+chr21 46544772 46565167 uc002zja.2 9 -
+chr21 46544772 46562562 uc002ziz.2 7 -
+chr21 46545474 46563479 uc002zjc.1 7 -
+chr21 46545474 46568213 uc002zjf.1 8 -
+chr21 46545477 46568213 uc010gqj.1 9 -
+chr21 46559057 46568213 uc002zjg.1 6 -
+chr21 46568463 46690110 uc002zji.2 47 +
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+chr21 46578738 46594162 uc010gqk.1 6 +
+chr21 46699327 46703021 uc002zjk.1 2 -
+chr21 46703317 46790647 uc002zjl.1 20 +
+chr21 46703317 46791548 uc002zjm.1 21 +
+chr21 46703317 46791548 uc010gql.1 20 +
+chr21 46703317 46813028 uc002zjo.1 38 +
+chr21 46703317 46794451 uc002zjn.1 22 +
+chr21 46748653 46789614 uc002zjp.1 14 +
+chr21 46783075 46791548 uc002zjq.1 5 +
+chr21 46797251 46803437 uc002zjr.2 7 +
+chr21 46805625 46813028 uc002zjs.1 5 +
+chr21 46808123 46813028 uc002zjt.1 4 +
+chr21 46842958 46849463 uc002zjv.1 4 -
+chr21 46842958 46849463 uc002zju.1 3 -
+chr21 46879954 46904483 uc002zjw.2 7 +
+chr21 46879954 46909291 uc002zjx.1 12 +
+chr21 46879954 46909291 uc002zjy.1 11 +
+chr21 46879954 46909291 uc010gqm.1 9 +
+chr21 46887625 46906276 uc002zjz.1 6 +
diff --git a/src/intersectBed/chr21.genes.txt b/src/intersectBed/chr21.genes.txt
new file mode 100644
index 0000000000000000000000000000000000000000..841b687392be9648a34cb16319bf60dae3471665
--- /dev/null
+++ b/src/intersectBed/chr21.genes.txt
@@ -0,0 +1,828 @@
+uc002yip.1 chr21 - 9928613 10012791 24
+uc002yiq.1 chr21 - 9928613 10012791 23
+uc002yir.1 chr21 - 9928613 10012791 22
+uc010gkv.1 chr21 - 9928613 10012791 19
+uc002yis.1 chr21 - 9928613 10061300 33
+uc002yiu.1 chr21 - 10042683 10120808 9
+uc002yit.1 chr21 - 10042683 10120796 10
+uc002yiv.1 chr21 - 10079666 10120808 4
+uc002yiw.1 chr21 - 10080031 10081687 2
+uc002yix.2 chr21 - 10081660 10120796 3
+uc002yiy.2 chr21 + 13332351 13346202 5
+uc002yiz.2 chr21 + 13336975 13346202 4
+uc002yja.2 chr21 + 13361138 13412440 3
+uc002yjb.1 chr21 + 13904368 13935777 11
+uc002yjc.1 chr21 + 13944438 13944477 1
+uc002yjd.1 chr21 + 13945076 13945106 1
+uc002yje.1 chr21 - 13973491 13975330 1
+uc002yjf.1 chr21 - 14137333 14142556 6
+uc002yjg.1 chr21 + 14200023 14200052 1
+uc002yjh.1 chr21 - 14202070 14202096 1
+uc002yji.1 chr21 - 14237966 14274631 6
+uc002yjj.2 chr21 - 14270940 14274631 2
+uc002yjk.2 chr21 + 14321612 14438647 3
+uc002yjl.2 chr21 + 14321612 14438730 3
+uc002yjm.1 chr21 - 14403005 14501125 10
+uc010gkw.1 chr21 - 14459414 14483611 4
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+uc002yjn.2 chr21 + 14510336 14522564 5
+uc002yjo.2 chr21 + 14510336 14522564 5
+uc002yjq.1 chr21 + 14567990 14585577 5
+uc002yjr.1 chr21 + 14567990 14595563 6
+uc010gkx.1 chr21 + 14567990 14595563 5
+uc002yjs.2 chr21 + 14567990 14632206 14
+uc002yjt.1 chr21 - 14665307 14677380 5
+uc002yjv.1 chr21 - 14779419 14877594 9
+uc010gky.1 chr21 - 14779419 14840535 4
+uc002yju.1 chr21 - 14779419 14840535 8
+uc002yjw.1 chr21 - 15117160 15151900 3
+uc002yjx.1 chr21 - 15255426 15262718 1
+uc010gkz.1 chr21 - 15258731 15358997 4
+uc010gla.1 chr21 + 16024366 16174248 11
+uc002yjz.1 chr21 + 16024366 16174248 25
+uc002yjy.1 chr21 + 16024366 16174248 24
+uc010glb.1 chr21 + 16085691 16113036 5
+uc002yka.1 chr21 + 16364712 16901413 8
+uc002ykb.1 chr21 + 16364712 16901413 8
+uc010glc.1 chr21 + 16365304 16365529 1
+uc002ykc.1 chr21 + 16488569 16901413 6
+uc002ykd.1 chr21 + 16833279 16833360 1
+uc002yke.1 chr21 + 16834014 16834106 1
+uc002ykf.1 chr21 + 16884427 16884516 1
+uc002ykg.1 chr21 + 17733107 17743132 4
+uc002yki.1 chr21 + 17807200 17861137 7
+uc010gle.1 chr21 + 17807200 17859800 3
+uc010gld.1 chr21 + 17807200 17859800 4
+uc002ykh.1 chr21 + 17807200 17859800 5
+uc002ykj.1 chr21 + 17841215 17887768 7
+uc002ykk.1 chr21 - 17887841 17907033 5
+uc002ykl.1 chr21 - 17887841 17907033 6
+uc002ykn.2 chr21 - 18071593 18086697 3
+uc002ykm.2 chr21 - 18071593 18086697 4
+uc002ykq.2 chr21 - 18083154 18113574 5
+uc002yko.2 chr21 - 18083154 18113574 5
+uc002ykp.2 chr21 - 18083154 18113574 4
+uc002ykr.1 chr21 + 18195450 18561558 7
