void ProcessFile(void (*funct)(UNCH *n, FILE *f), UNCH *e, UNCH *fln){
UNCH s[100], s2[100]; s2[0] = 0;
makefilename(s, fln,e);
if(dtdfilename != 0)makefilename(s2, dtdfilename,e);
FILE *f = fopen((char *)s, "r");
if (f != 0) funct(s, f);
else if(s2[0] != 0){
f = fopen((char *)s2, "r");
if (f) funct(s2, f);
}
else {
/*RES OLD MSG 586
Neither %0 file "%1" or "%2" was found. SGML2TDB will stop.
*/
ResFile->MsgData(e);
ResFile->MsgData(s);
ResFile->MsgData(s2);
ResFile->PutResError( /*RES REM INS*/ 586);
exit(100);
}
};
int c0x_mkdirname(char *path, size_t max, const char *dir, const char *sub)
{
#if DEBUGS
printf("$ mkdirname(path=%08p, max=%u, dir=%08p='%.9999s',\n"
"$ sub=%08p='%.9999s')\n",
path, max,
dir, (dir != NULL ? dir : ""),
sub, (sub != NULL ? sub : ""));
#endif
/* Construct a directory pathname */
return (makefilename(path, max, dir, sub));
}
int c0x_mkfilename(char *path, size_t max, const char *dir, const char *file)
{
#if DEBUGS
printf("$ mkfilename(path=%08p, max=%u, dir=%08p='%.9999s',\n"
"$ file=%08p='%.9999s')\n",
path, max,
dir, (dir != NULL ? dir : ""),
file, (file != NULL ? file : ""));
#endif
/* Construct a file pathname */
return (makefilename(path, max, dir, file));
}
void readsetupfiles(UNCH * fln){
initialalpData();
globalvars = new varnamestype;
localvars = new varnamestype;
ProcessFile(processalpfile, ".alp", fln);
BuildAlphabetXlate(AlphaLines, DiacRetLines,DiacNonLines, ContinuText, WordSepSeq);
ProcessFile(processepmfile, ".epm", fln);
delete globalvars;
delete localvars;
UNCH s[100];
makefilename(s, fln,(UNCH *)".tdb");
StartTDBFile(s, TitleText, RefTemText);
makemytagstk();
PgmSetup();
startdynamicdata(vtype);
initpgm->Execute();
delete initpgm;
};
//#pragma argsused
short PD_style _ASK_Distinct( OpndType *lpOpnd, short ParaNum, short *OpndTop, \
short *CurState )
{
dFIELDWHENACTION *p;
char buf[256];
dFIELD *field;
extern WSToMT FromToStru fFrTo;
extern char tmpPath[MAXPATH]; //asqlana.c
if( *CurState == 0 ) {
short i;
if( fFrTo.distinctBh != NULL ) {
*OpndTop -= ParaNum; /* maintain the opnd stack */
return 0;
}
if( xIsOpndField( &lpOpnd[0] ) == 0 )
{
i = (short)xGetOpndLong( &lpOpnd[0] );
if( i < 1 ) {
return 1;
}
} else {
i = -1;
}
sprintf(buf, "DT%03X%03X.NDX", (fFrTo.insideInt)++, intOfThread&0xFFF);
makefilename(buf, tmpPath, buf);
if( i < 1 ) {
p = (dFIELDWHENACTION *)lpOpnd[0].oval;
field=getFieldInfo(p->pSourceDfile, p->wSourceid);
fFrTo.distinctBh=BppTreeBuild(buf, (short)(field->fieldlen));
} else {
fFrTo.distinctBh=BppTreeBuild(buf, i);
}
} else if( *CurState > 0 ) {
if( xIsOpndField( &lpOpnd[0] ) == 0 )
{
char *sz = xGetOpndString( &lpOpnd[1] );
strZcpy(buf, sz, 256);
} else {
p = (dFIELDWHENACTION *)lpOpnd[0].oval;
get_fld(p->pSourceDfile, p->wSourceid, buf);
}
if( IndexSeek(fFrTo.distinctBh, buf) == LONG_MIN ) {
IndexRecIns(fFrTo.distinctBh, buf, LONG_MAX);
} else {
return 2;
}
} else {
