// main function
int TrimBam::execute(int argc, char ** argv)
{
SamFile samIn;
SamFile samOut;
int numTrimBaseL = 0;
int numTrimBaseR = 0;
bool noeof = false;
bool ignoreStrand = false;
bool noPhoneHome = false;
std::string inName = "";
std::string outName = "";
if ( argc < 5 ) {
usage();
std::cerr << "ERROR: Incorrect number of parameters specified\n";
return(-1);
}
inName = argv[2];
outName = argv[3];
static struct option getopt_long_options[] = {
// Input options
{ "left", required_argument, NULL, 'L'},
{ "right", required_argument, NULL, 'R'},
{ "ignoreStrand", no_argument, NULL, 'i'},
{ "noeof", no_argument, NULL, 'n'},
{ "noPhoneHome", no_argument, NULL, 'p'},
{ "nophonehome", no_argument, NULL, 'P'},
{ "phoneHomeThinning", required_argument, NULL, 't'},
{ "phonehomethinning", required_argument, NULL, 'T'},
{ NULL, 0, NULL, 0 },
};
int argIndex = 4;
if(argv[argIndex][0] != '-')
{
// This is the number of bases to trim off both sides
// so convert to a number.
numTrimBaseL = atoi(argv[argIndex]);
numTrimBaseR = numTrimBaseL;
++argIndex;
}
int c = 0;
int n_option_index = 0;
// Process any additional parameters
while ( ( c = getopt_long(argc, argv,
"L:R:in", getopt_long_options, &n_option_index) )
!= -1 )
{
switch(c)
{
case 'L':
numTrimBaseL = atoi(optarg);
break;
case 'R':
numTrimBaseR = atoi(optarg);
break;
case 'i':
ignoreStrand = true;
break;
case 'n':
noeof = true;
break;
case 'p':
case 'P':
noPhoneHome = true;
break;
case 't':
case 'T':
PhoneHome::allThinning = atoi(optarg);
break;
default:
fprintf(stderr,"ERROR: Unrecognized option %s\n",
getopt_long_options[n_option_index].name);
return(-1);
}
}
if(!noPhoneHome)
{
PhoneHome::checkVersion(getProgramName(), VERSION);
}
if(noeof)
{
// Set that the eof block is not required.
BgzfFileType::setRequireEofBlock(false);
}
if ( ! samIn.OpenForRead(inName.c_str()) ) {
fprintf(stderr, "***Problem opening %s\n",inName.c_str());
return(-1);
}
if(!samOut.OpenForWrite(outName.c_str())) {
fprintf(stderr, "%s\n", samOut.GetStatusMessage());
return(samOut.GetStatus());
}
fprintf(stderr,"Arguments in effect: \n");
fprintf(stderr,"\tInput file : %s\n",inName.c_str());
fprintf(stderr,"\tOutput file : %s\n",outName.c_str());
if(numTrimBaseL == numTrimBaseR)
{
fprintf(stderr,"\t#Bases to trim from each side : %d\n", numTrimBaseL);
}
else
{
fprintf(stderr,"\t#Bases to trim from the left of forward strands : %d\n",
numTrimBaseL);
fprintf(stderr,"\t#Bases to trim from the right of forward strands: %d\n",
numTrimBaseR);
if(!ignoreStrand)
{
// By default, reverse strands are treated the opposite.
fprintf(stderr,"\t#Bases to trim from the left of reverse strands : %d\n",
numTrimBaseR);
fprintf(stderr,"\t#Bases to trim from the right of reverse strands : %d\n",
numTrimBaseL);
}
else
{
// ignore strand, treating forward & reverse strands the same
fprintf(stderr,"\t#Bases to trim from the left of reverse strands : %d\n",
numTrimBaseL);
fprintf(stderr,"\t#Bases to trim from the right of reverse strands : %d\n",
numTrimBaseR);
}
}
// Read the sam header.
SamFileHeader samHeader;
if(!samIn.ReadHeader(samHeader))
{
fprintf(stderr, "%s\n", samIn.GetStatusMessage());
return(samIn.GetStatus());
}
// Write the sam header.
if(!samOut.WriteHeader(samHeader))
{
fprintf(stderr, "%s\n", samOut.GetStatusMessage());
return(samOut.GetStatus());
}
SamRecord samRecord;
char seq[65536];
char qual[65536];
int i, len;
// Keep reading records until ReadRecord returns false.
while(samIn.ReadRecord(samHeader, samRecord)) {
// Successfully read a record from the file, so write it.
strcpy(seq,samRecord.getSequence());
strcpy(qual,samRecord.getQuality());
// Number of bases to trim from the left/right,
// set based on ignoreStrand flag and strand info.
int trimLeft = numTrimBaseL;
int trimRight = numTrimBaseR;
if(!ignoreStrand)
{
if(SamFlag::isReverse(samRecord.getFlag()))
{
// We are reversing the reverse reads,
// so swap the left & right trim counts.
trimRight = numTrimBaseL;
trimLeft = numTrimBaseR;
}
}
len = strlen(seq);
// Do not trim if sequence is '*'
if ( strcmp(seq, "*") != 0 ) {
bool qualValue = true;
if(strcmp(qual, "*") == 0)
{
qualValue = false;
}
int qualLen = strlen(qual);
if ( (qualLen != len) && qualValue ) {
fprintf(stderr,"ERROR: Sequence and Quality have different length\n");
return(-1);
}
if ( len < (trimLeft + trimRight) ) {
// Read Length is less than the total number of bases to trim,
// so trim the entire read.
for(i=0; i < len; ++i) {
seq[i] = 'N';
if ( qualValue ) {
qual[i] = '!';
}
}
}
else
{
// Read Length is larger than the total number of bases to trim,
// so trim from the left, then from the right.
for(i=0; i < trimLeft; ++i)
{
// Trim the bases from the left.
seq[i] = 'N';
if ( qualValue )
{
qual[i] = '!';
}
}
for(i = 0; i < trimRight; i++)
{
seq[len-i-1] = 'N';
if(qualValue)
{
qual[len-i-1] = '!';
}
}
}
samRecord.setSequence(seq);
samRecord.setQuality(qual);
}
if(!samOut.WriteRecord(samHeader, samRecord)) {
// Failed to write a record.
fprintf(stderr, "Failure in writing record %s\n", samOut.GetStatusMessage());
return(-1);
}
}
if(samIn.GetStatus() != SamStatus::NO_MORE_RECS)
{
// Failed to read a record.
fprintf(stderr, "%s\n", samIn.GetStatusMessage());
}
std::cerr << std::endl << "Number of records read = " <<
samIn.GetCurrentRecordCount() << std::endl;
std::cerr << "Number of records written = " <<
samOut.GetCurrentRecordCount() << std::endl;
if(samIn.GetStatus() != SamStatus::NO_MORE_RECS)
{
// Failed reading a record.
return(samIn.GetStatus());
}
// Since the reads were successful, return the status based
samIn.Close();
samOut.Close();
return 0;
}