+uc002yku.1 chr21 + 18211407 18561558 5
+uc002ykt.1 chr21 + 18211407 18561558 6
+uc002yks.1 chr21 + 18211407 18561558 7
+uc002ykv.1 chr21 + 18539020 18561558 6
+uc002ykw.1 chr21 - 18563560 18697844 25
+uc010glf.1 chr21 - 18855455 19032214 4
+uc002ykx.2 chr21 - 18855455 19054001 4
+uc002ylc.2 chr21 - 21036784 21097287 7
+uc002ylb.2 chr21 - 21036784 21097287 7
+uc002yla.2 chr21 - 21036784 21097287 7
+uc002ykz.2 chr21 - 21036784 21097287 8
+uc002yky.2 chr21 - 21036784 21097287 8
+uc002yld.1 chr21 + 21292503 21833085 18
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+uc002ylh.1 chr21 - 22462158 22462605 1
+uc002yli.1 chr21 + 24722924 24784492 6
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+uc002ylk.1 chr21 - 25680009 25725884 5
+uc010glg.1 chr21 - 25680009 25725884 4
+uc002ylm.2 chr21 + 25856312 25869344 3
+uc002yll.1 chr21 + 25856375 25869344 1
+uc002yln.1 chr21 - 25879838 25901672 11
+uc002ylo.1 chr21 - 25879838 25901672 10
+uc010gli.1 chr21 + 25933459 26009106 8
+uc010glh.1 chr21 + 25933459 26009106 10
+uc002ylr.1 chr21 + 25933459 26009106 9
+uc002ylq.1 chr21 + 25933459 26009106 10
+uc002ylp.1 chr21 + 25933459 26009106 10
+uc002yls.1 chr21 - 26018661 26029836 4
+uc002ylt.1 chr21 - 26018661 26029836 4
+uc002ylu.1 chr21 - 26018661 26029836 4
+uc002ylv.1 chr21 - 26018661 26029836 4
+uc002ylw.1 chr21 - 26018661 26029836 4
+uc002ylx.2 chr21 + 26028751 26066642 10
+uc002yly.2 chr21 + 26029199 26066642 10
+uc010glj.1 chr21 - 26174731 26465003 15
+uc002ylz.1 chr21 - 26174731 26465003 18
+uc002yma.1 chr21 - 26174731 26465003 17
+uc002ymb.1 chr21 - 26174731 26465003 16
+uc010glk.1 chr21 - 26316026 26434649 6
+uc002ymc.1 chr21 - 26460085 26461513 1
+uc002ymd.1 chr21 - 26760398 26867452 4
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+uc002ymf.1 chr21 - 27130476 27139599 9
+uc002ymg.1 chr21 - 27212111 27260703 8
+uc002ymh.2 chr21 - 27653075 27742769 4
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+uc002ymk.1 chr21 + 28342603 28431799 5
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+uc002ymm.2 chr21 + 28833510 28834547 2
+uc002ymn.2 chr21 + 28833510 28834547 2
+uc002ymp.1 chr21 - 29166383 29179564 5
+uc002ymo.1 chr21 - 29166383 29179564 6
+uc002ymq.1 chr21 - 29166384 29179564 7
+uc002ymr.1 chr21 - 29222336 29287095 30
+uc010gll.1 chr21 - 29260562 29281126 10
+uc002ymv.1 chr21 - 29299950 29313554 4
+uc002ymu.1 chr21 - 29299950 29313554 4
+uc002ymt.1 chr21 - 29299950 29313554 6
+uc002yms.1 chr21 - 29299950 29313554 5
+uc002ymw.1 chr21 + 29318808 29348678 19
+uc002ymy.1 chr21 + 29318808 29348678 18
+uc002ymx.1 chr21 + 29318808 29348678 18
+uc010glm.1 chr21 - 29350518 29367881 14
+uc002ync.1 chr21 - 29350518 29367881 15
+uc002ynb.1 chr21 - 29350518 29367881 15
+uc002yna.1 chr21 - 29350518 29367827 15
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+uc010glo.1 chr21 + 29416245 29470073 4
+uc002yng.1 chr21 + 29424835 29470073 5
+uc010glp.1 chr21 + 29439770 29470073 4
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+uc002yni.2 chr21 + 29487685 29582396 2
+uc002ynj.1 chr21 + 29593090 29640340 5
+uc002ynk.1 chr21 + 29593607 29640340 5
+uc002ynl.1 chr21 + 29599430 29656086 8
+uc002ynn.1 chr21 - 29831124 30234153 16
+uc002yno.1 chr21 - 29847736 30234153 17
+uc010glq.1 chr21 - 29875615 30234153 10
+uc002ynp.1 chr21 + 29890230 29924938 3
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diff --git a/src/intersectBed/intersectBed.cpp b/src/intersectBed/intersectBed.cpp
index 7b4fde87e2b30b098f0eeab7b7458a35c7fa4e0b..8971ff974f66f6735008fcf06e57bec38963abb6 100755
--- a/src/intersectBed/intersectBed.cpp
+++ b/src/intersectBed/intersectBed.cpp
@@ -1,5 +1,5 @@
/*****************************************************************************
- intersectBed.h
+ intersectBed.cpp
(c) 2009 - Aaron Quinlan
Hall Laboratory
@@ -45,47 +45,61 @@ BedIntersect::~BedIntersect(void) {
void BedIntersect::FindOverlaps(BED &a, vector<BED> &hits) {
- // find all of the overlaps between a and B.
