void SamBam_read_ref_info(SamBam_FILE * ret)
{
unsigned int ref_info_size = 0;
ret ->bam_chro_table_size = 0;
//printf("CKK0\n");
SB_FETCH(ret);
if(SB_EOF(ret))
return;
//printf("CKK1\n");
memcpy(&ref_info_size, SB_READ(ret),4);
SB_RINC(ret, 4);
int xk1;
ret -> bam_chro_table = malloc(sizeof(SamBam_Reference_Info) * ref_info_size);
for(xk1=0;xk1<ref_info_size;xk1++)
{
SB_FETCH(ret);
if(SB_EOF(ret))
break;
int ref_name_len = 0;
memcpy(&ref_name_len, SB_READ(ret),4);
SB_RINC(ret, 4);
int ref_readin_len = min(ref_name_len, BAM_MAX_CHROMOSOME_NAME_LEN-1);
int ref_skip_len = ref_name_len - ref_readin_len;
memcpy(ret -> bam_chro_table[xk1].chro_name, SB_READ(ret), ref_readin_len);
ret -> bam_chro_table[xk1].chro_name[ref_readin_len] = 0;
SB_RINC(ret, ref_readin_len + ref_skip_len);
memcpy(&(ret -> bam_chro_table[xk1].chro_length), SB_READ(ret),4);
SB_RINC(ret, 4);
//SUBREADprintf("CHRO[%d] : %s [%d]\n", xk1+1, ret -> bam_chro_table[xk1].chro_name , ret -> bam_chro_table[xk1].chro_length);
}
ret ->bam_chro_table_size = ref_info_size;
}
static void
suboption(void)
{
unsigned char subchar;
printsub('<', subbuffer, SB_LEN()+2);
switch (subchar = SB_GET()) {
case TELOPT_TTYPE:
if (my_want_state_is_wont(TELOPT_TTYPE))
return;
if (SB_EOF() || SB_GET() != TELQUAL_SEND) {
return;
} else {
const char *name;
unsigned char temp[50];
int len;
name = gettermname();
len = strlen(name) + 4 + 2;
if (len < NETROOM()) {
sprintf(temp, "%c%c%c%c%s%c%c", IAC, SB, TELOPT_TTYPE,
TELQUAL_IS, name, IAC, SE);
ring_supply_data(&netoring, temp, len);
printsub('>', &temp[2], len-2);
} else {
ExitString("No room in buffer for terminal type.\n", 1);
/*NOTREACHED*/
}
}
break;
case TELOPT_TSPEED:
if (my_want_state_is_wont(TELOPT_TSPEED))
return;
if (SB_EOF())
return;
if (SB_GET() == TELQUAL_SEND) {
long ospeed, ispeed;
unsigned char temp[50];
int len;
TerminalSpeeds(&ispeed, &ospeed);
sprintf((char *)temp, "%c%c%c%c%ld,%ld%c%c", IAC, SB, TELOPT_TSPEED,
TELQUAL_IS, ospeed, ispeed, IAC, SE);
len = strlen((char *)temp+4) + 4; /* temp[3] is 0 ... */
if (len < NETROOM()) {
ring_supply_data(&netoring, temp, len);
printsub('>', temp+2, len - 2);
}
/*@*/ else printf("lm_will: not enough room in buffer\n");
}
break;
case TELOPT_LFLOW:
if (my_want_state_is_wont(TELOPT_LFLOW))
return;
if (SB_EOF())
return;
switch(SB_GET()) {
case LFLOW_RESTART_ANY:
restartany = 1;
break;
case LFLOW_RESTART_XON:
restartany = 0;
break;
case LFLOW_ON:
localflow = 1;
break;
case LFLOW_OFF:
localflow = 0;
break;
default:
return;
}
setcommandmode();
setconnmode(0);
break;
case TELOPT_LINEMODE:
if (my_want_state_is_wont(TELOPT_LINEMODE))
return;
if (SB_EOF())
return;
switch (SB_GET()) {
case WILL:
lm_will(subpointer, SB_LEN());
break;
case WONT:
lm_wont(subpointer, SB_LEN());
break;
case DO:
lm_do(subpointer, SB_LEN());
break;
case DONT:
lm_dont(subpointer, SB_LEN());
break;
case LM_SLC:
slc(subpointer, SB_LEN());
break;
case LM_MODE:
lm_mode(subpointer, SB_LEN(), 0);
break;
default:
break;
}
break;
#ifdef OLD_ENVIRON
case TELOPT_OLD_ENVIRON:
#endif
case TELOPT_NEW_ENVIRON:
if (SB_EOF())
return;
switch(SB_PEEK()) {
case TELQUAL_IS:
case TELQUAL_INFO:
if (my_want_state_is_dont(subchar))
return;
break;
case TELQUAL_SEND:
if (my_want_state_is_wont(subchar)) {
return;
}
break;
default:
return;
}
env_opt(subpointer, SB_LEN());
break;
case TELOPT_XDISPLOC:
if (my_want_state_is_wont(TELOPT_XDISPLOC))
return;
if (SB_EOF())
return;
if (SB_GET() == TELQUAL_SEND) {
unsigned char temp[50], *dp;
int len;
if ((dp = env_getvalue("DISPLAY")) == NULL ||
strlen(dp) > sizeof(temp) - 7) {
/*
* Something happened, we no longer have a DISPLAY
* variable. Or it is too long. So, turn off the option.
