GenomicRegion::GenomicRegion(const std::string& tchr, const std::string& tpos1, const std::string& tpos2, const SeqLib::BamHeader& hdr)
{
strand = '*';
// convert the pos strings
// throws invalid_argument if conversion can't be performed
// or throws an out_of_range if it is too big for result
#ifdef HAVE_C11
pos1 = std::stoi(tpos1);
pos2 = std::stoi(tpos2);
#else
pos1 = std::atoi(tpos1.c_str());
pos2 = std::atoi(tpos2.c_str());
#endif
// if no header, assume that it is "standard"
if (hdr.isEmpty()) {
if (tchr == "X" || tchr == "chrX")
chr = 22;
else if (tchr == "Y" || tchr == "chrY")
chr = 23;
else
#ifdef HAVE_C11
chr = std::stoi(SeqLib::scrubString(tchr, "chr")) - 1;
#else
chr = std::atoi(SeqLib::scrubString(tchr, "chr").c_str());
#endif
return;
} else {
chr = hdr.Name2ID(tchr); //bam_name2id(hdr.get(), tchr.c_str());
}
}
int main(int argc, char** argv) {
int c;
FastaReference reference;
bool has_ref = false;
bool suppress_output = false;
bool debug = false;
bool isuncompressed = true;
int maxiterations = 50;
if (argc < 2) {
printUsage(argv);
exit(1);
}
while (true) {
static struct option long_options[] =
{
{"help", no_argument, 0, 'h'},
{"debug", no_argument, 0, 'd'},
{"fasta-reference", required_argument, 0, 'f'},
{"max-iterations", required_argument, 0, 'm'},
{"suppress-output", no_argument, 0, 's'},
{"compressed", no_argument, 0, 'c'},
{0, 0, 0, 0}
};
int option_index = 0;
c = getopt_long (argc, argv, "hdcsf:m:",
long_options, &option_index);
/* Detect the end of the options. */
if (c == -1)
break;
switch (c) {
case 'f':
reference.open(optarg); // will exit on open failure
has_ref = true;
break;
case 'm':
maxiterations = atoi(optarg);
break;
case 'd':
debug = true;
break;
case 's':
suppress_output = true;
break;
case 'c':
isuncompressed = false;
break;
case 'h':
printUsage(argv);
exit(0);
break;
case '?':
printUsage(argv);
exit(1);
break;
default:
abort();
break;
}
}
if (!has_ref) {
cerr << "no FASTA reference provided, cannot realign" << endl;
exit(1);
}
BAMSINGLEREADER reader;
if (!reader.Open(STDIN)) {
cerr << "could not open stdin for reading" << endl;
exit(1);
}
#ifdef HAVE_BAMTOOLS
BamWriter writer;
if (isuncompressed) {
writer.SetCompressionMode(BamWriter::Uncompressed);
}
if (!suppress_output && !writer.Open("stdout", reader.GetHeaderText(), reader.GetReferenceData())) {
cerr << "could not open stdout for writing" << endl;
exit(1);
}
#else
SeqLib::BamWriter writer(isuncompressed ? SeqLib::SAM : SeqLib::BAM);
SeqLib::BamHeader hdr = reader.Header();
if (hdr.isEmpty()) {
cerr << "could not open header for input" << endl;
exit(1);
}
writer.SetHeader(hdr);
if (!suppress_output && !writer.Open("-")) {
cerr << "could not open stdout for writing" << endl;
exit(1);
}
#endif
// store the names of all the reference sequences in the BAM file
map<int, string> referenceIDToName;
REFVEC referenceSequences = reader.GETREFDATA;
int i = 0;
for (REFVEC::iterator r = referenceSequences.begin(); r != referenceSequences.end(); ++r) {
referenceIDToName[i] = r->REFNAME;
++i;
}
BAMALIGN alignment;
while (GETNEXT(reader, alignment)) {
DEBUG("--------------------------- read --------------------------" << endl);
DEBUG("| " << referenceIDToName[alignment.REFID] << ":" << alignment.POSITION << endl);
DEBUG("| " << alignment.QNAME << ":" << alignment.ENDPOSITION << endl);
DEBUG("| " << alignment.QNAME << ":" << (alignment.ISMAPPED ? " mapped" : " unmapped") << endl);
DEBUG("| " << alignment.QNAME << ":" << " cigar data size: " << alignment.GETCIGAR.size() << endl);
DEBUG("--------------------------- realigned --------------------------" << endl);
// skip unmapped alignments, as they cannot be left-realigned without CIGAR data
if (alignment.ISMAPPED) {
int endpos = alignment.ENDPOSITION;
int length = endpos - alignment.POSITION + 1;
if (alignment.POSITION >= 0 && length > 0) {
if (!stablyLeftAlign(alignment,
reference.getSubSequence(
referenceIDToName[alignment.REFID],
alignment.POSITION,
length),
maxiterations, debug)) {
cerr << "unstable realignment of " << alignment.QNAME
<< " at " << referenceIDToName[alignment.REFID] << ":" << alignment.POSITION << endl
<< alignment.QUERYBASES << endl;
}
}
}
DEBUG("----------------------------------------------------------------" << endl);
DEBUG(endl);
if (!suppress_output)
WRITEALIGNMENT(writer, alignment);
}
reader.Close();
if (!suppress_output)
writer.Close();
return 0;
}