- //bedB->binKeeperFind(bedB->bedMap[a.chrom], a.start, a.end, hits);
- bedB->binKeeperFind(a.chrom, a.start, a.end, hits);
-
- int numOverlaps = 0;
+ // grab _all_ of the features in B that overlap with a.
+ bedB->FindOverlapsPerBin(a.chrom, a.start, a.end, a.strand, hits, this->forceStrand);
+
+ // how many overlaps are there b/w a and B?
+ int numOverlaps = 0;
- // should we print each overlap, or does the
- // user want summary information?
+ // should we print each overlap, or does the user want summary information?
bool printable = true;
if (anyHit || noHit || writeCount) {
printable = false;
}
- for (vector<BED>::const_iterator h = hits.begin(); h != hits.end(); ++h) {
+ // loop through the hits and report those that meet the user's criteria
+ vector<BED>::const_iterator h = hits.begin();
+ vector<BED>::const_iterator hitsEnd = hits.end();
+ for (; h != hitsEnd; ++h) {
- // if forcing strandedness, move on if the hit
- // is not on the same strand as A.
- if ((this->forceStrand) && (a.strand != h->strand)) {
- continue; // continue force the next iteration of the for loop.
- }
- else {
- int s = max(a.start, h->start);
- int e = min(a.end, h->end);
+ int s = max(a.start, h->start);
+ int e = min(a.end, h->end);
+ int overlapBases = (e - s); // the number of overlapping bases b/w a and b
+ int aLength = (a.end - a.start); // the length of a in b.p.
+
+ // is there enough overlap relative to the user's request? (default ~ 1bp)
+ if ( ( (float) overlapBases / (float) aLength ) >= this->overlapFraction ) {
+
+ // Report the hit if the user doesn't care about reciprocal overlap between A and B.
+ if (!reciprocal) {
- // is there enough overlap relative to the user's request?
- // (default ~ 1bp)
- if ( ((float)(e-s) / (float)(a.end - a.start)) >= this->overlapFraction ) {
+ numOverlaps++; // we have another hit for A
+ if (!writeB && printable) {
+ if (writeA) bedA->reportBedNewLine(a);
+ else bedA->reportBedRangeNewLine(a,s,e);
+ }
+ else if (printable) {
+ if (writeA) {
+ bedA->reportBedTab(a);
+ bedB->reportBedNewLine(*h);
+ }
+ else {
+ bedA->reportBedRangeTab(a,s,e);
+ bedB->reportBedNewLine(*h);
+ }
+ }
+ }
+ else { // the user wants there to be sufficient reciprocal overlap
+ int bLength = (h->end - h->start);
+ float bOverlap = ( (float) overlapBases / (float) bLength );
- // Report the hit if the user doesn't care about reciprocal overlap
- // between A and B.
- if (!reciprocal) {
+ if (bOverlap >= this->overlapFraction) {
numOverlaps++; // we have another hit for A
if (!writeB && printable) {
- if (writeA) {
- bedA->reportBedNewLine(a);
- }
- else {
- bedA->reportBedRangeNewLine(a,s,e);
- }
+ if (writeA) bedA->reportBedNewLine(a);
+ else bedA->reportBedRangeNewLine(a,s,e);
}
else if (printable) {
if (writeA) {
@@ -98,34 +112,6 @@ void BedIntersect::FindOverlaps(BED &a, vector<BED> &hits) {
}
}
}
- else {
-
- float bOverlap = ((float)(e-s) / (float)(h->end - h->start));
-
- if (bOverlap >= this->overlapFraction) {
-
- numOverlaps++; // we have another hit for A
-
- if (!writeB && printable) {
- if (writeA) {
- bedA->reportBedNewLine(a);
- }
- else {
- bedA->reportBedRangeNewLine(a,s,e);
- }
- }
- else if (printable) {
- if (writeA) {
- bedA->reportBedTab(a);
- bedB->reportBedNewLine(*h);
- }
- else {
- bedA->reportBedRangeTab(a,s,e);
- bedB->reportBedNewLine(*h);
- }
- }
- }
- }
}
}
}
diff --git a/src/pairToBed/pairToBed.cpp b/src/pairToBed/pairToBed.cpp
index 6913b8cc22b16e8995f39b26c50aa9611db4e2f6..f0317bd0e7f2c71ae475074b948af61d459fa76f 100755
--- a/src/pairToBed/pairToBed.cpp
+++ b/src/pairToBed/pairToBed.cpp
@@ -99,7 +99,7 @@ void BedIntersectPE::FindOverlaps(BEDPE &a, vector<BED> &hits1, vector<BED> &hit
/*
Find the quality hits between ***end1*** of the BEDPE and the B BED file
*/
- bedB->binKeeperFind(bedB->bedMap[a.chrom1], a.start1, a.end1, hits1);
+ bedB->binKeeperFind(a.chrom1, a.start1, a.end1, hits1);
for (vector<BED>::iterator h = hits1.begin(); h != hits1.end(); ++h) {
@@ -127,7 +127,7 @@ void BedIntersectPE::FindOverlaps(BEDPE &a, vector<BED> &hits1, vector<BED> &hit
/*
Now find the quality hits between ***end2*** of the BEDPE and the B BED file
*/