*/
send_wont(TELOPT_XDISPLOC, 1);
break;
}
snprintf(temp, sizeof(temp), "%c%c%c%c%s%c%c", IAC, SB,
TELOPT_XDISPLOC, TELQUAL_IS, dp, IAC, SE);
len = strlen((char *)temp+4) + 4; /* temp[3] is 0 ... */
if (len < NETROOM()) {
ring_supply_data(&netoring, temp, len);
printsub('>', temp+2, len - 2);
}
/*@*/ else printf("lm_will: not enough room in buffer\n");
}
break;
#ifdef AUTHENTICATION
case TELOPT_AUTHENTICATION: {
if (!autologin)
break;
if (SB_EOF())
return;
switch(SB_GET()) {
case TELQUAL_IS:
if (my_want_state_is_dont(TELOPT_AUTHENTICATION))
return;
auth_is(subpointer, SB_LEN());
break;
case TELQUAL_SEND:
if (my_want_state_is_wont(TELOPT_AUTHENTICATION))
return;
auth_send(subpointer, SB_LEN());
break;
case TELQUAL_REPLY:
if (my_want_state_is_wont(TELOPT_AUTHENTICATION))
return;
auth_reply(subpointer, SB_LEN());
break;
case TELQUAL_NAME:
if (my_want_state_is_dont(TELOPT_AUTHENTICATION))
return;
auth_name(subpointer, SB_LEN());
break;
}
}
break;
#endif
#ifdef ENCRYPTION
case TELOPT_ENCRYPT:
if (SB_EOF())
return;
switch(SB_GET()) {
case ENCRYPT_START:
if (my_want_state_is_dont(TELOPT_ENCRYPT))
return;
encrypt_start(subpointer, SB_LEN());
break;
case ENCRYPT_END:
if (my_want_state_is_dont(TELOPT_ENCRYPT))
return;
encrypt_end();
break;
case ENCRYPT_SUPPORT:
if (my_want_state_is_wont(TELOPT_ENCRYPT))
return;
encrypt_support(subpointer, SB_LEN());
break;
case ENCRYPT_REQSTART:
if (my_want_state_is_wont(TELOPT_ENCRYPT))
return;
encrypt_request_start(subpointer, SB_LEN());
break;
case ENCRYPT_REQEND:
if (my_want_state_is_wont(TELOPT_ENCRYPT))
return;
/*
* We can always send an REQEND so that we cannot
* get stuck encrypting. We should only get this
* if we have been able to get in the correct mode
* anyhow.
