/*
int relayFile2Fifo(FILE *rfp,PCStr(regfile),PCStr(fifo)){
*/
int relayFile2Fifo(FILE *fs,FILE *rfp,PCStr(regfile),PCStr(fifo)){
FILE *ffp;
CStr(buf,8*1024);
int siz,rem,rcc,rcc1;
int start;
int last = time(0);
ffp = fopen(fifo,"w+");
if( lGATEWAY() )
sv1log("----FIFO relay OPEN %X %s\n",p2i(ffp),fifo);
if( rfp == 0 || ffp == 0 )
return -1;
rcc = 0;
start = time(0);
for(;;){
siz = File_size(regfile);
if( siz < 0 ){
break;
}
rem = siz - ftell(rfp);
if( lVERB() )
DEBUG("--SFTP-DATA rem[%d] = %d (%d - %d)\n",
fileno(rfp),rem,iftell(rfp),File_size(regfile));
if( 0 < rem ){
rcc1 = fread(buf,1,sizeof(buf),rfp);
if( rcc1 <= 0 )
break;
rcc += rcc1;
fwrite(buf,1,rcc1,ffp);
last = time(0);
}else{
if( !File_is(fifo) ){
/* fifo is unlinked on recv. complete */
break;
}
fflush(ffp);
if( 10 < time(0)-start ){
if( fPollIn(fs,1) == 0
//&& IsAlive(fileno(fifo))
&& time(0)-last < SFTP_DATA_TIMEOUT ){
/* no prompt for the next command yet */
}else
break;
}
msleep(100);
}
}
fflush(ffp);
fclose(ffp);
if( lGATEWAY() )
sv1log("####@@@@ FIFO relay DONE %d %s\n",rcc,fifo);
return rcc;
}
bool VcfFileReader::processNewSection()
{
myNewSection = false;
// Check to see if the index file has been read.
if(myVcfIndex == NULL)
{
myStatus.setStatus(StatGenStatus::FAIL_ORDER,
"Cannot read section since there is no index file open");
throw(std::runtime_error("SOFTWARE BUG: trying to read a VCF record by section prior to opening the VCF Index file."));
return(false);
}
if(myFilePtr == NULL)
{
myStatus.setStatus(StatGenStatus::FAIL_ORDER,
"Cannot read section without first opening the VCF file.");
throw(std::runtime_error("SOFTWARE BUG: trying to read a VCF record by section prior to opening the VCF file."));
return(false);
}
// Using random access, so can't buffer
myFilePtr->disableBuffering();
uint64_t startPos = 0;
// Find where this section starts in the file.
if(!myVcfIndex->getStartPos(mySectionChrom.c_str(),
mySection1BasedStartPos,
startPos))
{
// Didn't find the position.
myStatus = StatGenStatus::NO_MORE_RECS;
return(false);
}
if(startPos != (uint64_t)iftell(myFilePtr))
{
// Seek to the start position.
if(ifseek(myFilePtr, startPos, SEEK_SET) != true)
{
// seek failed, return failure.
myStatus.setStatus(StatGenStatus::FAIL_IO,
"Failed to seek to the specified section");
return(false);
}
}
return(true);
}
void put_cde_slots(IFILE *file, int ifaxq) /*;put_cde_slots*/
{
long dpos;
dpos = iftell(file); /* get current position */
putnum(file, "n-code_slots", tup_size(CODE_SLOTS));
putnum(file, "n-data-slots", tup_size(DATA_SLOTS));
putnum(file, "n-exception-slots", tup_size(EXCEPTION_SLOTS));
put_slot(file, CODE_SLOTS);
put_slot(file, DATA_SLOTS);
put_slot(file, EXCEPTION_SLOTS);
/* now replace word at start of file with long giving offset to
*start of information just written.
*/
file->fh_slots = dpos;
ifclose(file);
}
bool SamFile::ensureIndexedReadPosition()
{
// If no sections are specified, return true.
if(myRefID == BamIndex::REF_ID_ALL)
{
return(true);
}
// Check to see if we have more to read out of the current chunk.
// By checking the current position in relation to the current
// end chunk. If the current position is >= the end of the
// current chunk, then we must see to the next chunk.
uint64_t currentPos = iftell(myFilePtr);
if(currentPos >= myCurrentChunkEnd)
{
// If there are no more chunks to process, return failure.
if(myChunksToRead.empty())
{
myStatus = SamStatus::NO_MORE_RECS;
return(false);
}
// There are more chunks left, so get the next chunk.
Chunk newChunk = myChunksToRead.pop();
// Move to the location of the new chunk if it is not adjacent
// to the current chunk.
if(newChunk.chunk_beg != currentPos)
{
// New chunk is not adjacent, so move to it.
if(ifseek(myFilePtr, newChunk.chunk_beg, SEEK_SET) != true)
{
// seek failed, cannot retrieve next record, return failure.
myStatus.setStatus(SamStatus::FAIL_IO,
"Failed to seek to the next record");
return(false);
}
}
// Seek succeeded, set the end of the new chunk.
myCurrentChunkEnd = newChunk.chunk_end;
}
return(true);
}