- bedB->binKeeperFind(bedB->bedMap[a.chrom2], a.start2, a.end2, hits2);
+ bedB->binKeeperFind(a.chrom2, a.start2, a.end2, hits2);
for (vector<BED>::iterator h = hits2.begin(); h != hits2.end(); ++h) {
@@ -218,7 +218,7 @@ void BedIntersectPE::FindSpanningOverlaps(BEDPE &a, vector<BED> &hits, string &t
}
spanLength = spanEnd - spanStart;
- bedB->binKeeperFind(bedB->bedMap[a.chrom1], spanStart, spanEnd, hits);
+ bedB->binKeeperFind(a.chrom1, spanStart, spanEnd, hits);
for (vector<BED>::iterator h = hits.begin(); h != hits.end(); ++h) {
diff --git a/src/pairToPair/pairToPair.cpp b/src/pairToPair/pairToPair.cpp
index c3fde14003edb3cb2ab13b183b6128d79b4d4366..1ef5a402a6330f1a0aca7076a15b166d2f070bd8 100755
--- a/src/pairToPair/pairToPair.cpp
+++ b/src/pairToPair/pairToPair.cpp
@@ -117,10 +117,10 @@ void PairToPair::FindOverlaps(BEDPE &a, vector<BED> &hitsA1B1, vector<BED> &hits
// Find the _potential_ hits between each end of A and B
- bedB->binKeeperFind(bedB->bedMapEnd1[a.chrom1], a.start1, a.end1, hitsA1B1); // hits between A1 to B1
- bedB->binKeeperFind(bedB->bedMapEnd1[a.chrom2], a.start2, a.end2, hitsA2B1); // hits between A2 to B1
- bedB->binKeeperFind(bedB->bedMapEnd2[a.chrom1], a.start1, a.end1, hitsA1B2); // hits between A1 to B2
- bedB->binKeeperFind(bedB->bedMapEnd2[a.chrom2], a.start2, a.end2, hitsA2B2); // hits between A2 to B2
+ bedB->binKeeperFind(a.chrom1, a.start1, a.end1, hitsA1B1); // hits between A1 to B1
+ bedB->binKeeperFind(a.chrom2, a.start2, a.end2, hitsA2B1); // hits between A2 to B1
+ bedB->binKeeperFind(a.chrom1, a.start1, a.end1, hitsA1B2); // hits between A1 to B2
+ bedB->binKeeperFind(a.chrom2, a.start2, a.end2, hitsA2B2); // hits between A2 to B2
// Now, reduce to the set of hits on each end of A and B that meet the required overlap fraction and orientation.
diff --git a/src/shuffleBed/shuffleBed.cpp b/src/shuffleBed/shuffleBed.cpp
index 91633b270a2a100deea4a247ddd994acfa8c852e..51ff1a298fbe3bdcf11286cc1cde13a03c49a79d 100755
--- a/src/shuffleBed/shuffleBed.cpp
+++ b/src/shuffleBed/shuffleBed.cpp
@@ -145,7 +145,7 @@ void BedShuffle::ShuffleWithExclusions(istream &bedInput) {
// test to see if the chosen locus overlaps
// with an exclude region
- exclude->binKeeperFind(exclude->bedMap[bedEntry.chrom], bedEntry.start, bedEntry.end, hits);
+ exclude->binKeeperFind(bedEntry.chrom, bedEntry.start, bedEntry.end, hits);
bool haveOverlap = false;
for (vector<BED>::const_iterator h = hits.begin(); h != hits.end(); ++h) {
diff --git a/src/subtractBed/new b/src/subtractBed/new
new file mode 100644
index 0000000000000000000000000000000000000000..d2d55542572008f381df6d247f7e7b2e2941ccec
--- /dev/null
+++ b/src/subtractBed/new
@@ -0,0 +1 @@
+chr1 100 180
diff --git a/src/subtractBed/old b/src/subtractBed/old
new file mode 100644
index 0000000000000000000000000000000000000000..d2d55542572008f381df6d247f7e7b2e2941ccec
--- /dev/null
+++ b/src/subtractBed/old
@@ -0,0 +1 @@
+chr1 100 180
diff --git a/src/subtractBed/subtractBed.cpp b/src/subtractBed/subtractBed.cpp
index d2ceff8b7eef683ebfe35eda139adc53504741f6..8380428dccddf9287d6cbe2a93b416328de06caf 100755
--- a/src/subtractBed/subtractBed.cpp
+++ b/src/subtractBed/subtractBed.cpp
@@ -39,7 +39,7 @@ BedSubtract::~BedSubtract(void) {
void BedSubtract::FindOverlaps(BED &a, vector<BED> &hits) {
// find all of the overlaps between a and B.
- bedB->binKeeperFind(bedB->bedMap[a.chrom], a.start, a.end, hits);
+ bedB->FindOverlapsPerBin(a.chrom, a.start, a.end, a.strand, hits, this->forceStrand);
// is A completely spanned by an entry in B?
// if so, A should not be reported.
@@ -47,21 +47,19 @@ void BedSubtract::FindOverlaps(BED &a, vector<BED> &hits) {
int numOverlaps = 0;
vector<BED> bOverlaps; // list of hits in B. Special processing if there are multiple.
- for (vector<BED>::iterator h = hits.begin(); h != hits.end(); ++h) {
+ vector<BED>::const_iterator h = hits.begin();
+ vector<BED>::const_iterator hitsEnd = hits.end();
+ for (; h != hitsEnd; ++h) {
- // if forcing strandedness, move on if the hit
- // is not on the same strand as A.
- if ((this->forceStrand) && (a.strand != h->strand)) {
- continue; // continue force the next iteration of the for loop.
