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Commit 58b1ce0b authored by Aaron's avatar Aaron
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src/utils/bedFile/bedFile.cpp
+ 59
− 34
View file @ 58b1ce0b
......@@ -102,7 +102,9 @@ void BedFile::Open(void) {
_bedStream = new igzstream(bedFile.c_str(), ios::in);
}
if ( !(_bedStream->good()) ) {
cerr << "Error: The requested bed file (" << bedFile << ") could not be opened. Exiting!" << endl;
cerr << "Error: The requested bed file ("
<< bedFile
<< ") could not be opened. Exiting!" << endl;
exit (1);
}
}
......@@ -270,9 +272,12 @@ bool BedFile::GetNextMergedBed(BED &merged_bed) {
}
void BedFile::allHits(string chrom, CHRPOS start, CHRPOS end, string strand,
vector<BED> &hits, bool sameStrand, bool diffStrand,
float overlapFraction, bool reciprocal) {
void BedFile::allHits(string chrom, CHRPOS start,
CHRPOS end, string strand,
vector<BED> &hits, bool sameStrand,
bool diffStrand, float overlapFraction,
bool reciprocal)
{
BIN startBin, endBin;
startBin = (start >> _binFirstShift);
......@@ -297,7 +302,10 @@ void BedFile::allHits(string chrom, CHRPOS start, CHRPOS end, string strand,
CHRPOS e = min(end, bedItr->end);
int overlapBases = (e - s);
// 1. is there sufficient overlap w.r.t A?
if ( (float) overlapBases / (float) aLength >= overlapFraction) {
if ( (float) overlapBases
/
(float) aLength >= overlapFraction)
{
CHRPOS bLength = (bedItr->end - bedItr->start);
float bOverlap = ( (float) overlapBases / (float) bLength );
bool strands_are_same = (strand == bedItr->strand);
......@@ -352,7 +360,10 @@ bool BedFile::anyHits(string chrom, CHRPOS start, CHRPOS end, string strand,
CHRPOS e = min(end, bedItr->end);
int overlapBases = (e - s);
// 1. is there sufficient overlap w.r.t A?
if ( (float) overlapBases / (float) aLength >= overlapFraction) {
if ( (float) overlapBases
/
(float) aLength >= overlapFraction)
{
CHRPOS bLength = (bedItr->end - bedItr->start);
float bOverlap = ( (float) overlapBases / (float) bLength );
bool strands_are_same = (strand == bedItr->strand);
......@@ -393,9 +404,9 @@ void BedFile::countHits(const BED &a, bool sameStrand, bool diffStrand, bool cou
// loop through each bin at this level of the hierarchy
BIN offset = _binOffsetsExtended[i];
for (BIN 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.
// 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<BEDCOV>::iterator bedItr = bedCovMap[a.chrom][j].begin();
vector<BEDCOV>::iterator bedEnd = bedCovMap[a.chrom][j].end();
for (; bedItr != bedEnd; ++bedItr) {
......@@ -408,8 +419,9 @@ void BedFile::countHits(const BED &a, bool sameStrand, bool diffStrand, bool cou
{
continue;
}
else if (overlaps(bedItr->start, bedItr->end, a.start, a.end) > 0) {
else if (overlaps(bedItr->start, bedItr->end, a.start, a.end)
> 0)
{
bedItr->count++;
if (countsOnly == false) {
if (a.zeroLength == false) {
......@@ -417,9 +429,10 @@ void BedFile::countHits(const BED &a, bool sameStrand, bool diffStrand, bool cou
bedItr->depthMap[a.end].ends++;
}
else {
// correct for the fact that we artificially expanded the zeroLength feature
// correct for the fact that we artificially
// expanded the zeroLength feature
bedItr->depthMap[a.start+2].starts++;
bedItr->depthMap[a.end-1].ends++;
bedItr->depthMap[a.end-1].ends++;
}
if (a.start < bedItr->minOverlapStart) {
......@@ -456,15 +469,16 @@ void BedFile::countSplitHits(const vector<BED> &bedBlocks, bool sameStrand, bool
// loop through each bin at this level of the hierarchy
BIN offset = _binOffsetsExtended[i];
for (BIN 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<BEDCOV>::iterator bedItr = bedCovMap[blockItr->chrom][j].begin();