/*sprintf(buf, "DIST_%03X.NDX", intOfThread&0xFFF);
makefilename(buf, tmpPath, buf);
*/
strcpy(buf, fFrTo.distinctBh->ndxName);
IndexDispose(fFrTo.distinctBh);
fFrTo.distinctBh = NULL;
unlink(buf);
}
return 0;
} //end of _ASK_Distinct()
/* asqlBlobPut()
*
*************************************************************************/
_declspec(dllexport) long asqlBlobPut(TS_CLIENT_CURSOR *tscc,
LPCSTR lpszUser, \
LPCSTR lpszUserDir,\
void *df, \
long recNo, \
LPSTR fieldName, \
EXCHNG_BUF_INFO *exbuf )
{
TS_COM_PROPS tscp;
unsigned short iw;
char buf[4096];
char szCn[128];
// int i;
memset(&tscp, 0, sizeof(TS_COM_PROPS));
while( tscc != NULL ) {
if( tscc->p == (void *)df )
goto agdr_dfTrueR;
tscc = tscc->pNext;
}
df = NULL;
agdr_dfTrueR:
tscp.packetType = 'R';
tscp.msgType = 'E';
tscp.len = 0;
if( df == NULL || recNo <= 0 ) {
tscp.lp = -1;
memcpy(buf, &tscp, sizeof(TS_COM_PROPS));
SrvWriteExchngBuf(exbuf, buf, sizeof(TS_COM_PROPS));
return -1;
}
iw = GetFldid((dFILE *)df, fieldName);
if( iw == 0xFFFF ) {
tscp.lp = -4;
memcpy(buf, &tscp, sizeof(TS_COM_PROPS));
SrvWriteExchngBuf(exbuf, buf, sizeof(TS_COM_PROPS));
return -4;
}
if( lServerAsRunning ) {
/*i = 32;
GetComputerName(szCn, &i);
i = MAXPATH;
if( GetUserHomeDir(szCn, lpszUser, buf, &i) != 0 )
{
tscp.packetType = 'R';
tscp.msgType = 'E';
tscp.len = 4096-sizeof(TS_COM_PROPS);
tscp.lp = 0;
memcpy(buf, &tscp, sizeof(TS_COM_PROPS));
strcpy(&buf[sizeof(TS_COM_PROPS)], "ERR:4 INF:No Thread service");
SrvWriteExchngBuf(exbuf, buf, 4096);
return 4;
}*/
strZcpy(buf, lpszUserDir, MAXPATH);
beSurePath(buf);
sprintf(szCn, "%s.DTM", fieldName);
makefilename(buf, buf, szCn);
} else {
sprintf(buf, "%s.DTM", fieldName);
}
wmtDbfLock((dFILE *)df);
//((dFILE *)df)->rec_p = recNo;
dseek((dFILE *)df, recNo-1, dSEEK_SET);
if( get1rec((dFILE *)df) == NULL ) {
wmtDbfUnLock((dFILE *)df);
tscp.lp = -4;
memcpy(buf, &tscp, sizeof(TS_COM_PROPS));
SrvWriteExchngBuf(exbuf, buf, 4096);
return -4;
}
if( (tscp.lp=dbtFromFile((dFILE *)df, iw, buf)) >= 0 ) {
tscp.msgType = 'D';
}
wmtDbfUnLock((dFILE *)df);
memcpy(buf, &tscp, sizeof(TS_COM_PROPS));
SrvWriteExchngBuf(exbuf, buf, tscp.len+sizeof(TS_COM_PROPS));
return 0;
} //end of asqlBlobPut()
int
main (int argc, char * argv[])
{
int i, trim_len_fw, trim_len_rev;
//struct reads_info ** ri_left;
//struct reads_info ** ri_right;
// int cnt_reads_left;
// int cnt_reads_right;
int read_size;
char * out[4];
FILE * fd[4];
int ass;
double uncalled_forward, uncalled_reverse;
struct user_args sw;
struct emp_freq * ef;
struct block_t fwd_block;
struct block_t rev_block;
char two_piece;
int elms;
if (!decode_switches (argc, argv, &sw))
{
/* TODO: Validate reads names */
usage ();
return (EXIT_FAILURE);
}
ef = (struct emp_freq *)malloc (sizeof(struct emp_freq));
ef->freqa = ef->freqc = ef->freqg = ef->freqt = ef->total = ef->pa = ef->pc = ef->pg = ef->pt = ef->q = 0.25;
init_scores(sw->phred_base, ef);
