// return 0 on sucess, 1 otherwise
inline int validate_entry(char *hdr,char *hdr2,char *seq,char *qual,unsigned long linenum,const char* filename) {
// Sequence identifier
if ( hdr[0]!='@' ) {
fprintf(stderr,"Error in file %s, line %lu: sequence identifier should start with an @ - %s\n",filename,linenum,hdr);
return 1;
}
if ( hdr[1]=='\0' || hdr[1]=='\n' || hdr[1]=='\r') {
fprintf(stderr,"Error in file %s, line %lu: sequence identifier should be longer than 1\n",filename,linenum);
return 1;
}
// sequence
unsigned int slen=0;
while ( seq[slen]!='\0' && seq[slen]!='\n' && seq[slen]!='\r' ) {
// check content: ACGT acgt nN 0123....include the .?
if ( seq[slen]!='A' && seq[slen]!='C' && seq[slen]!='G' && seq[slen]!='T' &&
seq[slen]!='a' && seq[slen]!='c' && seq[slen]!='g' && seq[slen]!='t' &&
seq[slen]!='0' && seq[slen]!='1' && seq[slen]!='2' && seq[slen]!='3' &&
seq[slen]!='n' && seq[slen]!='N' && seq[slen]!='.' ) {
fprintf(stderr,"Error in file %s, line %lu: invalid character '%c' (hex. code:'%x'), expected ACGTacgt0123nN.\n",filename,linenum+1,seq[slen],seq[slen]);
return 1;
}
slen++;
}
// check len
if (slen < MIN_READ_LENGTH ) {
fprintf(stderr,"Error in file %s, line %lu: read length too small - %u\n",filename,linenum+1,slen);
return 1;
}
// hdr2=+
// be tolerant
//if (hdr2[1]!='\0' && hdr2[1]!='\n' && hdr2[1]!='\r') {
// fprintf(stderr,"Error in file %s, line %lu: header2 wrong. The line should contain only '+' followed by a newline.\n",filename,linenum+2);
// return 1;
//}
if (hdr2[0]!='+') {
fprintf(stderr,"Error in file %s, line %lu: header2 wrong. The line should contain only '+' followed by a newline or read name (header1).\n",filename,linenum+2);
return 1;
}
// length of hdr2 should be 1 or be the same has the hdr1
// ignore the + sign
hdr2=&hdr2[1];
hdr=&hdr[1];
if (hdr2[0]!='\0' && hdr2[0]!='\r' ) {
if ( !compare_headers(&hdr[1],&hdr2[1]) ) {
fprintf(stderr,"Error in file %s, line %lu: header2 differs from header1\nheader 1 \"%s\"\nheader 2 \"%s\"\n",filename,linenum,hdr,hdr2);
return 1;
}
}
// qual length==slen
unsigned int qlen=0;
while ( qual[qlen]!='\0' && qual[qlen]!='\n' && qual[qlen]!='\r') {
qlen++;
}
if ( qlen!=slen ) {
fprintf(stderr,"Error in file %s, line %lu: sequence and quality don't have the same length %u!=%u\n",filename,linenum+3,slen,qlen);
return 1;
}
return 0;
}
bool TCPStreamDialog::compareHeaders(segment *seg)
{
return (compare_headers(&graph_.src_address, &graph_.dst_address,
graph_.src_port, graph_.dst_port,
&seg->ip_src, &seg->ip_dst,
seg->th_sport, seg->th_dport,
COMPARE_CURR_DIR));
}