vector<BEDCOV>::iterator bedEnd = bedCovMap[blockItr->chrom][j].end();
// 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<BEDCOV>::iterator
bedItr = bedCovMap[blockItr->chrom][j].begin();
vector<BEDCOV>::iterator
bedEnd = bedCovMap[blockItr->chrom][j].end();
for (; bedItr != bedEnd; ++bedItr) {
bool strands_are_same = (blockItr->strand == bedItr->strand);
bool strands_are_same =
(blockItr->strand == bedItr->strand);
// skip the hit if not on the same strand (and we care)
if ((sameStrand == true && strands_are_same == false) ||
(diffStrand == true && strands_are_same == true)
......@@ -472,14 +486,17 @@ void BedFile::countSplitHits(const vector<BED> &bedBlocks, bool sameStrand, bool
{
continue;
}
else if (overlaps(bedItr->start, bedItr->end, blockItr->start, blockItr->end) > 0) {
else if (overlaps(bedItr->start, bedItr->end,
blockItr->start, blockItr->end) > 0)
{
if (countsOnly == false) {
if (blockItr->zeroLength == false) {
bedItr->depthMap[blockItr->start+1].starts++;
bedItr->depthMap[blockItr->end].ends++;
}
else {
// correct for the fact that we artificially expanded the zeroLength feature
// correct for the fact that we artificially
// expanded the zeroLength feature
bedItr->depthMap[blockItr->start+2].starts++;
bedItr->depthMap[blockItr->end-1].ends++;
}
......@@ -501,8 +518,8 @@ void BedFile::countSplitHits(const vector<BED> &bedBlocks, bool sameStrand, bool
set< vector<BEDCOV>::iterator >::iterator validHitsItr = validHits.begin();
set< vector<BEDCOV>::iterator >::iterator validHitsEnd = validHits.end();
for (; validHitsItr != validHitsEnd; ++validHitsItr)
// the validHitsItr points to another itr, hence the (*itr)-> dereferencing.
// ugly, but that's C++.
// the validHitsItr points to another itr, hence
// the (*itr)-> dereferencing. ugly, but that's C++.
(*validHitsItr)->count++;
}
......@@ -520,11 +537,13 @@ void BedFile::countListHits(const BED &a, int index, bool sameStrand, bool diffS
BIN offset = _binOffsetsExtended[i];
for (BIN 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<BEDCOVLIST>::iterator bedItr = bedCovListMap[a.chrom][j].begin();
vector<BEDCOVLIST>::iterator bedEnd = bedCovListMap[a.chrom][j].end();
// 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 tothe list of hits.
vector<BEDCOVLIST>::iterator
bedItr = bedCovListMap[a.chrom][j].begin();
vector<BEDCOVLIST>::iterator
bedEnd = bedCovListMap[a.chrom][j].end();
for (; bedItr != bedEnd; ++bedItr) {
bool strands_are_same = (a.strand == bedItr->strand);
......@@ -535,16 +554,19 @@ void BedFile::countListHits(const BED &a, int index, bool sameStrand, bool diffS
{
continue;
}
else if (overlaps(bedItr->start, bedItr->end, a.start, a.end) > 0) {
else if (overlaps(bedItr->start, bedItr->end,
a.start, a.end) > 0)
{
bedItr->counts[index]++;
if (a.zeroLength == false) {
bedItr->depthMapList[index][a.start+1].starts++;
bedItr->depthMapList[index][a.end].ends++;
}
else {
// correct for the fact that we artificially expanded the zeroLength feature
// correct for the fact that we artificially expanded
// the zeroLength feature
bedItr->depthMapList[index][a.start+2].starts++;
bedItr->depthMapList[index][a.end-1].ends++;
bedItr->depthMapList[index][a.end-1].ends++;
}
if (a.start < bedItr->minOverlapStarts[index]) {
......@@ -656,7 +678,10 @@ void BedFile::loadBedFileIntoMapNoBin() {
// sort the BED entries for each chromosome
// in ascending order of start position
for (masterBedMapNoBin::iterator m = this->bedMapNoBin.begin(); m != this->bedMapNoBin.end(); ++m) {
for (masterBedMapNoBin::iterator m = this->bedMapNoBin.begin();
m != this->bedMapNoBin.end();
++m)
{
sort(m->second.begin(), m->second.end(), sortByStart);
}
}
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