/* returns pointer to the first new line char position */
const char* recv_line (SYS_socket s, char ** pbuf, size_t buf_left)
{
while (buf_left > 0)
{
ssize_t rcved_size;
char *buf_start = *pbuf;
const char *nl_ptr;
rcved_size = recv (s, buf_start, buf_left, 0);
if (0 > rcved_size)
{
int err = SYS_sock_errno;
fprintf (stderr, "Network error: %u\n",
(unsigned)err);
SYS_set_sock_errno (err);
return NULL;
}
*pbuf += rcved_size;
buf_left -= rcved_size;
nl_ptr = find_chr (buf_start, '\n', rcved_size);
if (nl_ptr)
return nl_ptr;
}
fprintf (stderr, "No buffer space left.\n");
return NULL;
}
void mapper( char *ref, int length, int start_base_pos, const char *bam )
{
anal_t input;
gzFile pRef;
kseq_t * seq = NULL;
char chr[8] = { 0, };
int ret;
bam_plbuf_t *buf;
bam1_t *b;
/*
fprintf( stderr, "ref: %s\n", ref );
fprintf( stderr, "length: %d\n", length );
fprintf( stderr, "start_base_pos: %d\n", start_base_pos );
fprintf( stderr, "bam: %s\n", bam );
*/
input.beg = 0; input.end = 0x7fffffff;
input.in = samopen(bam, "rb", 0);
if (input.in == 0)
{
fprintf(stderr, "Fail to open BAM file %s\n", bam);
return;
}
pRef = gzopen( ref, "r" );
fprintf( stderr, "ref : %s\n", ref );
fprintf( stderr, "pRef: %p\n", pRef );
if( pRef == NULL )
{
fprintf( stderr, "ref : %s\n", ref );
fprintf( stderr, "pRef: %p\n", pRef );
return;
}
seq = kseq_init( pRef );
b = bam_init1(); // alloc memory size of bam1_t
//fprintf( stderr, "%\pn", b );
buf = bam_plbuf_init(pileup_func, &input); // alloc memory
bam_plbuf_set_mask(buf, -1);
while ((ret = samread( input.in, b)) >= 0)
{
bam_plbuf_push(b, buf);
//fprintf( stderr, "%x\n", b->core.flag );
if( b->core.flag & 0x0004 ) // unmapped
{ // do nothing
/*
qname1 = strtok(bam1_qname(b), ":\t\n ");
qname2 = strtok(NULL, ":\t\n ");
qname3 = atoi(qname2);
fprintf( stderr, "%s:%10d:%s:%d\t%c:%d:%d:%d\n",
qname1, qname3, "*", b->core.pos,
'*', b->core.flag, b->core.qual, ret );
*/
fprintf( stdout, "%s:%s:%d\t%c:0x%x:%d:%d\n",
bam1_qname(b), "*", b->core.pos+1,
'*', b->core.flag, b->core.qual, ret );
/*
fprintf( stderr, "%s:%s:%d\t%c:0x%x:%d:%d\n",
bam1_qname(b), "*", b->core.pos,
'*', b->core.flag, b->core.qual, ret );
*/
}
else
{
// to find a base in the reference genome, seq.
if( ( seq != NULL ) &&
( strcmp( input.in->header->target_name[b->core.tid], chr ) == 0 ) )
{
// already found that
// fprintf( stderr, "found : %s\n", chr );
}else
{
if( find_chr(input.in->header->target_name[b->core.tid], seq, chr) < 0 )
{
fprintf( stderr, "ERROR : cannot find chromosome %s\n", \
input.in->header->target_name[b->core.tid] );
}else
{
fprintf( stderr, "FOUND CHR : %s\n", chr );
}
}
// remove not aligned to the chromosome
fprintf( stdout, "%s:%s:%d\t%c:%d:%d:%d\n",
bam1_qname(b),
input.in->header->target_name[b->core.tid],
b->core.pos+1,
seq->seq.s[b->core.pos], b->core.flag, b->core.qual, ret );
/*
fprintf( stderr, "%s:%s:%d\t%c:%d:%d:%d\n",
bam1_qname(b),
input.in->header->target_name[b->core.tid],
b->core.pos,
seq->seq.s[b->core.pos], b->core.flag, b->core.qual, ret );
*/
}
}
// for the last bases...
// printf("pos:%d(%c), flag:%d qual: %d(ret %d)\n",
// b->core.pos+1, seq->seq.s[b->core.pos], b->core.flag, b->core.qual, ret );
bam_plbuf_push(0, buf);
bam_plbuf_destroy(buf); // release memory
bam_destroy1(b); // release memory size of bam1_t
samclose(input.in);
kseq_destroy( seq );
gzclose( pRef );
return;
}
static int SdpMedia(const char *data, int len, sdp_msg *msg)
{
const char *next_token;
const char *lineend;
char number[256];
int tokenlen, token;
short mcnt;
mcnt = msg->transp.count;
if (mcnt == SDP_MAX_RTP_CHANNELS)
return -1;
lineend = data + len;
/* The first token media type */
tokenlen = get_token_len(data, lineend, &next_token);
if (tokenlen == 0 || data[tokenlen] != ' ') {
return -1;
}
msg->transp.type[mcnt] = SDP_MEDIA_UNKNOW;
if (strncmp(data, "audio", tokenlen) == 0) {
msg->transp.type[mcnt] = SDP_MEDIA_AUDIO;
}
else if (strncmp(data, "video", tokenlen) == 0) {
msg->transp.type[mcnt] = SDP_MEDIA_VIDEO;
}
else {
LogPrintf(LV_WARNING, "New media type");
}
data = next_token;
/* port */
tokenlen = get_token_len(data, lineend, &next_token);
if (tokenlen == 0 || data[tokenlen] != ' ') {
return -1;
}
token = find_chr(data, tokenlen, '/');
if (token != -1) {
memcpy(number, data, token);
number[token] = '\0';
msg->transp.port[mcnt] = atoi(number);
LogPrintf(LV_WARNING, "Port count to be complete");
}
else {
msg->transp.port[mcnt] = atoi(data);
}
data = next_token;
/* media protocol */
tokenlen = get_token_len(data, lineend, &next_token);
if (tokenlen == 0 || data[tokenlen] != ' ') {
return -1;
}
msg->transp.proto[mcnt] = DMemMalloc(tokenlen+1);
memcpy(msg->transp.proto[mcnt], data, tokenlen);
msg->transp.proto[mcnt][tokenlen] = '\0';
data = next_token;
/* pt */
tokenlen = get_token_len(data, lineend, &next_token);
if (strcmp(msg->transp.proto[mcnt], "RTP/AVP") == 0) {
while (tokenlen != 0) {
#if 0
memcpy(number, data, tokenlen);
number[tokenlen] = '\0';
msg->transp.media[mcnt].pt[msg->transp.media[mcnt].pt_count] = atoi(number);
#else
msg->transp.media[mcnt].pt[msg->transp.media[mcnt].pt_count] = atoi(data);
#endif
msg->transp.media[mcnt].pt_count++;
data = next_token;
tokenlen = get_token_len(data, lineend, &next_token);
}
}
msg->transp.count++;
return 0;
}