- }
-
int s = max(a.start, h->start);
- int e = min(a.end, h->end);
-
+ int e = min(a.end, h->end);
+ int overlapBases = (e - s); // the number of overlapping bases b/w a and b
+ int aLength = (a.end - a.start); // the length of a in b.p.
+
if (s < e) {
// is there enough overlap (default ~ 1bp)
- float overlap = ((float)(e-s) / (float)(a.end - a.start));
+ float overlap = ((float) overlapBases / (float) aLength);
if (overlap >= 1.0) {
numOverlaps++;
diff --git a/src/utils/bedFile/bedFile.cpp b/src/utils/bedFile/bedFile.cpp
index 0cc6b2b58bb15ee53613edc3e760b097641c58b7..bbec52f4cd091dca05d7166b44e7dfb595222d11 100755
--- a/src/utils/bedFile/bedFile.cpp
+++ b/src/utils/bedFile/bedFile.cpp
@@ -1,92 +1,29 @@
-//
-// bedFile.cpp
-// BEDTools
-//
-// Created by Aaron Quinlan Spring 2009.
-// Copyright 2009 Aaron Quinlan. All rights reserved.
-//
-// Summary: Contains common functions for finding BED overlaps.
-//
-// Acknowledgments: Much of the code herein is taken from Jim Kent's
-// BED processing code. I am grateful for his elegant
-// genome binning algorithm and therefore use it extensively.
+/*****************************************************************************
+ bedFile.cpp
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan@gmail.com
+
+ Licensed under the GNU General Public License 2.0+ license.
+******************************************************************************/
#include "lineFileUtilities.h"
#include "bedFile.h"
-// return the amount of overlap between two features. Negative if none.
-int overlaps(const int aS, const int aE, const int bS, const int bE) {
- return min(aE, bE) - max(aS, bS);
-}
-
-
-bool leftOf(const int a, const int b) {
- return (a < b);
-}
-
-// return the lesser of two values.
-int min(const int a, int b) {
- if (a <= b) {
- return a;
- }
- else {
- return b;
- }
-}
-
-// return the greater of two values.
-int max(const int a, int b) {
- if (a >= b) {
- return a;
- }
- else {
- return b;
- }
-}
-
-
-int getBin(int start, int end)
-/*
- NOTE: Taken ~verbatim from kent source.
-
- Given start,end in chromosome coordinates assign it
- * a bin. There's a bin for each 128k segment, for each
- * 1M segment, for each 8M segment, for each 64M segment,
- * and for each chromosome (which is assumed to be less than
- * 512M.) A range goes into the smallest bin it will fit in. */
-{
- int startBin = start;
- int endBin = end-1;
- startBin >>= _binFirstShift;
- endBin >>= _binFirstShift;
-
- for (int i=0; i<6; ++i) {
- if (startBin == endBin) {
- return binOffsetsExtended[i] + startBin;
- }
- startBin >>= _binNextShift;
- endBin >>= _binNextShift;
- }
-
- cerr << "start " << start << ", end " << end << " out of range in findBin (max is 512M)" << endl;
- return 0;
-}
-
-//*********************************************
-// Sorting functions
-//*********************************************
-bool sortByChrom(BED const & a, BED const & b){
+bool sortByChrom(BED const & a, BED const & b) {
if (a.chrom < b.chrom) return true;
else return false;
};
-bool sortByStart(const BED &a, const BED &b){
+bool sortByStart(const BED &a, const BED &b) {
if (a.start < b.start) return true;
else return false;
};
-bool sortBySizeAsc(const BED &a, const BED &b){
+bool sortBySizeAsc(const BED &a, const BED &b) {
unsigned int aLen = a.end - a.start;
unsigned int bLen = b.end - b.start;
@@ -95,7 +32,7 @@ bool sortBySizeAsc(const BED &a, const BED &b){
else return false;
};
-bool sortBySizeDesc(const BED &a, const BED &b){
+bool sortBySizeDesc(const BED &a, const BED &b) {
unsigned int aLen = a.end - a.start;
unsigned int bLen = b.end - b.start;
@@ -104,18 +41,18 @@ bool sortBySizeDesc(const BED &a, const BED &b){
else return false;
};
-bool sortByScoreAsc(const BED &a, const BED &b){
+bool sortByScoreAsc(const BED &a, const BED &b) {
if (a.score < b.score) return true;
else return false;
};
-bool sortByScoreDesc(const BED &a, const BED &b){
+bool sortByScoreDesc(const BED &a, const BED &b) {
if (a.score > b.score) return true;
else return false;
};
-bool byChromThenStart(BED const & a, BED const & b){
+bool byChromThenStart(BED const & a, BED const & b) {
if (a.chrom < b.chrom) return true;
else if (a.chrom > b.chrom) return false;
@@ -126,31 +63,64 @@ bool byChromThenStart(BED const & a, BED const & b){
return false;
};
-
-/*
+int getBin(int start, int end)
+/*
NOTE: Taken ~verbatim from kent source.
- Return a list of all items in binKeeper that intersect range.
- Free this list with slFreeList.
