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best_sam_hits4longreads.c
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best_sam_hits4longreads.c
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#include "mem_share.h"
#include "filereader.h"
#include "list.h"
#include "hashset.h"
typedef struct {
u4i stroff, strlen;
u4i taglen, flag;
u4i qlen, qb, qe;
u4i refidx, reflen;
} lr_hit_t;
define_list(lrhitv, lr_hit_t);
int select_best_hit(lrhitv *hits, String *lines, u4i minlen, float mincov, FILE *out){
lr_hit_t *h1, *h2;
u4i i, j, pass;
int x, y, ret;
sort_array(hits->buffer, hits->size, lr_hit_t, num_cmpgt(b.qe - b.qb, a.qe - a.qb));
ret = 0;
for(i=0;i<hits->size;i++){
h1 = ref_lrhitv(hits, i);
if(h1->qe - h1->qb < minlen) break;
if(h1->qe - h1->qb < UInt(mincov * h1->qlen)) break;
pass = 1;
for(j=0;j<i;j++){
h2 = ref_lrhitv(hits, j);
x = num_max(h1->qb, h2->qb);
y = num_min(h1->qe, h2->qe);
if(y - x >= (1 - mincov) * (h1->qe - h1->qb)){
pass = 0;
break;
}
}
if(pass){
fprintf(out, "%s\n", lines->string + h1->stroff);
ret ++;
}
}
clear_lrhitv(hits);
clear_string(lines);
return ret;
}
int usage(char *prog){
printf(
"Usage: %s [-h] [-v] [-B:retain secondary aligment] [-l min_map_len:100] [-f min_map_cov:0.70]\n"
, prog
);
return 1;
}
int main(int argc, char **argv){
FileReader *fr;
FILE *out;
cuhash *refs;
cplist *reftags;
u4v *reflens;
String *lines;
lrhitv *hits;
lr_hit_t *hit, HIT;
char *str, *reftag;
u4i minlen, i, reflen;
float mincov;
int c, primary_hit, verbose;
u1i movs[256];
minlen = 100;
mincov = 0.70;
primary_hit = 1;
verbose = 0;
out = stdout;
while((c = getopt(argc, argv, "hvBl:f:")) != -1){
switch(c){
case 'l': minlen = atoi(optarg); break;
case 'f': mincov = atof(optarg); break;
case 'B': primary_hit = 0; break;
case 'v': verbose = 1; break;
default: return usage(argv[0]);
}
}
fr = open_filereader(NULL, 1);
refs = init_cuhash(13);
reftags = init_cplist(8);
reflens = init_u4v(8);
hits = init_lrhitv(4);
lines = init_string(1024);
memset(movs, 0, 256);
movs[(int)'M'] = 0b11;
movs[(int)'I'] = 0b10;
movs[(int)'D'] = 0b01;
movs[(int)'N'] = 0b01;
movs[(int)'S'] = 0b10;
movs[(int)'H'] = 0b10;
movs[(int)'P'] = 0b00;
movs[(int)'='] = 0b11;
movs[(int)'X'] = 0b11;
while((c = readline_filereader(fr))){
if(fr->line->string[0] == '@'){
fprintf(out, "%s\n", fr->line->string);
if(fr->line->string[1] == 'S' && fr->line->string[2] == 'Q'){
if((c = split_line_filereader(fr, '\t')) > 2){
reftag = NULL;
reflen = 0;
for(i=1;i<3;i++){
if(get_col_len(fr, i) <= 3){
continue;
}
str = get_col_str(fr, i);
if(str[0] == 'S' && str[1] == 'N' && str[2] == ':'){
reftag = strdup(str + 3);
} else if(str[0] == 'L' && str[1] == 'N' && str[2] == ':'){
reflen = atol(str + 3);
}
}
if(strlen(reftag) && reflen){
push_cplist(reftags, reftag);
push_u4v(reflens, reflen);
put_cuhash(refs, (cuhash_t){reftag, reftags->size - 1});
}
}
}
} else {
hit = &HIT;
str = index(fr->line->string, '\t');
if(str == NULL){
fprintf(stderr, "[WARNNING:too_few_column] %s\n", fr->line->string);
continue;
}
hit->taglen = str - fr->line->string;
if(hits->size && (hits->buffer[0].taglen != hit->taglen || strncmp(lines->string + hits->buffer[0].stroff, fr->line->string, hit->taglen))){
select_best_hit(hits, lines, minlen, mincov, out);
}
hit->stroff = lines->size;
hit->strlen = fr->line->size;
append_string(lines, fr->line->string, fr->line->size);
add_char_string(lines, '\0');
if((c = split_line_filereader(fr, '\t')) < 11){
fprintf(stderr, "[WARNNING:too_few_columns] %s\n", lines->string + hit->stroff);
continue;
}
hit->taglen = get_col_len(fr, 0);
hit->flag = atol(get_col_str(fr, 1));
if(primary_hit && (hit->flag & 0x900)){
continue;
}
if(get_col_str(fr, 2)[0] == '*'){
continue;
}
hit->refidx = getval_cuhash(refs, get_col_str(fr, 2));
if(hit->refidx == MAX_U4){
fprintf(stderr, "[WARNNING:unknown_refname] %s\n", lines->string + hit->stroff);
continue;
}
hit->reflen = reflens->buffer[hit->refidx];
hit->qlen = 0;
u4i tb, te, qb, qe, len, cnt, tmp;
u4i ln;
char op;
tb = atoi(get_col_str(fr, 3));
te = tb;
qb = qe = 0;
len = 0;
tmp = cnt = 0;
str = get_col_str(fr, 5); // CIGAR
ln = 0;
op = 0;
while(str[0]){
if(str[0] >= '0' && str[0] <= '9'){
ln = ln * 10 + str[0] - '0';
} else {
op = movs[(int)str[0]];
if(op & 0b01){
te += ln;
qe += tmp;
tmp = 0;
if(cnt == 0){
qb = qe;
cnt = 1;
}
if(op & 0b10){
qe += ln;
len += ln;
}
} else if(op & 0b10){
tmp += ln;
len += ln;
}
ln = 0;
}
str ++;
}
if(hit->flag & 0x10){
tmp = len - qb;
qb = len - qe;
qe = tmp;
}
hit->qlen = len;
hit->qb = qb;
hit->qe = qe;
if(verbose){
fprintf(out, "#%s\t%u\t+\t%u\t%u\t%s\t%c\t%u\t%u\n", get_col_str(fr, 0), len, qb, qe, get_col_str(fr, 2), "+-"[(hit->flag & 0x10) >> 4], tb, te);
}
push_lrhitv(hits, HIT);
}
}
select_best_hit(hits, lines, minlen, mincov, out);
free_string(lines);
free_lrhitv(hits);
free_cuhash(refs);
for(i=0;i<reftags->size;i++){
free(reftags->buffer[i]);
}
free_cplist(reftags);
free_u4v(reflens);
close_filereader(fr);
return 0;
}