void getRefAltCounts(BamReader& reader, const BamRegion &r, int& nReadsRef, int& nReadsAlt, vcfRecord record)
{
// Return the number of reads aligning reference and alternate allele
if (!reader.IsOpen())
{
cout << "Can't access BAM file" << endl;
return;
}
if (!reader.HasIndex())
{
cout << "Can't access BAM file index" << endl;
return;
}
BamAlignment al;
assert(reader.SetRegion(r));
while ( reader.GetNextAlignment(al) )
{
// int baseAlignment = al.Position;
bool found = false;
int index = 0;
int indexPosition = al.Position;
for ( size_t i = 0; i < al.CigarData.size(); i++ )
{
switch ( al.CigarData.at(i).Type )
{
case 'H' : break; // Hard clip
case 'S' : break; // Soft clip
case 'M' : // Match or mismatch
case 'D' :
case 'N' :
case 'P' :
if ( indexPosition + al.CigarData.at(i).Length > (record.pos-1) )
{
index += (record.pos-1) - indexPosition;
found = true;
}
else
{
index += al.CigarData.at(i).Length;
indexPosition += al.CigarData.at(i).Length;
}
break;
case 'I' :
index += al.CigarData.at(i).Length;
break;
}
if ( found )
break;
}
if ( !found || index >= al.AlignedBases.size())
{
cerr << "Problem with finding variant in read:\n";
for ( unsigned int i = 0; i < al.AlignedBases.size(); i++ )
cout << al.AlignedBases.at(i) << " ";
cout << endl;
for ( unsigned int i = 0; i < al.CigarData.size(); i++ )
cout << al.CigarData.at(i).Type << al.CigarData.at(i).Length << " ";
cout << endl;
cout << "Read position: " << al.RefID+1 << " " << al.Position+1 << endl;
cout << "Variant position: " << record.chr << " " << record.pos << endl;
exit(1);
}
if ( al.AlignedBases.at(index) == record.ref.at(0) )
nReadsRef++;
else if ( al.AlignedBases.at(index) == record.alt.at(0) )
nReadsAlt++;
}
}
int main(int argc, char** argv) {
FILE *fsp = 0, *fep = 0;
int flag; // 0
char chrom[255]; // 1
int pos; // 2
int quality; // 3
char *cigar; // 4
size_t len = 0;
char chromcopy[255] = { 0 };
char fn[255];
int i;
int forward, reverse;
bool direction; // 0
bool leftflag;
const char *prefix = "";
int cnt = 0;
BamReader reader;
//if (argc < 2 || argc > 4) usage();
for (i=1; i<argc; i++) {
if ((strcmp(argv[i], "-p") == 0) && (i != argc-1)) {
prefix = argv[++i];
} else {
if (!reader.IsOpen()) {
try {
reader.Open(argv[i]);
} catch (exception& e) {
cout << e.what();
throw;
}
} else {
usage();
}
}
}
if (!reader.IsOpen()) usage();
const SamHeader header = reader.GetHeader();
const RefVector references = reader.GetReferenceData();
BamAlignment al;
while(reader.GetNextAlignmentCore(al)) {
flag = al.AlignmentFlag;
if ((flag & 256) || (flag & 4) || (flag & 512) || (flag & 1024)) continue;
direction = ( (flag & 16) == 16);
strcpy(chrom, references[al.RefID].RefName.c_str());
pos = al.Position+1;
quality = al.MapQuality;
if (quality == 0) continue;
if (strcmp(chromcopy, chrom) != 0) {
if (fsp) fclose(fsp);
if (fep) fclose(fep);
fn[0] = 0;
if (prefix != "") {
strcat(fn, prefix);
}
strcat(fn, chrom);
strcat(fn, "_forward.txt");
fsp = fopen(fn, "w");
fn[0] = 0;
if (prefix != "") {
strcat(fn, prefix);
}
strcat(fn, chrom);
strcat(fn, "_reverse.txt");
fep = fopen(fn, "w");
strcpy(chromcopy, chrom);
}
vector<CigarOp> cigars = al.CigarData;
forward = pos;
reverse = pos;
leftflag = true;
for (i = 0; i < cigars.size(); i++) {
if (cigars[i].Type == 'S' || cigars[i].Type == 'H') {
if (leftflag == false) break;
continue;
} else {
if (cigars[i].Type != 'I') reverse += cigars[i].Length;
leftflag = false;
}
}
if (direction == 0)
fprintf(fsp, "%d\n", forward);
else
fprintf(fep, "%d\n", reverse-1);
cnt++;
if (cnt % 500000 == 0)
printf("%d ", cnt);
}
reader.Close();
printf("\n");
if (fsp) fclose(fsp);
if (fep) fclose(fep);
}
