std::string Breakpoint::to_string(RefVector ref) {
std::stringstream ss;
ss << "(";
ss << get_chr(get_coordinates().start.min_pos, ref);
ss << ":";
ss << calc_pos(get_coordinates().start.min_pos, ref);
ss << "-";
ss << get_chr(get_coordinates().stop.max_pos, ref);
ss << ":";
ss << calc_pos(get_coordinates().stop.max_pos, ref);
ss << " ";
ss << positions.support.size();
ss << " ";
ss << this->sv_debug;
ss << " ";
ss << this->get_strand(2);
ss << "\n";
int num = 0;
for (std::map<std::string, read_str>::iterator i = positions.support.begin(); i != positions.support.end() && num < Parameter::Instance()->report_n_reads; i++) {
ss << "\t";
ss << (*i).first;
ss << " ";
ss << (*i).second.type;
if ((*i).second.strand.first) {
ss << "+";
} else {
ss << "-";
}
if ((*i).second.strand.second) {
ss << "+";
} else {
ss << "-";
}
num++;
ss << "\n";
}
ss << " ";
return ss.str();
}
void msg_edit::mbeditmenu()
{
int x, result, page = 0;
unsigned char ch;
while ( pass->session->isActive() )
{
pass->session->puts ( "\x1b[0m\x1b[2J" );
pass->session->puts ( ".----------------------------------------------------------------.\r\n" );
pass->session->puts ( "| Message Forum Editor |\r\n" );
pass->session->puts ( "`----------------------------------------------------------------'\r\n" );
x=list_message_bases ( page );
pass->session->puts ( "\r\n [d]elete, [e]dit, [i]nsert, [m]ove, [q]uit : \x1b[1;44m \x1b[D" );
get_chr ( pass,ch );
switch ( toupper ( ch ) )
{
case 'D':
delete_mbase();
break;
case 'I':
insert_mbase();
break;
case 'E':
modify_mbase();
break;
case 'M':
move_mbase();
break;
//case 'B': import_backbone(); break;
case 'Q':
return;
case '[':
page--;
if ( page < 0 )
page = 0;
break;
case ']':
if ( x )
page++;
break;
default :
break;
}
}
}
void msg_edit::mod_mbase ( int mbnum )
{
mb_list_rec mbl;
char faka[41]= {0};
char sigtxt[3][21]= {"None","Short Sig.","Long Sig."};
std::string TF;
char rBuffer[200]= {0};
_mfunc.read_mbaselist ( &mbl, mbnum );
if ( mbl.sigtype < 0 || mbl.sigtype > 2 ) mbl.sigtype = 0;
int total_mbases = _mfunc.msg_count();
int result;
unsigned char ch;
while ( pass->session->isActive() )
{
faddr2char ( faka,&mbl.aka );
strcpy ( rBuffer,"" );
pass->session->puts ( "\x1b[0m\x1b[2J" );
pass->session->puts ( ".----------------------------------------------------------------.\r\n" );
pass->session->puts ( "| Message Forum Editor |\r\n" );
pass->session->puts ( "`----------------------------------------------------------------'\r\n" );
pass->session->printf ( " Forum: %d of %d", mbnum+1,total_mbases );
pass->session->puts ( "\r\n" );
pass->session->puts ( ".-------------------------." );
pass->session->puts ( "\r\n" );
pass->session->printf ( "| [A]. Description | %s", mbl.mbdisplay );
pass->session->puts ( "\r\n" );
pass->session->printf ( "| [B]. Filename | %s", mbl.mbfile );
if ( mbl.Type == MSGTYPE_JAM ) TF = "JAM";
else TF = "SQUISH";
pass->session->puts ( "\r\n" );
pass->session->printf ( "| [C]. Message Type | %s", TF.c_str() );
pass->session->puts ( "\r\n" );
pass->session->printf ( "| [D]. Forum Kind | %s", mbtypes[mbl.Kind] );
