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#include <iostream>
#include <getopt.h>
#include <fstream>
#include <iostream>
#include <sstream>
#include <signal.h>
#include <stdlib.h>
#include <cmath>
#include <algorithm>
#include <map>
#include <vector>
#include "FBFasta.h"
#include "LeftAlign.h"
#ifdef VERBOSE_DEBUG
#define DEBUG(msg) \
if (debug) { cerr << msg; }
#else
#define DEBUG(msg)
#endif
using namespace std;
void printUsage(char** argv) {
cerr << "usage: [BAM data stream] | " << argv[0] << " [options]" << endl
<< endl
<< "Left-aligns and merges the insertions and deletions in all alignments in stdin." << endl
<< "Iterates until each alignment is stable through a left-realignment step." << endl
<< endl
<< "arguments:" << endl
<< " -f --fasta-reference FILE FASTA reference file to use for realignment (required)" << endl
<< " -d --debug Print debugging information about realignment process" << endl
<< " -s --suppress-output Don't write BAM output stream (for debugging)" << endl
<< " -m --max-iterations N Iterate the left-realignment no more than this many times" << endl
<< " -c --compressed Write compressed BAM on stdout, default is uncompressed" << endl;
}
int main(int argc, char** argv) {
int c;
FB::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(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);
}
writer.WriteHeader();
#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;
}
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