/**
* Clip off some of the high-numbered positions.
*/
void Edit::clipHi(EList<Edit>& ed, size_t len, size_t amt) {
assert_leq(amt, len);
size_t max = len - amt;
size_t nrm = 0;
for(size_t i = 0; i < ed.size(); i++) {
size_t ii = ed.size() - i - 1;
assert_lt(ed[ii].pos, len);
if(ed[ii].pos > max) {
nrm++;
} else if(ed[ii].pos == max && !ed[ii].isReadGap()) {
nrm++;
} else {
break;
}
}
ed.resize(ed.size() - nrm);
}
/**
* Merman main driver function. Does the following:
*
* 1. Parses command-line options
*/
int merman(int argc, char **argv) {
reset();
try {
parseCommandLine(argc, argv);
Timer tov(cerr, "Overall time: ", timing);
EList<string> refstrs;
ReferenceSet refs;
EList<string> refnames;
EList<size_t> reflens;
string refstr = argv[optind++];
tokenize(refstr, ",", refstrs);
auto_ptr<MerIndex> ind(
new MerIndex(ap, rp, readLen, seedWidth, nk.first, nk.second,
specificity, begin, naiveCheck, nthreads));
{
Timer t(cerr, "... ", timing);
if(timing) cerr << "Reading reference sequences..." << endl;
for(size_t i = 0; i < refstrs.size(); i++) {
if(timing) {
cerr << " Sequence " << (i+1) << " of " << refstrs.size() << endl;
}
if(refIsStr) {
refs.addOrigReferenceString(refstrs[i].c_str(), rp);
} else {
refs.addOrigReferenceFasta(refstrs[i].c_str(), rp);
}
}
for(size_t i = 0; i < refs.numRefs(); i++) {
refnames.push_back(string(refs[i].name.toZBuf()));
reflens.push_back(refs[i].seq.length(color));
}
if(refs.numRefs() == 0) {
cerr << "Warning: No references were found" << endl;
}
if(rp.genCrick) {
if(timing) {
cerr << " Crickizing" << endl;
}
// Add the crick strand. If there were bisulfite
// transformations to the Watson strand, they are
// removed from the Watson strand before the Crick copy
// is made. Transformations are then applied to the
// new Crick strand. This has the effect of correctly
// producing either Watson / Crick in the non-bisulfite
// case, or BS Watson / BS Crick in the bisulfite case.
refs.addReferenceRevComps(rp, false, 1, 0);
}
if(rp.genRevcomps) {
if(timing) {
cerr << " Adding reverse comps" << endl;
}
// Add reverse complements of all existing references
// (after the transformations have already been
// applied).
refs.addReferenceRevComps(rp, true, -1, 1);
}
assert(refs.repOk());
}
pair<size_t, size_t> mers = make_pair(0, 0);
EList<MerIndexThread> threads;
{
Timer t(cerr, "... ", timing);
if(timing) cerr << "Preparing to extract sub-sequences..." << endl;
// Instantiate and run index threads
assert_gt(nthreads, 0);
threads.resize(nthreads);
for(int i = 0; i < nthreads; i++) {
threads[i].runCount(&refs, ind.get(), i, nthreads, color);
}
for(int i = 0; i < nthreads; i++) {
pair<size_t, size_t> mrs = threads[i].join();
mers.first += mrs.first;
mers.second += mrs.second;
}
ind->allocateMers();
}
if(timing || verbose || justBlowup) {
cerr << "Expecting index footprint of ";
printBytes(mers.first * sizeof(mer_ent), cerr);
cerr << endl;
if(mers.first > mers.second) {
cerr.setf(ios::fixed);
cerr << " base footprint is ";
printBytes(mers.second * sizeof(mer_ent), cerr);
cerr << endl
<< " blowup factor: " << setprecision(2) << ((double)mers.first / (double)mers.second) << endl;
}
if(justBlowup) throw 0;
}
{
Timer t(cerr, "... ", timing);