pass->session->puts ( "\r\n" );
pass->session->printf ( "| [E]. Posting Type | %s", posttyp[mbl.Pubpriv] );
pass->session->puts ( "\r\n" );
pass->session->printf ( "| [F]. Info Filename | %s", mbl.infofile );
if ( mbl.Allowalias ) TF = "yes";
else TF = "no";
pass->session->puts ( "\r\n" );
pass->session->printf ( "| [G]. Allow Aliases | %s", TF.c_str() );
pass->session->puts ( "\r\n" );
pass->session->printf ( "| [H]. Post ACS | " );
pass->session->puts ( "\r\n" );
pass->session->printf ( "| [I]. Read ACS | " );
pass->session->puts ( "\r\n" );
pass->session->printf ( "| [J]. Sysop ACS | " );
pass->session->puts ( "\r\n" );
pass->session->printf ( "| [K]. Signature | %s", sigtxt[mbl.sigtype] );
pass->session->puts ( "\r\n" );
pass->session->printf ( "| [L]. Mail address | %s", faka );
/*
mci("%sQuoted (%d)`0F, ",
ansic(mbl.colors[MSG_QUOTE]),
mbl.colors[MSG_QUOTE]);
mci("%sText (%d)`0F,",
ansic(mbl.colors[MSG_TEXT]),
mbl.colors[MSG_TEXT]);
mci("%sTear (%d)`0F,",
ansic(mbl.colors[MSG_TEAR]),
mbl.colors[MSG_TEAR]);
mci("%sOrigin (%d)~SM",
ansic(mbl.colors[MSG_ORIGIN]),
mbl.colors[MSG_ORIGIN]);
*/
pass->session->puts ( "\r\n" );
pass->session->printf ( "| [M]. Origin Line | %s", mbl.OriginLine );
pass->session->puts ( "\r\n" );
pass->session->puts ( "`-------------------------'\r\n\r\n" );
pass->session->puts ( " [d]elete, [e]dit, [i]nsert, [m]ove, [q]uit : \x1b[1;44m \x1b[D" );
get_chr ( pass,ch );
switch ( toupper ( ch ) )
{
case 'A':
pass->session->puts ( "\r\n\r\n Description: \x1b[1;44m \x1b[30D" );
get_str ( pass,rBuffer );
if ( strcmp ( rBuffer," " ) == 0 ) break;
strcpy ( mbl.mbdisplay,rBuffer );
break;
case 'B':
pass->session->puts ( "\r\n\r\n New Filename: \x1b[1;44m \x1b[30D" );
get_str ( pass,rBuffer );
if ( strcmp ( rBuffer," " ) == 0 ) break;
strcpy ( mbl.mbfile,rBuffer );
break;
case 'C':
if ( mbl.Type == MSGTYPE_JAM ) mbl.Type = MSGTYPE_SQUISH;
else mbl.Type = MSGTYPE_JAM;
break;
case 'D':
++mbl.Kind;
if ( mbl.Kind > 4 )
mbl.Kind = 0;
switch ( mbl.Kind )
{
case LOCAL :
mbl.Pubpriv = PUBLIC;
break;
case ECHOMAIL :
mbl.Pubpriv = PUBLIC;
break;
case NETMAIL :
mbl.Pubpriv = PRIVATE;
break;
case EMAIL :
mbl.Pubpriv = PRIVATE;
break;
case NEWS :
mbl.Pubpriv = PUBLIC;
break;
}
break;
case 'E':
if ( mbl.Pubpriv==PUBLIC )
{
switch ( mbl.Kind )
{
case LOCAL :
mbl.Pubpriv = PRIVATE;
break;
case ECHOMAIL :
mbl.Pubpriv = PUBLIC;
break;
case NETMAIL :
mbl.Pubpriv = PRIVATE;
break;
case EMAIL :
mbl.Pubpriv = PRIVATE;
break;
case NEWS :
mbl.Pubpriv = PUBLIC;
break;
}
}
else
{
switch ( mbl.Kind )
{
case LOCAL :
mbl.Pubpriv = PUBLIC;
break;
case ECHOMAIL :
mbl.Pubpriv = PUBLIC;
break;
case NETMAIL :
mbl.Pubpriv = PRIVATE;
break;
case EMAIL :
mbl.Pubpriv = PRIVATE;
break;
case NEWS :
mbl.Pubpriv = PUBLIC;
break;
}
}
break;
case 'F':
pass->session->puts ( "\r\n\r\n Info File: \x1b[1;44m \x1b[30D" );
get_str ( pass,rBuffer );
if ( strcmp ( rBuffer," " ) == 0 ) break;
strcpy ( mbl.infofile,rBuffer );
break;
case 'G':
mbl.Allowalias = ( mbl.Allowalias ) ?0:1;
break;
case 'H':
ACS ( &mbl.WriteACS,mbl.mbdisplay );