/* read the two fastq files containing the left-end and right-end reads */
//ri_left = read_fastq(sw.fastq_left, &cnt_reads_left);
//ri_right = read_fastq(sw.fastq_right, &cnt_reads_right);
//if (!validate_input (cnt_reads_left, cnt_reads_right))
// {
// return (EXIT_FAILURE);
// }
// read_size = strlen (ri_left[0]->data);
/* TODO: THIS IS WRONG!!!! TO GET EMPIRICAL FREQUENCIES WE NEED TO READ THE WHOLE FILE :-( */
//ef = get_emp_freq (cnt_reads_right, read_size, fwd_block.reads, rev_block.reads);
/* reverse the right ends */
/* allocate memory for the assembled results */
/*
ai = (struct asm_info *) malloc (cnt_reads_left * sizeof(struct asm_info));
for (i = 0; i < cnt_reads_left; ++i)
{
ai[i].data = (char *) malloc ((2 * read_size + 1) * sizeof(char));
ai[i].quality_score = (char *) malloc ((2 * read_size + 1) * sizeof(char));
}
*/
init_fastq_reader (sw.fastq_left, sw.fastq_right, sw.memory, &fwd_block, &rev_block);
/* construct output file names */
out[0] = makefilename (sw.outfile, ".assembled.fastq");
out[1] = makefilename (sw.outfile, ".unassembled.forward.fastq");
out[2] = makefilename (sw.outfile, ".unassembled.reverse.fastq");
out[3] = makefilename (sw.outfile, ".discarded.fastq");
fd[0] = fopen (out[0], "w");
fd[1] = fopen (out[1], "w");
fd[2] = fopen (out[2], "w");
fd[3] = fopen (out[3], "w");
while (1)
{
elms = get_next_reads (&fwd_block, &rev_block);
if (!elms) break;
read_size = strlen (fwd_block.reads[0]->data);
// printf ("%d elms (Seq)\n", elms);
//#pragma omp parallel shared(fwd_block.reads, rev_block.reads, ai) private(i, ass, uncalled, kassian_result)
#pragma omp parallel private(i, ass)
{
/* flags[i] = 1 (assembled) 0 (discarded) 2 (unassembled) */
#pragma omp for schedule (guided)
for (i = 0; i < elms; ++ i)
{
mstrrev (rev_block.reads[i]->data);
mstrcpl (rev_block.reads[i]->data);
mstrrev (rev_block.reads[i]->qscore);
if (sw.emp_freqs == 0)
{
ass = assembly (fwd_block.reads[i], rev_block.reads[i], &sw);
*(fwd_block.reads[i]->qscore - 1) = ass;
}
else
{
ass = assembly_ef (fwd_block.reads[i], rev_block.reads[i], ef, &sw);
*(fwd_block.reads[i]->qscore - 1) = ass;
}
}
}
for ( i = 0; i < elms; ++ i)
{
two_piece = *(fwd_block.reads[i]->data - 1);
*(fwd_block.reads[i]->data - 1) = 0;
if (*(fwd_block.reads[i]->qscore - 1) == 1) /* assembled */
{
*(fwd_block.reads[i]->qscore - 1) = 0;
fprintf (fd[0], "%s\n", fwd_block.reads[i]->header);
if (!two_piece)
{
fprintf (fd[0], "%s\n", fwd_block.reads[i]->data);
}
else
{
fprintf (fd[0], "%s", fwd_block.reads[i]->data);
fprintf (fd[0], "%s\n", rev_block.reads[i]->data);
}
fprintf (fd[0], "+\n");
if (!two_piece)
{
fprintf (fd[0], "%s\n", fwd_block.reads[i]->qscore);
}
else
{
fprintf (fd[0], "%s", fwd_block.reads[i]->qscore);
fprintf (fd[0], "%s\n", rev_block.reads[i]->qscore);
}
}
else /* not assembled */
{
*(fwd_block.reads[i]->qscore - 1) = 0;
trim_len_fw = trim (fwd_block.reads[i], &sw, read_size, &uncalled_forward);