*/
encrypt_request_end();
break;
case ENCRYPT_IS:
if (my_want_state_is_dont(TELOPT_ENCRYPT))
return;
encrypt_is(subpointer, SB_LEN());
break;
case ENCRYPT_REPLY:
if (my_want_state_is_wont(TELOPT_ENCRYPT))
return;
encrypt_reply(subpointer, SB_LEN());
break;
case ENCRYPT_ENC_KEYID:
if (my_want_state_is_dont(TELOPT_ENCRYPT))
return;
encrypt_enc_keyid(subpointer, SB_LEN());
break;
case ENCRYPT_DEC_KEYID:
if (my_want_state_is_wont(TELOPT_ENCRYPT))
return;
encrypt_dec_keyid(subpointer, SB_LEN());
break;
default:
break;
}
break;
#endif /* ENCRYPTION */
default:
break;
}
}
SamBam_FILE * SamBam_fopen(char * fname , int file_type)
{
SamBam_FILE * ret = (SamBam_FILE *)malloc(sizeof(SamBam_FILE));
ret -> file_type = file_type;
if(file_type ==SAMBAM_FILE_SAM)
{
ret -> os_file = f_subr_open(fname, "rb");
if(!ret -> os_file)
{
free(ret);
return NULL;
}
fseek(ret -> os_file,0,SEEK_SET);
}
else
{
ret -> os_file = f_subr_open(fname, "rb");
if(ret -> os_file == NULL)
{
free(ret);
return NULL;
}
unsigned char first_ch = fgetc(ret->os_file);
unsigned char second_ch = fgetc(ret->os_file);
if(first_ch!=31 || second_ch!=139)
{
free(ret);
return NULL;
}
fseek(ret->os_file, 0, SEEK_SET);
ret -> input_binary_stream_buffer = (char *)malloc(SAMBAM_INPUT_STREAM_SIZE);
ret -> input_binary_stream_read_ptr = 0;
ret -> input_binary_stream_write_ptr = 0;
ret -> input_binary_stream_buffer_start_ptr = 0;
ret -> bam_file_stage = BAM_FILE_STAGE_HEADER;
ret -> is_eof = 0;
SB_FETCH(ret);
if(SB_EOF(ret))
{
free(ret->input_binary_stream_buffer);
free(ret);
SUBREADprintf("FEOF 0!\n");
return NULL;
}
int magic_4 = 0;
memcpy(&magic_4 , SB_READ(ret), 4);
SB_RINC(ret, 4);
if(magic_4 != 21840194) // this number is the four bytes of "BAM1"
{
free(ret->input_binary_stream_buffer);
free(ret);
SUBREADprintf("FEOF 4 == %d!\n", magic_4);
return NULL;
}
int l_text = 0;
memcpy(&l_text, SB_READ(ret), 4);
SB_RINC(ret, 4);
ret -> bam_file_next_section_start = ret -> input_binary_stream_read_ptr + l_text;
}
return ret;
}
char * SamBam_fgets(SamBam_FILE * fp, char * buff , int buff_len, int seq_needed)
{
if(fp->file_type==SAMBAM_FILE_SAM){
char * ret = fgets(buff, buff_len, fp->os_file);
int strlenbuff = strlen(buff);
if(strlenbuff < 1 || ret == NULL) return NULL;
else{
if(ret[strlenbuff-1]!='\n')
{
while(1)
{
int ch = getc(fp->os_file);
if(ch == EOF || ch == '\n')break;
}
ret[strlenbuff-1] = '\n';
}
return ret;
}
}
else
{
int xk1;
// decrypt the BAM mess.
if(fp-> bam_file_stage == BAM_FILE_STAGE_HEADER)
{
char nch;
xk1=0;
SB_FETCH(fp);
if(SB_EOF(fp))
return NULL;
while(1)
{
if(fp -> input_binary_stream_read_ptr >= fp -> bam_file_next_section_start)
break;
nch = *(SB_READ(fp));
SB_RINC(fp,1);
//printf("NNCH=%c\n", nch);
if(nch == '\r'||nch=='\n' || nch <0) break;
if(xk1 < buff_len-2)
{
buff[xk1]=nch;
xk1++;
}
}
buff[xk1]='\n';
buff[xk1+1]=0;
// printf("%d > %d\n", fp -> input_binary_stream_read_ptr , fp -> bam_file_next_section_start);
if(fp -> input_binary_stream_read_ptr >= fp -> bam_file_next_section_start)
{
SamBam_read_ref_info(fp);
fp -> bam_file_stage = BAM_FILE_STAGE_ALIGNMENT;
}
return buff;
}
else
{
SamBam_Alignment *aln = &fp->aln_buff;
int chunk_ptr = 0;
SB_FETCH(fp);
if(SB_EOF(fp)) return NULL;