+ Given start,end in chromosome coordinates assign it
+ * a bin. There's a bin for each 128k segment, for each
+ * 1M segment, for each 8M segment, for each 64M segment,
+ * and for each chromosome (which is assumed to be less than
+ * 512M.) A range goes into the smallest bin it will fit in. */
+{
+ int startBin = start;
+ int endBin = end-1;
+ startBin >>= _binFirstShift;
+ endBin >>= _binFirstShift;
+
+ for (int i=0; i<6; ++i) {
+ if (startBin == endBin) {
+ return binOffsetsExtended[i] + startBin;
+ }
+ startBin >>= _binNextShift;
+ endBin >>= _binNextShift;
+ }
+
+ cerr << "start " << start << ", end " << end << " out of range in findBin (max is 512M)" << endl;
+ return 0;
+}
+
+/*
+ Adapted from kent source "binKeeperFind"
*/
-void BedFile::binKeeperFind(string chrom, const int start, const int end, vector<BED> &hits) {
+void BedFile::FindOverlapsPerBin(string chrom, int start, int end, string strand, vector<BED> &hits, bool forceStrand) {
int startBin, endBin;
- startBin = (start >>_binFirstShift);
- endBin = ((end-1) >>_binFirstShift);
+ startBin = (start >> _binFirstShift);
+ endBin = ((end-1) >> _binFirstShift);
+ // loop through each bin "level" in the binning hierarchy
for (int i = 0; i < 6; ++i) {
+
+ // loop through each bin at this level of the hierarchy
int offset = binOffsetsExtended[i];
-
for (int j = (startBin+offset); j <= (endBin+offset); ++j) {
+ // loop through each feature in this chrom/bin and see if it overlaps
+ // with the feature that was passed in. if so, add the feature to
+ // the list of hits.
vector<BED>::const_iterator bedItr = bedMap[chrom][j].begin();
vector<BED>::const_iterator bedEnd = bedMap[chrom][j].end();
-
for (; bedItr != bedEnd; ++bedItr) {
- if (overlaps(bedItr->start, bedItr->end, start, end) > 0) {
- hits.push_back(*bedItr);
- }
+
+ // skip the hit if not on the same strand (and we care)
+ if (forceStrand && (strand != bedItr->strand)) {
+ continue;
+ }
+ else if (overlaps(bedItr->start, bedItr->end, start, end) > 0) {
+ hits.push_back(*bedItr); // it's a hit, add it.
+ }
+
}
}
startBin >>= _binNextShift;
@@ -159,34 +129,40 @@ void BedFile::binKeeperFind(string chrom, const int start, const int end, vector
}
+void BedFile::countHits(const BED &a, bool forceStrand) {
-void BedFile::countHits(map<int, vector<BED>, std::less<int> > &bk, BED &a, bool &forceStrand) {
int startBin, endBin;
- int i,j;
+ startBin = (a.start >> _binFirstShift);
+ endBin = ((a.end-1) >> _binFirstShift);
- startBin = (a.start>>_binFirstShift);
- endBin = ((a.end-1)>>_binFirstShift);
- for (i=0; i<6; ++i) {
+ // loop through each bin "level" in the binning hierarchy
+ for (int i = 0; i < 6; ++i) {
+
+ // loop through each bin at this level of the hierarchy
int offset = binOffsetsExtended[i];
-
- for (j = (startBin+offset); j <= (endBin+offset); ++j) {
+ for (int j = (startBin+offset); j <= (endBin+offset); ++j) {
- for (vector<BED>::iterator el = bk[j].begin(); el != bk[j].end(); ++el) {
+ // loop through each feature in this chrom/bin and see if it overlaps
+ // with the feature that was passed in. if so, add the feature to
+ // the list of hits.
+ vector<BED>::iterator bedItr = bedMap[a.chrom][j].begin();
+ vector<BED>::iterator bedEnd = bedMap[a.chrom][j].end();
+ for (; bedItr != bedEnd; ++bedItr) {
- if (forceStrand && (a.strand != el->strand)) {
- continue; // continue force the next iteration of the for loop.
+ // skip the hit if not on the same strand (and we care)
+ if (forceStrand && (a.strand != bedItr->strand)) {
+ continue;
}
- else if (overlaps(el->start, el->end, a.start, a.end) > 0) {
+ else if (overlaps(bedItr->start, bedItr->end, a.start, a.end) > 0) {
- el->count++;
- el->depthMap[a.start+1].starts++;
- el->depthMap[a.end].ends++;
+ bedItr->count++;
+ bedItr->depthMap[a.start+1].starts++;
+ bedItr->depthMap[a.end].ends++;
- if (a.start < el->minOverlapStart) {
- el->minOverlapStart = a.start;
+ if (a.start < bedItr->minOverlapStart) {
+ bedItr->minOverlapStart = a.start;
}
}
-
}
}
startBin >>= _binNextShift;
diff --git a/src/utils/bedFile/bedFile.h b/src/utils/bedFile/bedFile.h
index e9743f0bef9574cfbbe2d9e6fe379e07c2a9daca..327a1eec9646d1e776a787b905f8622a6e6caa24 100755
--- a/src/utils/bedFile/bedFile.h
+++ b/src/utils/bedFile/bedFile.h
@@ -1,3 +1,14 @@
+/*****************************************************************************
+ bedFile.h
+
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan@gmail.com
+
+ Licensed under the GNU General Public License 2.0+ license.
+******************************************************************************/
#ifndef BEDFILE_H
#define BEDFILE_H
@@ -11,7 +22,7 @@
#include <algorithm>
#include <limits.h>
#include <cstdio>
-
+#include <tr1/unordered_map>
using namespace std;
//*************************************************
@@ -58,23 +69,29 @@ struct BED {
};
-
-//*************************************************
-// Common functions
-//*************************************************
-
-int getBin(int, int);
+// return the genome "bin" for a feature with this start and end
+int getBin(int start, int end);
-// BED sorting
-bool sortByChrom(BED const &, BED const &);
-bool sortByStart(const BED &, const BED &);
-bool byChromThenStart(BED const &, BED const &);
+// return the amount of overlap between two features. Negative if none and the the
+// number of negative bases is the distance between the two.