trim_len_rev = trim_cpl (rev_block.reads[i], &sw, read_size, &uncalled_reverse);
if (trim_len_fw < sw.min_trim_len || trim_len_rev < sw.min_trim_len || uncalled_forward >= sw.max_uncalled || uncalled_reverse >= sw.max_uncalled)
{ /* discarded reads*/
/* Maybe consider printing the untrimmed sequences */
fprintf (fd[3], "%s\n", fwd_block.reads[i]->header);
fprintf (fd[3], "%s\n+\n%s\n", fwd_block.reads[i]->data, fwd_block.reads[i]->qscore);
fprintf (fd[3], "%s\n", rev_block.reads[i]->header);
fprintf (fd[3], "%s\n+\n%s\n", rev_block.reads[i]->data, rev_block.reads[i]->qscore); /* printing the reverse compliment of the original sequence */
}
else /* unassembled reads*/
{
fprintf (fd[1], "%s\n", fwd_block.reads[i]->header);
fprintf (fd[2], "%s\n", rev_block.reads[i]->header);
fprintf (fd[1], "%s\n+\n%s\n", fwd_block.reads[i]->data, fwd_block.reads[i]->qscore);
fprintf (fd[2], "%s\n+\n%s\n", rev_block.reads[i]->data, rev_block.reads[i]->qscore); /* printing the reverse compliment of the original sequence */
}
}
}
}
free (ef);
free (out[0]);
free (out[1]);
free (out[2]);
free (out[3]);
destroy_reader ();
/* TODO: Fix those file closings */
fclose (fd[0]);
fclose (fd[1]);
fclose (fd[2]);
fclose (fd[3]);
return (0);
}
int main(int argc, char *argv[])
{
char *dev; // The device to sniff on
char errbuf[PCAP_ERRBUF_SIZE]; // Error string if any operation fails
struct bpf_program fp; // The compiled filter (not used)
char filter_exp[] = "port 23"; // The filter expression (not used)
bpf_u_int32 mask; // Our subnet mask
bpf_u_int32 net; // Our network ID
struct pfring_pkthdr header; // The header that pfring gives us
u_char *packet; // The actual packet
int flags,num_pkts=0; // Flags to pass for opening pfring instance, number of packets captured
memset(&header,0,sizeof(header));
signal(SIGINT,sigproc);
dev = argv[1]; // Set the device manually to arg[1]
printf("\nCapture device: %s\n", dev);
makefilename();
flags = PF_RING_PROMISC;
if((handle = pfring_open(dev, 1520, flags)) == NULL) { //MAX_CAPLEN instead of 1520
printf("pfring_open error");
return(-1);
} else {
pfring_set_application_name(handle, "packetcapture");
}
pfring_enable_ring(handle);
dumper = pcap_dump_open(pcap_open_dead(DLT_EN10MB, 16384), filename); //16384 is MTU
if(dumper == NULL) {
printf("Unable to create dump file %s\n", filename);
return(-1);
}
while(1) {
if(pfring_recv(handle, &packet, 0, &header, 1 ) > 0) { //wait for packet, blocking call
if(num_pkts>=PACKETS_PER_FILE)
{
num_pkts = 0;
pcap_dump_close(dumper);
filenumber++;
makefilename();
dumper = pcap_dump_open(pcap_open_dead(DLT_EN10MB, 16384), filename);
if(dumper == NULL) {
printf("Unable to create dump file %s\n", filename);
exit(1);
}
}
pcap_dump((u_char*)dumper, (struct pcap_pkthdr*)&header, packet);
fprintf(stdout, ".");
fflush(stdout);
num_pkts++;
}
}
pcap_dump_close(dumper);
pfring_close(handle);
return 0;
}