int main(int argc, char* argv[]) {
if (argc < 3) {
cout << "usage: buildLengthHistogram.cpp input.cmp.h5 output.txt" << endl;
exit(0);
}
string cmpH5FileName = argv[1];
string outputFileName = argv[2];
CmpFile cmpFile;
HDFCmpReader<CmpAlignment> cmpFileReader;
if (cmpFileReader.Initialize(cmpH5FileName) == 0) {
cout << "Could not read the cmp file." << endl;
exit(0);
}
ofstream outFile;
CrucialOpen(outputFileName, outFile, std::ios::out);
cmpFileReader.Read(cmpFile);
vector<int> readLengths;
int a;
cout << "Processing " << cmpFile.alnInfo.alignments.size() << " alignments." << endl;
for (a = 0; a < cmpFile.alnInfo.alignments.size(); a++ ) {
readLengths.push_back(abs(cmpFile.alnInfo.alignments[a].GetQueryEnd() - cmpFile.alnInfo.alignments[a].GetQueryStart()));
}
sort(readLengths.begin(), readLengths.end());
int r = 0;
while(r < readLengths.size()) {
int rn = r;
while(rn < readLengths.size() and readLengths[rn] == readLengths[r]) { rn++;}
outFile << readLengths[r] << " " << rn - r << endl;
r = rn;
}
}
int main(int argc, char* argv[]) {
string cmpFileName;
string refFileName;
string readsFileName;
string mapqvTrackName;
if (argc < 2) {
cout << " printMapqvTrack: print a gff file of the average mapping quality value" << endl;
exit(1);
}
vector<int> refPositions;
cmpFileName = argv[1];
refFileName = argv[2];
mapqvFileName = argv[3];
CmpFile cmpFile;
FASTASequence ref;
FASTAReader reader;
reader.Initialize(refFileName);
reader.GetNext(ref);
HDFBasReader basReader;
SMRTSequence seq, *seqPtr;
vector<int> refCoverage;
refCoverage.resize(ref.length);
std::fill(refCoverage.begin(), refCoverage.end(), 0);
/*
* These guys pull information from the same pls file.
*/
HDFCmpReader<CmpAlignment> cmpReader;
if (cmpReader.Initialize(cmpFileName) == 0) {
cout << "ERROR, could not open the cmp file." << endl;
exit(1);
}
cmpReader.Read(cmpFile);
UInt alignmentIndex;
// movieIndexSets.resize(nMovies);
for (alignmentIndex = 0; alignmentIndex < cmpFile.alnInfo.alignments.size(); alignmentIndex++) {
int refSeqId = cmpFile.alnInfo.alignments[alignmentIndex].GetRefSeqId();
int readGroupId = cmpFile.alnInfo.alignments[alignmentIndex].GetReadGroupId();
int refSeqIdIndex;
if (cmpFile.refSeqTable.GetIndexOfId(refSeqId, refSeqIdIndex) == false) {
//
// Sanity check -- we're only looking at alignments to references in the cmp file.
//
cout << "ERROR, ref seq id: " << refSeqId << " should exist in the cmp file but it does not." << endl;
assert(0);
}
int readGroupIdIndex;
cmpFile.readGroupTable.GetIndexOfId(readGroupId, readGroupIdIndex);
string readGroupPath = cmpFile.readGroupTable.names[readGroupIdIndex];
string readGroup = cmpReader.readGroupPathToReadGroup[readGroupPath];
int readGroupArrayIndex = cmpReader.refAlignGroups[refSeqIdIndex]->experimentNameToIndex[readGroup];
vector<char> alignedSequence, alignedTarget;
//
// This read overlaps one of the ref positions.
UInt offsetEnd, offsetBegin;
offsetEnd = cmpFile.alnInfo.alignments[alignmentIndex].GetOffsetEnd();
offsetBegin = cmpFile.alnInfo.alignments[alignmentIndex].GetOffsetBegin();
vector<unsigned char> byteAlignment;
int alignedSequenceLength = offsetEnd - offsetBegin;
if (alignedSequenceLength >= 0) {
alignedSequence.resize(alignedSequenceLength);
alignedTarget.resize(alignedSequenceLength);
byteAlignment.resize(alignedSequenceLength);
}
cmpReader.refAlignGroups[refSeqIdIndex]->readGroups[readGroupArrayIndex]->alignmentArray.Read(offsetBegin, offsetEnd, &byteAlignment[0]);
UInt refStart = cmpFile.alnInfo.alignments[alignmentIndex].GetRefStart();
UInt refEnd = cmpFile.alnInfo.alignments[alignmentIndex].GetRefEnd();
UInt readStart= cmpFile.alnInfo.alignments[alignmentIndex].GetQueryStart();
UInt readEnd = cmpFile.alnInfo.alignments[alignmentIndex].GetQueryEnd();
//
// Read the alignment string.
//
if (refSeqIdIndex > 0) continue;
//
// Convert to something we can compare easily.
//
alignedSequence[alignedSequence.size()-1]= '\0';
ByteAlignmentToQueryString(&byteAlignment[0], byteAlignment.size(), &alignedSequence[0]);
ByteAlignmentToRefString(&byteAlignment[0], byteAlignment.size(), &alignedTarget[0]);
int gi, i;
gi = 0;
int refStrand = cmpFile.alnInfo.alignments[alignmentIndex].GetRCRefStrand();
if (refStrand == 1) {
// revcomp the ref strand
vector<char> rcAlignedTarget, rcAlignedQuery;
int t;
rcAlignedTarget.resize(alignedTarget.size());
rcAlignedQuery.resize(alignedSequence.size());
for (t = 0; t < alignedTarget.size(); t++) {
if (alignedTarget[t] == ' ') {
rcAlignedTarget[alignedTarget.size() - t - 1] = ' ';
}
else {
rcAlignedTarget[alignedTarget.size() - t - 1] = ReverseComplementNuc[alignedTarget[t]];
}
if (alignedSequence[t] == ' '){
rcAlignedQuery[alignedTarget.size() - t - 1] = ' ';
}
else {
rcAlignedQuery[alignedTarget.size() - t - 1] = ReverseComplementNuc[alignedTarget[t]];
}
}
alignedTarget = rcAlignedTarget;
alignedSequence = rcAlignedQuery;
}
int holeNumber = cmpFile.alnInfo.alignments[alignmentIndex].GetHoleNumber();
int ri = readStart;
gi = refStart;
for (i = 0; i < alignedTarget.size(); i++, gi++, ri++ ) {
while(i < alignedTarget.size() and alignedTarget[i] == ' ') {
i++;
}
if (alignedSequence[i] != ' ') {
refCoverage[gi]++;
}
}
} // end looping over regions
// Now compute the number of gaps.
UInt pos;
int numNotCovered = 0;
for (pos = 0; pos < refCoverage.size(); pos++ ){
if (refCoverage[pos] < 1) { numNotCovered++;}
}
if (numNotCovered > 100) {
cout << "TOO Many!!!" << endl;
}
else {
for (pos = 0; pos < refCoverage.size(); pos++ ){
// cout << refCoverage[pos] << endl;
if (refCoverage[pos] < 1) {
int left, right;
left = right = -1;
if (pos > 0) { left = refCoverage[pos-1];}
if (pos < refCoverage.size()-1) {right = refCoverage[pos+1];}
cout << pos << " " << left << " " << right << endl;
}
}
}
}
