//-------------------------------------------------------------------------------------------------------------------------------
//
// 硬盘初始化函数
//
//-------------------------------------------------------------------------------------------------------------------------------
void HardDiskInit (void)
{
ConsolePrintf("Set the hard disk driver");
if(GetIDENum()==0)
{
ConsolePrintFault();
ConsoleMsg("\n");
ConsoleMsg(" System had no hard disk!\n");
ConsoleMsg("\n");
return;}
ConsolePrintOK();
ConsoleMsg("\n");
if(NR_HD_DEV==1)
ConsoleMsg(" System only one hard disk\n");
else if(NR_HD_DEV==2)
ConsoleMsg(" System have two hard disk\n");
ConsoleMsg(" Hard disk Type: %s\n", HardDiskName );
ConsoleMsg("\n");
//for(i=0 ; i<NR_BLK_REQUEST ; i++) {
// hd_req[i].flag = -1;
// hd_req[i].next = NULL;
// semaphore_init (&(hd_req[i].sem), 0);
//}
//semaphore_init(&request_sem, NR_BLK_REQUEST);
SetIntrGate(0x2E,(void*)HardDiskInterrupt);
outb_p(inb_p(0x21)&0xfb,0x21);
outb(inb_p(0xA1)&0xbf,0xA1);
TickDelay(1);
ReadPartition(); //Must before fs!!!
TickDelay(1);
}
// loads the next read from the alignment archive
bool CAlignmentReader::LoadNextRead(Mosaik::AlignedRead& ar) {
if(!mIsOpen) {
cout << "ERROR: An attempt was made to get reads from an alignment archive that hasn't been opened yet." << endl;
exit(1);
}
// check if we have already processed all of the reads
if(mCurrentRead >= mNumReads) return false;
// read the partition
if(mPartitionMembers == mPartitionSize) {
if(!ReadPartition()) return false;
}
// initialize
unsigned char readStatus = RF_UNKNOWN;
int numMate1Alignments = 0;
int numMate2Alignments = 0;
int numMate1OriginalAlignments = 0;
int numMate2OriginalAlignments = 0;
int numMate1Hash = 0;
int numMate2Hash = 0;
// load the read header
LoadReadHeader(ar.Name, ar.ReadGroupCode, readStatus, numMate1Alignments, numMate2Alignments,
numMate1OriginalAlignments, numMate2OriginalAlignments, numMate1Hash, numMate2Hash);
// interpret the read status
const bool haveMate1 = ((readStatus & RF_HAVE_MATE1) != 0 ? true : false);
const bool haveMate2 = ((readStatus & RF_HAVE_MATE2) != 0 ? true : false);
const bool isResolvedAsPair = ((readStatus & RF_RESOLVED_AS_PAIR) != 0 ? true : false);
ar.hasCsString = ((readStatus & RF_HAS_CS_STRING) != 0 ? true : false);
ar.IsLongRead = ((readStatus & RF_IS_LONG_READ) != 0 ? true : false);
ar.IsPairedEnd = ((readStatus & RF_IS_PAIRED_IN_SEQUENCING) != 0 ? true : false);
ar.IsResolvedAsPair = ((readStatus & RF_RESOLVED_AS_PAIR) != 0 ? true : false);
// =================================
// deserialize each mate 1 alignment
// =================================
ar.Mate1Alignments.clear();
ar.Mate1Alignments.resize(numMate1Alignments);
if (haveMate1)
ReadAlignments(ar.Mate1Alignments, ar.IsLongRead, ar.IsPairedEnd,
isResolvedAsPair, ar.ReadGroupCode, numMate1OriginalAlignments,
numMate2OriginalAlignments, numMate1Hash, numMate2Hash, ar.hasCsString);
// =================================
// deserialize each mate 2 alignment
// =================================
ar.Mate2Alignments.clear();
ar.Mate2Alignments.resize(numMate2Alignments);
if (haveMate2)
ReadAlignments(ar.Mate2Alignments, ar.IsLongRead, ar.IsPairedEnd,
isResolvedAsPair, ar.ReadGroupCode, numMate1OriginalAlignments,
numMate2OriginalAlignments, numMate1Hash, numMate2Hash, ar.hasCsString);
// increment the read counter
++mCurrentRead;
++mPartitionMembers;
return true;
}