if(timing) cerr << "Extracting index sub-sequences..." << endl;
// Instantiate and run index threads
for(int i = 0; i < nthreads; i++) {
threads[i].runIndex(&refs, ind.get(), i, nthreads, color);
}
for(int i = 0; i < nthreads; i++) threads[i].join();
}
assert_eq(mers.first, ind->size());
if(verbose) {
cout << " read " << refs.numRefs() << " reference strings" << endl;
}
if(refs.empty() && iformat != INPUT_CHAININ) {
cerr << "Index is empty; not enough reference sequence supplied" << endl;
throw 1;
}
if(refs.numRefs() == 0 && iformat != INPUT_CHAININ) {
cerr << "No reference strings provided; aborting..." << endl;
throw 1;
}
{
Timer t(cerr, "Sorting reference mers: ", timing);
ind->sort(nthreads); // sort mers
}
{
Timer t(cerr, "... ", timing);
if(timing) cerr << "Aligning reads..." << endl;
string rstr = argv[optind++];
// Instantiate reference map, which translates to new reference
// coordinate system prior to alignment output
auto_ptr<ReferenceMap> rmap(
refmapFile == NULL ? NULL : new ReferenceMap(refmapFile, !refidx));
// Instantiate annotation map, which encodes SNP locations & alleles
auto_ptr<AnnotationMap> amap(
annotFile == NULL ? NULL : new AnnotationMap(annotFile));
// Instantiate the read-input object
auto_ptr<Reads> rs(
(iformat == INPUT_CMDLINE) ?
(Reads*)new StringReads(rstr, begin) :
((iformat == INPUT_FASTA) ?
(Reads*)new FastaReads(rstr, begin, bufsz) :
((iformat == INPUT_FASTA_CONT) ?
(Reads*)new FastaContinuousReads(
rstr, begin, fastaContLen,
fastaContFreq, fcontBis, fcontRc,
color) :
((iformat == INPUT_FASTQ) ?
(Reads*)new FastqReads(rstr, solexaScale, sixty4off, begin, bufsz) :
((iformat == INPUT_CHAININ) ?
(Reads*)new ChainReads(rstr, begin, bufsz) :
((iformat == INPUT_CSFASTA) ?
(Reads*)new CSFastaReads(rstr, begin, bufsz) :
((iformat == INPUT_CSFASTA_AND_QV) ?
(Reads*)new CSFastaAndQVReads(rstr, qualFile, begin, bufsz) :
(Reads*)new CSFastqReads(rstr, solexaScale, sixty4off, begin, bufsz))))))));
// Set output stream
string of = "-";
if(optind < argc) of = argv[optind++];
// Instantiate the alignment-output object
auto_ptr<AlignOutput> outs(
(oformat == OUTPUT_SAM) ?
(AlignOutput*)new SamOutput(of, fullref, refidx, rp.bisulfiteC || rp.bisulfiteCpG, !samNoCsCq) :
(AlignOutput*)new BowtieOutput(of, fullref, printCost, refidx, rp.bisulfiteC || rp.bisulfiteCpG));
outs->printHeader(refnames, reflens);
// Run the progress thread, if requested
ProgressThread proThread;
if(progress) proThread.run();
// Instantiate and run search threads
EList<SearchThread> sthreads;
sthreads.resize(nthreads);
for(int i = 0; i < (int)sthreads.size(); i++) {
sthreads[i].init(
i, (int)sthreads.size(), ind.get(), rs.get(), &refs,
outs.get(), rmap.get(), amap.get());
sthreads[i].run();
}
// Wait until search sthreads are finished
for(size_t i = 0; i < sthreads.size(); i++) {
sthreads[i].join();
}
if(progress) {
proThread.kill();
proThread.join();
}
outs->flush();
}
if(!quiet) ProgressThread::reportStats();
} catch(exception& e) {
cerr << "Command: ";
for(int i = 0; i < argc; i++) cerr << argv[i] << " ";
cerr << endl;
return 1;
} catch(int e) {
if(e != 0) {
cerr << "Command: ";
for(int i = 0; i < argc; i++) cerr << argv[i] << " ";
cerr << endl;
}
return e;
}
return 0;
}