+inline
+int overlaps(int aS, int aE, int bS, int bE) {
+ return min(aE, bE) - max(aS, bS);
+}
-// BED comparsions
-int overlaps(const int, const int, const int, const int);
-bool leftOf(const int, const int);
-int min(const int, int);
-int max(const int, int);
+// return the lesser of two values.
+inline
+int min(int a, int b) {
+ if (a <= b) return a;
+ else return b;
+}
+
+// return the greater of two values.
+inline
+int max(int a, int b) {
+ if (a >= b) return a;
+ else return b;
+}
// templated function to convert objects to strings
@@ -88,20 +105,25 @@ std::string ToString(const T & value)
// BED Sorting Methods
-bool sortByChrom(BED const &, BED const &);
-bool sortByStart(const BED &, const BED &);
-bool sortBySizeAsc(const BED &, const BED &);
-bool sortBySizeDesc(const BED &, const BED &);
-bool sortByScoreAsc(const BED &, const BED &);
-bool sortByScoreDesc(const BED &, const BED &);
-bool byChromThenStart(BED const &, BED const &);
+bool sortByChrom(const BED &a, const BED &b);
+bool sortByStart(const BED &a, const BED &b);
+bool sortBySizeAsc(const BED &a, const BED &b);
+bool sortBySizeDesc(const BED &a, const BED &b);
+bool sortByScoreAsc(const BED &a, const BED &b);
+bool sortByScoreDesc(const BED &a, const BED &b);
+bool byChromThenStart(BED const &a, BED const &b);
+
+
//*************************************************
// Common typedefs
//*************************************************
-
typedef map<int, vector<BED>, std::less<int> > binsToBeds;
+//typedef tr1::unordered_map<int, vector<BED> > binsToBeds;
+
typedef map<string, binsToBeds, std::less<string> > masterBedMap;
+//typedef tr1::unordered_map<string, binsToBeds> masterBedMap;
+
typedef map<string, vector<BED>, std::less<string> > masterBedMapNoBin;
@@ -118,36 +140,35 @@ public:
// Destructor
~BedFile(void);
- // parse an input line and determine how it should be handled
- bool parseLine (BED &bed, const vector<string> &lineVector, int &lineNum);
- // parse a BED line
- bool parseBedLine (BED &bed, const vector<string> &lineVector, int lineNum);
- // parse a GFF line
- bool parseGffLine (BED &bed, const vector<string> &lineVector, int lineNum);
-
+ // 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
+ // value is vector of BEDs
void loadBedFileIntoMapNoBin();
//void binKeeperFind(map<int, vector<BED>, std::less<int> > &, const int, const int, vector<BED> &);
- void binKeeperFind(string chrom, const int start, const int end, vector<BED> &);
-
-
- void countHits(map<int, vector<BED>, std::less<int> > &, BED &, bool &);
+ void FindOverlapsPerBin(string chrom, int start, int end, string strand, vector<BED> &hits, bool forceStrand);
+ //void countHits(map<int, vector<BED>, std::less<int> > &, BED &, bool &);
+ void countHits(const BED &a, bool forceStrand);
+
// printing methods
void reportBedTab(const BED &);
- void reportBedNewLine(const BED &);
-
+ void reportBedNewLine(const BED &);
void reportBedRangeTab(const BED &bed, int start, int end);
void reportBedRangeNewLine(const BED &bed, int start, int end);
-
+ // parse an input line and determine how it should be handled
+ bool parseLine (BED &bed, const vector<string> &lineVector, int &lineNum);
+
map<string, int> minPosMap;
map<string, int> maxPosMap;
// the bedfile with which this instance is associated
string bedFile;
- unsigned int bedType; // 3 -6 for BED
+ unsigned int bedType; // 3-6, 12 for BED
// 9 for GFF
vector<BED> bedVector;
@@ -155,9 +176,11 @@ public:
masterBedMapNoBin bedMapNoBin;
private:
-
-
+ // parse a BED line
+ bool parseBedLine (BED &bed, const vector<string> &lineVector, int lineNum);
+ // parse a GFF line
+ bool parseGffLine (BED &bed, const vector<string> &lineVector, int lineNum);
};
#endif /* BEDFILE_H */
diff --git a/src/utils/lineFileUtilities/lineFileUtilities.cpp b/src/utils/lineFileUtilities/lineFileUtilities.cpp
index e99267fc2d45ab0a1a69d94b8deca9b414a82dc4..f21cbc6fdc4cd0a5d1b1926c3af83a926bcddd84 100755
--- a/src/utils/lineFileUtilities/lineFileUtilities.cpp
+++ b/src/utils/lineFileUtilities/lineFileUtilities.cpp
@@ -15,7 +15,7 @@
// Common Functions
//***********************************************
-void Tokenize(const string& str, vector<string>& tokens)
+void Tokenize(string str, vector<string>& tokens)
{
/* method to tokenize on any whitespace
@@ -42,7 +42,6 @@ void Tokenize(const string& str, vector<string>& tokens)
// Find next "non-delimiter"
pos = str.find_first_of("\t", lastPos);
}
-
}
diff --git a/src/utils/lineFileUtilities/lineFileUtilities.h b/src/utils/lineFileUtilities/lineFileUtilities.h
index 53080b225dbd3683175a47c5f13dc1432c62d957..e384dc392d007d84b8c4e039a682548df4080240 100755
--- a/src/utils/lineFileUtilities/lineFileUtilities.h
+++ b/src/utils/lineFileUtilities/lineFileUtilities.h
@@ -9,7 +9,7 @@
using namespace std;
// split a line from a file into a vector of strings. token = "\t"
-void Tokenize(const string& str, vector<string>& tokens);
+void Tokenize(string str, vector<string>& tokens);
#endif /* LINEFILEUTILITIES_H */
diff --git a/src/windowBed/new b/src/windowBed/new
new file mode 100644
index 0000000000000000000000000000000000000000..e0d2ddede71d9849c7799c1832e4f3a92f18e5d7
--- /dev/null
+++ b/src/windowBed/new
@@ -0,0 +1,4 @@
+chr1 10000 20000 A.forward 1 + chr1 1000 8000 B1
+chr1 10000 20000 A.forward 1 + chr1 24000 32000 B2
+chr1 10000 20000 A.reverse 1 - chr1 1000 8000 B1
+chr1 10000 20000 A.reverse 1 - chr1 24000 32000 B2
diff --git a/src/windowBed/old b/src/windowBed/old
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/src/windowBed/windowBed.cpp b/src/windowBed/windowBed.cpp
index 05d9ff449cdd6c62dc20aa830e66696f9b063976..d6d48b55ec3d9d9bc00ddc2e0e85737a547a0c3b 100755
--- a/src/windowBed/windowBed.cpp
+++ b/src/windowBed/windowBed.cpp
@@ -47,64 +47,60 @@ BedWindow::~BedWindow(void) {
void BedWindow::FindWindowOverlaps(BED &a, vector<BED> &hits) {
+ /*
+ Adjust the start and end of a based on the requested window
+ */
+
// update the current feature's start and end
// according to the slop requested (slop = 0 by default)
int aFudgeStart = 0;
int aFudgeEnd;
-
// Does the user want to treat the windows based on strand?
