void TAlignmentOutput::add_align ( const string &seq , const string &quality , uint pos , int chromosome ) {
if ( align_full[pos] ) return ;
int lane , seql = seq.length() ;
for ( lane = 0 ; lane < MAXLINES ; lane++ ) {
if ( align[twotoone(lane,pos)] + align[twotoone(lane,pos+seql/2-1)] + align[twotoone(lane,pos+seql-1)] == 96 ) break ;
}
if ( lane >= MAXLINES ) {
align_full[pos] = true ;
return ; // HARD CUT OFF
}
for ( int i = 0 ; i < seql ; i++ ) {
uint p = twotoone(lane,pos+i) ;
align[p] = seq[i] ;
qalign[p] = quality[i] ;
}
}
void TAlignmentOutput::show_pileup ( FILE *pileup , bool snps_only ) {
int search_snps = 0 , found_snps = 0 , bogus = 0 ;
uint base , l , cnt , p , lastns ;
uchar common ;
char *s2 = new char[MAXLINES+5] ;
char *s3 = new char[MAXLINES+5] ;
char *t , *u ;
uint count[256] ;
for ( base = 0 ; base < chr->sequence.length() ; base++ ) {
if ( snps_only && !isIUPAC[chr->sequence[base]] ) continue ;
if ( isIUPAC[chr->sequence[base]] ) search_snps++ ;
count['A']=count['C']=count['G']=count['T']=0 ;
cnt = 0 ;
common = ' ' ;
lastns = 0 ;
p = twotoone(0,base) ;
t = s2 ;
u = s3 ;
char *c = align + p ;
char *q = qalign + p ;
for ( l = 0 ; l < MAXLINES ; l++ , c++ , q++ ) {
if ( *c && *c != ' ' ) {
lastns = l ;
cnt++ ;
count[*c]++ ;
common = MERGE_IUPAC ( *c , common ) ;
if ( *q < MINQUAL + 33 ) *t++ = to_lc[*c] ;
else *t++ = *c ;
*u++ = *q ;
} else {
*t++ = ' ' ;
*u++ = ' ' ;
}
}
s2[lastns+1] = 0 ;
s3[lastns+1] = 0 ;
bool confirmed_snp = false ;
uint n = 0 ;
if ( count['A'] >= MINOCCUR ) n++ ;
if ( count['C'] >= MINOCCUR ) n++ ;
if ( count['G'] >= MINOCCUR ) n++ ;
if ( count['T'] >= MINOCCUR ) n++ ;
if ( n > 1 ) {
confirmed_snp = true ;
found_snps++ ;
}
/*
if ( common != ' ' && isIUPAC[common] ) {
confirmed_snp = true ;
found_snps++ ;
}
*/
if ( common != ' ' && isIUPAC[common] && !isIUPAC[chr->sequence[base]] ) bogus++ ;
if ( snps_only && common == ' ' ) continue ;
char mark = confirmed_snp ? '*' : ' ' ;
string ref ;
if ( !chr->original_sequence.empty() ) {
ref += chr->original_sequence[base] ;
ref += "\t" ;
}
ref += chr->sequence[base] ;
fprintf ( pileup , "%s\t%s\t%d\t%c%c\t%d\t" , chr->name.c_str() , ref.c_str() , base+1 , common , mark , cnt ) ;
fprintf ( pileup , "%s\t%s\n" , s2 , s3 ) ;
}
}
