int32_t
checkLinkPairCandidate(const BamAlignment& al,
const RefVector& refs,
const int32_t critTail)
{
int32_t tail = readTail(al, refs);
return abs(tail) <= critTail ? tail : 0;
}
bool
processReadPair(const BamAlignment& al1,
const BamAlignment& al2,
const RefVector& refs,
const int32_t totalTail,
const int32_t critTail,
const bool diff_ref)
{
if ((al1.IsFirstMate() && al2.IsFirstMate())
|| (al1.IsSecondMate() && al2.IsSecondMate())) {
cerr << "Incompatible mate orders: name1 = " << al1.Name
<< " is1stmate " << al1.IsFirstMate() << " is2ndmate " << al1.IsSecondMate()
<< " name2 = " << al2.Name
<< " is1stmate " << al2.IsFirstMate() << " is2ndmate " << al2.IsSecondMate()
<< endl;
exit(1);
}
int32_t total_tail = -1;
if (! (total_tail = checkLinkPair(al1, al2, refs, totalTail, critTail, diff_ref))) {
return false; // reject all but link pairs
// continue;
}
if (critTail && ! checkLinkPairCandidate(al1, refs, critTail)
&& ! checkLinkPairCandidate(al2, refs, critTail)) {
return false; // neither read was a link pair candidate
}
if (debug_processReadPair) cout << "---------------------------------" << endl;
int32_t lpc_tail1 = checkLinkPairCandidate(al1, refs, critTail);
int32_t lpc_tail2 = checkLinkPairCandidate(al2, refs, critTail);
if (debug_processReadPair) {
printAlignmentInfo(al1, refs);
if (lpc_tail1) {
cout << "LINK PAIR CANDIDATE ";
cout << ((lpc_tail1 > 0) ? "--->" : "<---") << " " << lpc_tail1 << endl;
}
printAlignmentInfo(al2, refs);
if (lpc_tail2) {
cout << "LINK PAIR CANDIDATE ";
cout << ((lpc_tail2 > 0) ? "--->" : "<---") << " " << lpc_tail2 << endl;
}
cout << "TOTAL TAIL " << (abs(readTail(al1, refs)) + abs(readTail(al2, refs))) << endl;
}
return true;
}
void readIpc (unsigned char* bufferedData) {
// fix the data length so if the interrupt adds data
// during execution of this block, it will be read
// until the next readIpc
unsigned int tmpLen = getLength(protBuffer);
unsigned int i=0;
unsigned int availBytes = 0, sendMore = 0;
unsigned char failureTrue = 0;
//static unsigned long long timeStamp = 0;
// Set the output size accordingly
bufferedData[0] = (tmpLen > MAXLOGLEN)? MAXLOGLEN: tmpLen;
// TODO: Remove debugging info from readIPC
//if ((timeStamp % 1000)== 0){
// printToUart2("T: %6.0f\n\r\0",(float) timeStamp*0.01);
//}
//timeStamp++;
// write the data
for(i = 1; i <= bufferedData[0]; i += 1 )
{
bufferedData[i] = readFront(protBuffer);
}
if (getOverflow(protBuffer)>0) {
// disable the SPI module
SPI1STATbits.SPIEN = 0;
// Disable the interrupts
IEC0bits.SPI1IE = 0;
IFS0bits.SPI1IF = 0;
printToUart2("\n=== %s =====\n\r\n\r\n\r", "BEGIN DUMP ");
//printToUart2("Ts: %f\n\r\0",(float) timeStamp*0.01);
printToUart2("Ovrflw: %d\n\r", getOverflow(protBuffer));
printToUart2("Head: %d\n\r", readHead(protBuffer));
printToUart2("Tail: %d\n\r", readTail(protBuffer));
printToUart2("Len: %d\n\r", getLength(protBuffer));
printToUart2("Siz: %d\n\r", protBuffer->size);
for(i = 0; i <BSIZE; i ++ )
{
printToUart2("%d ", protBuffer->buffer[i]);
}
printToUart2("\n=== %s =====\n\r\n\r\n\r", "END ");
// Empty the buffer
makeEmpty(protBuffer);
// Enable the interrupts
IFS0bits.SPI1IF = 0;
IEC0bits.SPI1IE = 1;
// Enable the SPI module
SPI1STATbits.SPIEN = 1;
}
}