// If so,
// if "+", then left is left and right is right
// if "-", the left is right and right is left.
if (this->strandWindows) {
-
if (a.strand == "+") {
- if ((a.start - this->leftSlop) > 0) {
- aFudgeStart = a.start - this->leftSlop;
- }
- else {
- aFudgeStart = 0;
- }
+ if ((a.start - this->leftSlop) > 0) aFudgeStart = a.start - this->leftSlop;
+ else aFudgeStart = 0;
aFudgeEnd = a.end + this->rightSlop;
}
else {
- if ((a.start - this->rightSlop) > 0) {
- aFudgeStart = a.start - this->rightSlop;
- }
- else {
- aFudgeStart = 0;
- }
+ if ((a.start - this->rightSlop) > 0) aFudgeStart = a.start - this->rightSlop;
+ else aFudgeStart = 0;
aFudgeEnd = a.end + this->leftSlop;
}
}
+ // If not, add the windows irrespective of strand
else {
- if ((a.start - this->leftSlop) > 0) {
- aFudgeStart = a.start - this->leftSlop;
- }
- else {
- aFudgeStart = 0;
- }
+ if ((a.start - this->leftSlop) > 0) aFudgeStart = a.start - this->leftSlop;
+ else aFudgeStart = 0;
aFudgeEnd = a.end + this->rightSlop;
}
- bedB->binKeeperFind(bedB->bedMap[a.chrom], aFudgeStart, aFudgeEnd, hits);
+
+ /*
+ Now report the hits (if any) based on the window around a.
+ */
+ // get the hits in B for the A feature
+ bedB->FindOverlapsPerBin(a.chrom, aFudgeStart, aFudgeEnd, a.strand, hits, this->matchOnStrand);
int numOverlaps = 0;
- for (vector<BED>::iterator h = hits.begin(); h != hits.end(); ++h) {
- // if forcing strandedness, move on if the hit
- // is not on the same strand as A.
- if ((this->matchOnStrand) && (a.strand != h->strand)) {
- continue; // continue force the next iteration of the for loop.
- }
+ // loop through the hits and report those that meet the user's criteria
+ vector<BED>::const_iterator h = hits.begin();
+ vector<BED>::const_iterator hitsEnd = hits.end();
+ for (; h != hitsEnd; ++h) {
int s = max(aFudgeStart, h->start);
int e = min(aFudgeEnd, h->end);
-
+ int overlapBases = (e - s); // the number of overlapping bases b/w a and b
+ int aLength = (a.end - a.start); // the length of a in b.p.
+
if (s < e) {
// is there enough overlap (default ~ 1bp)
- if ( ((float)(e-s) / (float)(a.end - a.start)) > 0 ) {
+ if ( ((float) overlapBases / (float) aLength) > 0 ) {
numOverlaps++;
if (!anyHit && !noHit && !writeCount) {
bedA->reportBedTab(a);
@@ -146,7 +142,7 @@ void BedWindow::WindowIntersectBed(istream &bedInput) {
Tokenize(bedLine,bedFields);
BED a;
- // find the overlaps with B if it's a valid BED entry.
+ // find the overlaps between "a" and "B" if "a" is a valid BED entry.
if (bedA->parseLine(a, bedFields, lineNum)) {
FindWindowOverlaps(a, hits);
hits.clear();
diff --git a/src/windowBed/windowMain.cpp b/src/windowBed/windowMain.cpp
index dbe92896623841918014036725e85de43dc3837e..2507bc5833193d2b32584a74126b3801b66424b0 100755
--- a/src/windowBed/windowMain.cpp
+++ b/src/windowBed/windowMain.cpp
@@ -191,7 +191,6 @@ void ShowHelp(void) {
cerr << "\t\t- Default is 1000 bp." << endl;
cerr << "\t\t- (INTEGER)" << endl << endl;
-
cerr << "\t-sw\t" << "Define -l and -r based on strand. For example if used, -l 500" << endl;
cerr << "\t\tfor a negative-stranded feature will add 500 bp downstream." << endl;
cerr << "\t\t- Default = disabled." << endl << endl;