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#include <algorithm>
#include <iostream>
#include <string>
#include <vector>
#include <alignment/files/ReaderAgglomerate.hpp>
#include <alignment/utils/FileOfFileNames.hpp>
#include <alignment/utils/RegionUtils.hpp>
#include <hdf/HDFPlsReader.hpp>
#include <hdf/HDFRegionTableReader.hpp>
#include <pbdata/SMRTSequence.hpp>
#include <pbdata/amos/AfgBasWriter.hpp>
#include <pbdata/reads/ReadInterval.hpp>
#include <pbdata/reads/RegionTable.hpp>
#include <pbdata/utils.hpp>
void PrintUsage()
{
std::cout << "usage: toAfg input.filetype output.filetype" << std::endl
<< " [-minSubreadLength l] " << std::endl
<< " [-regionTable regions_file] "
<< std::endl
<< " [-noSplitSubreads]" << std::endl
<< " [-useccsdenovo]" << std::endl
<< " [-uniformQV QV]" << std::endl
<< "Print reads stored in a file (pls|fasta|fastq) as an afg." << std::endl;
}
int main(int argc, char* argv[])
{
std::string inputFileName, outputFileName;
if (argc < 2) {
PrintUsage();
std::exit(EXIT_FAILURE);
}
std::vector<std::string> inputFileNames;
inputFileName = argv[1];
outputFileName = argv[2];
int argi = 3;
RegionTable regionTable;
std::string regionsFOFNName = "";
std::vector<std::string> regionFileNames;
bool splitSubreads = true;
bool useCCS = false;
bool useUniformQV = false;
int uniformQV = 7;
int minSubreadLength = 1;
while (argi < argc) {
if (strcmp(argv[argi], "-regionTable") == 0) {
regionsFOFNName = argv[++argi];
} else if (strcmp(argv[argi], "-noSplitSubreads") == 0) {
splitSubreads = false;
} else if (strcmp(argv[argi], "-minSubreadLength") == 0) {
minSubreadLength = atoi(argv[++argi]);
} else if (strcmp(argv[argi], "-useccsdenovo") == 0) {
useCCS = true;
} else if (strcmp(argv[argi], "-uniformQV") == 0) {
useUniformQV = true;
uniformQV = atoi(argv[++argi]);
} else {
PrintUsage();
std::cout << "ERROR! Option " << argv[argi] << " is not supported." << std::endl;
}
argi++;
}
if (FileOfFileNames::IsFOFN(inputFileName)) {
FileOfFileNames::FOFNToList(inputFileName, inputFileNames);
} else {
inputFileNames.push_back(inputFileName);
}
if (regionsFOFNName == "") {
regionFileNames = inputFileNames;
} else {
if (FileOfFileNames::IsFOFN(regionsFOFNName)) {
FileOfFileNames::FOFNToList(regionsFOFNName, regionFileNames);
} else {
regionFileNames.push_back(regionsFOFNName);
}
}
std::ofstream fastaOut;
CrucialOpen(outputFileName, fastaOut);
HDFRegionTableReader hdfRegionReader;
AfgBasWriter afgWriter;
if (useUniformQV) {
afgWriter.SetDefaultQuality(uniformQV);
}
afgWriter.Initialize(outputFileName);
for (size_t plsFileIndex = 0; plsFileIndex < inputFileNames.size(); plsFileIndex++) {
if (splitSubreads) {
hdfRegionReader.Initialize(regionFileNames[plsFileIndex]);
hdfRegionReader.ReadTable(regionTable);
}
ReaderAgglomerate reader;
// reader.SkipReadQuality(); // should have been taken care of by *Filter modules
if (useCCS) {
reader.UseCCS();
} else {
reader.IgnoreCCS();
}
reader.Initialize(inputFileNames[plsFileIndex]);
CCSSequence seq;
int seqIndex = 0;
std::vector<ReadInterval> subreadIntervals;
while (reader.GetNext(seq)) {
++seqIndex;
if (useUniformQV && seq.qual.data != NULL) {
for (DNALength qvIndex = 0; qvIndex < seq.length; qvIndex++) {
seq.qual[qvIndex] = uniformQV;
}
}
if (splitSubreads == false) {
if (seq.length >= static_cast<DNALength>(minSubreadLength)) {
afgWriter.Write(seq);
}
seq.Free();
continue;
}
DNALength hqReadStart, hqReadEnd;
int score;
GetReadTrimCoordinates(seq, seq.zmwData, regionTable, hqReadStart, hqReadEnd, score);
if (regionTable.HasHoleNumber(seq.HoleNumber())) {
subreadIntervals =
regionTable[seq.HoleNumber()].SubreadIntervals(seq.length, true, true);
} else {
subreadIntervals = {};
}
if (seq.length == 0 and subreadIntervals.size() > 0) {
std::cout
<< "WARNING! A high quality interval region exists for a read of length 0."
<< std::endl;
std::cout << " The offending ZMW number is " << seq.HoleNumber() << std::endl;
seq.Free();
continue;
}
for (size_t intvIndex = 0; intvIndex < subreadIntervals.size(); intvIndex++) {
SMRTSequence subreadSequence;
DNALength subreadStart =
static_cast<DNALength>(subreadIntervals[intvIndex].start) > hqReadStart
? static_cast<DNALength>(subreadIntervals[intvIndex].start)
: hqReadStart;
DNALength subreadEnd =
static_cast<DNALength>(subreadIntervals[intvIndex].end) < hqReadEnd
? static_cast<DNALength>(subreadIntervals[intvIndex].end)
: hqReadEnd;
DNALength subreadLength = subreadEnd - subreadStart;
if (subreadLength < DNALength(minSubreadLength)) continue;
subreadSequence.SubreadStart(subreadStart);
subreadSequence.SubreadEnd(subreadEnd);
subreadSequence.ReferenceSubstring(seq, subreadStart, subreadLength);
std::stringstream titleStream;
titleStream << seq.title << "/" << subreadIntervals[intvIndex].start << "_"
<< subreadIntervals[intvIndex].end;
subreadSequence.CopyTitle(titleStream.str());
afgWriter.Write(subreadSequence);
}
seq.Free();
}
reader.Close();
hdfRegionReader.Close();
}
}
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