break;
case 'I':
ACS ( &mbl.ReadACS, mbl.mbdisplay );
break;
case 'J':
ACS ( &mbl.SysopACS,mbl.mbdisplay );
break;
case 'K':
mbl.sigtype++;
if ( mbl.sigtype<0 || mbl.sigtype>2 )
mbl.sigtype=0;
break;
case 'L':
edit_aka ( &mbl );
//mbl.fidoaddr=pick_aka();
break;
case 'M':
pass->session->puts ( "\r\n\r\n Origin Line: \x1b[1;44m \x1b[30D" );
get_str ( pass,rBuffer );
if ( strcmp ( rBuffer," " ) == 0 ) break;
strcpy ( mbl.OriginLine,rBuffer );
break;
case 'Q':
_mfunc.save_mbaselist ( &mbl, mbnum );
_mfunc.save_msgbase ( &mbl );
return;
}
}
}
// INS_CNV, DUP1, DUP2, DEL, INV
void rsv_gen(FILE *msg, reg_t *rsv_reg)
{
char msg_line[1024]; _reg_t r;
char chr[10]; int s,e,len; char type[10]; char xa[1024], ins_chr[10]; int ins_s, ins_e;
int left=1, offset=0, right;
while (fgets(msg_line, 1024, msg) != NULL)
{
sscanf(msg_line, "%s\t%d\t%d\t%d\t%s\t%[^\n]\n", chr, &s, &e, &len, type, xa);
switch(type[2])
{
case 'S': // INS
sscanf(xa, "%s\t%d\t%d", ins_chr, &ins_s, &ins_e);
right = s+offset; //M right
//fprintf(stdout, "%s\t%d\t%d\t%d\t%s\n", chr, left, right, right-left+1, "MAT");
r.chr = get_chr(chr), strcpy(r.type, "MAT");
r.left = left, r.right = right, r.len = right-left+1, r.offset=offset;
push_reg(rsv_reg, r);
left=e+offset; //I left
right=left+len-1; //I right
//fprintf(stdout, "%s\t%d\t%d\t%d\t%s\n", chr, left, right, len, "INS");
r.chr = get_chr(chr), strcpy(r.type, "INS_CNV");
r.left = left, r.right = right, r.len = len, r.offset=offset;
// ins_reg
r.ins_chr = get_chr(ins_chr);
r.ins_left = ins_s, r.ins_right = ins_e;
push_reg(rsv_reg, r);
left = e+offset+len;
offset+=len;
break;
case 'P': // DUP (DUP1, DUP2, ...)
right = s+offset; // M right
r.chr = get_chr(chr), strcpy(r.type, "MAT");
r.left = left, r.right = right, r.len = right-left+1, r.offset=offset;
push_reg(rsv_reg, r);
left=e+offset; // P left
right=left+len-1; // P right
r.chr = get_chr(chr), strcpy(r.type, type); // DUP1, DUP2, ...
r.left = left, r.right = right, r.len = len, r.offset=offset;
// dup_reg
r.ins_chr = get_chr(chr);
r.ins_left = s-(len)/atoi(type+3)+1; r.ins_right = s;
push_reg(rsv_reg, r);
left = e+offset+len;
offset+=len;
break;
case 'L': // DEL
right = s+offset;
//fprintf(stdout, "%s\t%d\t%d\t%d\t%s\n", chr, left, right, right-left+1, "MAT");
r.chr = get_chr(chr), strcpy(r.type, "MAT");
r.left = left, r.right = right, r.len = right-left+1, r.offset=offset;
push_reg(rsv_reg, r);
left=s+offset;
offset-=len;
right=e+offset;
//fprintf(stdout, "%s\t%d\t%d\t%d\t%s\n", chr, left, right, len, "DEL");
r.chr = get_chr(chr), strcpy(r.type, "DEL");
r.left = left, r.right = right, r.len = len, r.offset=offset;
push_reg(rsv_reg, r);
left=right;
break;
case 'V': // INV
right=s+offset; //M right
//fprintf(stdout, "%s\t%d\t%d\t%d\t%s\n", chr, left, right, right-left+1, "MAT");
r.chr = get_chr(chr), strcpy(r.type, "MAT");
r.left = left, r.right = right, r.len = right-left+1, r.offset=offset;
push_reg(rsv_reg, r);
left=right+1; //V left
right=e+offset-1;//V right
//fprintf(stdout, "%s\t%d\t%d\t%d\t%s\n", chr, left, right, len, "INV");
r.chr = get_chr(chr), strcpy(r.type, "INV");