int text_len = PBam_chunk_gets(SB_READ(fp) , &chunk_ptr, fp -> input_binary_stream_write_ptr - fp -> input_binary_stream_read_ptr , fp -> bam_chro_table, buff , buff_len, aln, seq_needed);
SB_RINC(fp, chunk_ptr);
if(text_len>0) return buff;
return NULL;
}
}
}
int SamBam_feof(SamBam_FILE * fp)
{
if(fp->file_type ==SAMBAM_FILE_SAM)
return feof(fp->os_file);
else return SB_EOF(fp);
}
static void
suboption(void)
{
unsigned char subchar;
printsub('<', subbuffer, SB_LEN()+2);
switch (subchar = SB_GET()) {
case TELOPT_TTYPE:
if (my_want_state_is_wont(TELOPT_TTYPE))
return;
if (SB_EOF() || SB_GET() != TELQUAL_SEND) {
return;
} else {
char *name;
unsigned char temp[50];
int len;
name = gettermname();
len = strlen(name) + 4 + 2;
if (len < NETROOM()) {
snprintf((char *)temp, sizeof(temp),
"%c%c%c%c%s%c%c", IAC, SB, TELOPT_TTYPE,
TELQUAL_IS, name, IAC, SE);
ring_supply_data(&netoring, temp, len);
printsub('>', &temp[2], len-2);
} else
ExitString("No room in buffer for terminal type.\n", 1);
}
break;
case TELOPT_TSPEED:
if (my_want_state_is_wont(TELOPT_TSPEED))
return;
if (SB_EOF())
return;
if (SB_GET() == TELQUAL_SEND) {
long ospeed, ispeed;
unsigned char temp[50];
int len;
TerminalSpeeds(&ispeed, &ospeed);
snprintf((char *)temp, sizeof(temp),
"%c%c%c%c%ld,%ld%c%c", IAC, SB, TELOPT_TSPEED,
TELQUAL_IS, ospeed, ispeed, IAC, SE);
len = strlen((char *)temp+4) + 4; /* temp[3] is 0 ... */
if (len < NETROOM()) {
ring_supply_data(&netoring, temp, len);
printsub('>', temp+2, len - 2);
}
/*@*/ else printf("lm_will: not enough room in buffer\n");
}
break;
case TELOPT_LFLOW:
if (my_want_state_is_wont(TELOPT_LFLOW))
return;
if (SB_EOF())
return;
switch(SB_GET()) {
case LFLOW_RESTART_ANY:
restartany = 1;
break;
case LFLOW_RESTART_XON:
restartany = 0;
break;
case LFLOW_ON:
localflow = 1;
break;
case LFLOW_OFF:
localflow = 0;
break;
default:
return;
}
setcommandmode();
setconnmode(0);
break;
case TELOPT_LINEMODE:
if (my_want_state_is_wont(TELOPT_LINEMODE))
return;
if (SB_EOF())
return;
switch (SB_GET()) {
case WILL:
lm_will(subpointer, SB_LEN());
break;
case WONT:
lm_wont(subpointer, SB_LEN());
break;
case DO:
lm_do(subpointer, SB_LEN());
break;
case DONT:
lm_dont(subpointer, SB_LEN());
break;
case LM_SLC:
slc(subpointer, SB_LEN());
break;
case LM_MODE:
lm_mode(subpointer, SB_LEN(), 0);
break;
default:
break;
}
break;
case TELOPT_NEW_ENVIRON:
if (SB_EOF())
return;
switch(SB_PEEK()) {
case TELQUAL_IS:
case TELQUAL_INFO:
if (my_want_state_is_dont(subchar))
return;
break;
case TELQUAL_SEND:
if (my_want_state_is_wont(subchar)) {
return;
}
break;
default:
return;
}
env_opt(subpointer, SB_LEN());
break;
case TELOPT_XDISPLOC:
if (my_want_state_is_wont(TELOPT_XDISPLOC))
return;
if (SB_EOF())
return;
if (SB_GET() == TELQUAL_SEND) {
unsigned char temp[50], *dp;
int len;
if ((dp = env_getvalue("DISPLAY", 0)) == NULL) {
/*
* Something happened, we no longer have a DISPLAY
* variable. So, turn off the option.
*/
send_wont(TELOPT_XDISPLOC, 1);
break;
}
snprintf((char *)temp, sizeof(temp),
"%c%c%c%c%s%c%c", IAC, SB, TELOPT_XDISPLOC,
TELQUAL_IS, dp, IAC, SE);
len = strlen((char *)temp+4) + 4; /* temp[3] is 0 ... */
if (len < NETROOM()) {
ring_supply_data(&netoring, temp, len);
printsub('>', temp+2, len - 2);
}
/*@*/ else printf("lm_will: not enough room in buffer\n");
}
break;
default:
break;
}
}
