int main (int argc, char *argv[])
{
if( argc != 3 ) {
usage( "%s <errors|noerrors> <gaps|nogaps>", argv[0]);
return -1;
}
MrfEntry *currEntry;
MrfBlock *currBlock;
int i, error, errorCode, numErrors;
int gaps = 0;
if( strEqual( "gaps", argv[2] ) )
gaps = 1;
seq_init();
mrf_init ("-");
printf( "%s\n", mrf_writeHeader());
numErrors = 0;
while (currEntry = mrf_nextEntry ()) {
error = 0;
for( i=0; i<arrayMax(currEntry->read1.blocks); i++) {
currBlock=arrp( currEntry->read1.blocks, i, MrfBlock);
if( i==0 ) {
errorCode = processBlock ( currBlock, NULL, gaps );
} else {
errorCode = processBlock ( currBlock, arrp( currEntry->read1.blocks, i-1, MrfBlock ), gaps );
}
if( errorCode != 0 ) {
warn( "Error code (read1): %d\t%s:%c:%d:%d:%d:%d", errorCode, currBlock->targetName, currBlock->strand, currBlock->targetStart,
currBlock->targetEnd, currBlock->queryStart, currBlock->queryEnd);
error++;
}
}
if (currEntry->isPairedEnd & error == 0) {
for( i=0; i<arrayMax(currEntry->read2.blocks); i++) {
currBlock=arrp( currEntry->read2.blocks, i, MrfBlock);
if( i==0 ) {
errorCode = processBlock ( currBlock, NULL , gaps );
} else {
errorCode = processBlock (currBlock, arrp( currEntry->read2.blocks, i-1, MrfBlock) , gaps);
}
if( errorCode !=0 ) {
warn( "Error code (read2): %d\t%s:%c:%d:%d:%d:%d", errorCode, currBlock->targetName, currBlock->strand, currBlock->targetStart,
currBlock->targetEnd, currBlock->queryStart, currBlock->queryEnd);
error++;
}
}
}
if( error > 0 && strEqual(argv[1], "errors")) {
printf( "%s\n", mrf_writeEntry( currEntry ));
error=0;
numErrors++;
}
if( error == 0 && strEqual(argv[1], "noerrors"))
printf( "%s\n", mrf_writeEntry( currEntry ));
}
mrf_deInit ();
warn("%s: done", argv[0]);
return 0;
}
static void processEntry (MrfEntry *currEntry, char *targetName, int targetStart, int targetEnd)
{
int containment;
containment = 0;
containment += isContained (&currEntry->read1,targetName,targetStart,targetEnd);
if (currEntry->isPairedEnd) {
containment += isContained (&currEntry->read2,targetName,targetStart,targetEnd);
}
if (containment != 0) {
puts (mrf_writeEntry (currEntry));
}
}
static void processEntry (MrfEntry *currEntry, int mode)
{
int containment;
containment = 0;
containment += isContained (&currEntry->read1);
if (currEntry->isPairedEnd) {
containment += isContained (&currEntry->read2);
}
if ((containment != 0 && mode == MODE_INCLUDE) ||
(containment == 0 && mode == MODE_EXCLUDE)) {
puts (mrf_writeEntry (currEntry));
}
}