r.left = left, r.right = right, r.len = len, r.offset=offset;
r.ins_left = s, r.ins_right = e; // inv_left, inv_right
push_reg(rsv_reg, r);
left=e+offset; //M left
break;
default: break;
}
//fprintf(stdout, "%s %d %d %d %s\n", chr, s, e, len, type);
}
right=CHR_MAX_LEN; len=right-left+1;
//fprintf(stdout, "%s\t%d\t%d\t%d\t%s\n", chr, left, right, len, "MAT");
r.chr = get_chr(chr), strcpy(r.type, "MAT");
r.left = left, r.right = right, r.len = len, r.offset=offset;
push_reg(rsv_reg, r);
}
void whole_gen_core(reg_t *rsv_reg, FILE *wgsim, reg_t *who_reg)
{
int i;
char msg_line[1024]; _reg_t r;
char chr[10]; int s,e,len; char type[10];
int offset=0, /*next*/left=1, right;
int cur_rsv_n = 0; _reg_t R_r, w_r; int indel=0;
reg_t *cur, *next;
//init cur/next
cur = (reg_t*)malloc(sizeof(reg_t));
cur->reg_m = 100;
cur->reg = (_reg_t*)malloc(100 * sizeof(_reg_t));
next = (reg_t*)malloc(sizeof(reg_t));
next->reg_m = 100;
next->reg = (_reg_t*)malloc(100 * sizeof(_reg_t));
cur->reg_n = 0;
next->reg_n = 0;
// first wgsim-region, stored in next
fgets(msg_line, 1024, wgsim);
sscanf(msg_line, "%s\t%d\t%d\t%d\t%s\n", chr, &s, &e, &len, type);
r.left = s, r.right = e, r.len = len, r.offset=0; r.chr=get_chr(chr), strcpy(r.type, type);
push_reg(next, r);
offset = 0;
while (cur_rsv_n < rsv_reg->reg_n) {
// clear cur
cur->reg_n = 0;
R_r = rsv_reg->reg[cur_rsv_n];
// find wgsim in the rsv-region, store in cur
// until one wgsim outbound this rsv-reg, store in next
if (next->reg_n>0 && R_r.type[2] != 'L') {
// push next to cur, if necessary
if (((next->reg[0].type[2] == 'S' || next->reg[0].type[2] == 'P') && next->reg[0].left <= rsv_reg->reg[cur_rsv_n].right)
|| (next->reg[0].type[2] == 'L' && next->reg[0].left < rsv_reg->reg[cur_rsv_n].right)) {
// split wgsim, if it acrosses two RSV-reg
if (next->reg[0].type[2] == 'L'&& next->reg[0].right > rsv_reg->reg[cur_rsv_n].right+1) {
r.left = next->reg[0].left;
r.right = rsv_reg->reg[cur_rsv_n].right+1;
r.len = r.right-r.left+1;
r.offset = 0;
r.chr = next->reg[0].chr, strcpy(r.type, "DEL");
push_reg(cur, r);
r.left = rsv_reg->reg[cur_rsv_n].right;
r.right = next->reg[0].right;
r.len = r.right-r.left+1;
r.offset = 0;
next->reg_n=0;
push_reg(next, r);
goto UPDATE;
}
push_reg(cur, next->reg[0]);
next->reg_n = 0;
// push wgsim to cur, if necessary
// until push wgsim to next, or reach EOF in wgsim
while (fgets(msg_line, 1024, wgsim) != NULL) {
sscanf(msg_line, "%s\t%d\t%d\t%d\t%s\n", chr, &(r.left), &(r.right), &(r.len), r.type);
r.chr = get_chr(chr);
if (((r.type[2]=='S' || r.type[2]=='P') && r.left <= rsv_reg->reg[cur_rsv_n].right)
|| (r.type[2]=='L' && r.left < rsv_reg->reg[cur_rsv_n].right)) {
// split wgsim, if necessary, same to upper
if (r.type[2] == 'L' && r.right > rsv_reg->reg[cur_rsv_n].right+1) {
left = r.left, right = r.right, len = r.len;
r.left = left, r.right = rsv_reg->reg[cur_rsv_n].right+1;
r.len = r.right-r.left+1;
r.offset=0;
push_reg(cur, r);
r.left = rsv_reg->reg[cur_rsv_n].right;
r.right = right;
r.len = r.right - r.left + 1;
push_reg(next, r);
break;
}
push_reg(cur, r);
}
else { push_reg(next, r); break; }
}
}
}
UPDATE:
// split cur_rsv, based on cur, push into whole_reg
switch (R_r.type[2]) {
case 'T': // MATCH
left = R_r.left+offset;
for (i = 0; i < cur->reg_n; ++i) {
// push (left, cur.s) and (cur.s, cur.e) into whole_reg
w_r = cur->reg[i];
switch (w_r.type[2]){
case 'S': // INS
// (left, cur.s)
r.left = left;
r.right = w_r.left+offset;
r.len = r.right-r.left+1;
r.offset = R_r.offset+offset;
r.wgsim_off = offset;
r.chr = w_r.chr, strcpy(r.type, R_r.type);
push_reg(who_reg, r);
// (wgsim)
r.left = w_r.right+offset;
r.len = w_r.len;
r.right = r.left+r.len-1;
r.wgsim_off = offset;
r.chr = w_r.chr, strcpy(r.type, "INS");
push_reg(who_reg, r);
// set next-left
left = r.right+1;
offset += len;
break;
case 'L': // DEL
// (left, cur.s)
r.left = left;
r.right = w_r.left+offset;
r.len = r.right-r.left+1;
r.offset = R_r.offset+offset;
r.wgsim_off = offset;
r.chr = w_r.chr, strcpy(r.type, R_r.type);
push_reg(who_reg, r);
// (cur.s, cur.e)
r.left = w_r.left+offset;
r.right = r.left+1;
r.len = w_r.len;
r.offset = R_r.offset+offset;
r.wgsim_off = offset;
r.chr = w_r.chr, strcpy(r.type, "DEL");
push_reg(who_reg, r);
// next left
left = r.right;
offset -= w_r.len;
break;
default: break;
}
}
// push (left, rsv.end) into whole_reg
r.left = left;
r.right = R_r.right+offset;
r.len = r.right-r.left+1;
r.offset = R_r.offset+offset;
r.wgsim_off = offset;
r.chr = R_r.chr, strcpy(r.type, R_r.type);
push_reg(who_reg, r);
break;
case 'V': // INV
indel = 0;
for (i = 0; i < cur->reg_n; ++i) { // calculate whole-indels
if (cur->reg[i].type[2] == 'S') // INS
indel += (cur->reg[i].len);
else if (cur->reg[i].type[2] == 'L') // DEL
indel -= (cur->reg[i].len);
else {fprintf(stderr, "[whole_gen] Error.\n"); exit(0);}
}
r.left = R_r.left + offset;
r.len = R_r.len + indel;
r.right = r.left + r.len - 1;
r.offset = R_r.offset + offset;
r.wgsim_off = offset;
r.chr = R_r.chr, strcpy(r.type, R_r.type);
r.ins_left = R_r.ins_left; r.ins_right = R_r.ins_right;
push_reg(who_reg, r);
offset += indel;
break;
case 'S': // INS
case 'P': // DUP
indel = 0;
for (i = 0; i < cur->reg_n; ++i) { // calculate whole-indels
if (cur->reg[i].type[2] == 'S') // INS
indel += (cur->reg[i].len);
else if (cur->reg[i].type[2] == 'L') // DEL
indel -= (cur->reg[i].len);
else {fprintf(stderr, "[whole_gen] Error.\n"); exit(0);}
}
r.left = R_r.left + offset;
r.len = R_r.len + indel;
if (r.len <=0 ) { fprintf(stderr, "[whole_gen] Error: indel >= RSV %s-len.\n", R_r.type); exit(0); }
r.right = r.left + r.len - 1;
r.offset = R_r.offset + offset;
r.wgsim_off = offset;
r.chr = R_r.chr, strcpy(r.type, R_r.type);
r.ins_chr = R_r.ins_chr;
r.ins_left = R_r.ins_left; r.ins_right = R_r.ins_right;
push_reg(who_reg, r);
offset += indel;
break;
case 'L': // DEL // no split
r.left = R_r.left+offset;
r.right = R_r.right+offset;
r.len = R_r.len;
r.offset = R_r.offset+offset;
r.wgsim_off = offset;
r.chr = R_r.chr, strcpy(r.type, "DEL");
push_reg(who_reg,r);
default: break;
}
// next rsv-reg
++cur_rsv_n;
}
free(cur->reg), free(cur); free(next->reg), free(next);
}
