mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-15 12:47:57 +08:00
r254: added --ex-list and --ex-iter
This commit is contained in:
Heng Li
175
extract.cpp
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175
extract.cpp
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@@ -0,0 +1,175 @@
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#include <zlib.h>
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#include <string.h>
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#include "Process_Read.h"
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#include "khashl.h"
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#include "kseq.h"
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typedef const char *cstr_t;
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KHASHL_CMAP_INIT(KH_LOCAL, strmap_t, ss, cstr_t, int, kh_hash_str, kh_eq_str)
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KSTREAM_INIT(gzFile, gzread, 65536)
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#define GFA_MALLOC(ptr, len) ((ptr) = (__typeof__(ptr))malloc((len) * sizeof(*(ptr))))
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#define GFA_REALLOC(ptr, len) ((ptr) = (__typeof__(ptr))realloc((ptr), (len) * sizeof(*(ptr))))
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char *gfa_strdup(const char *src)
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{
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int32_t len;
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char *dst;
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len = strlen(src);
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GFA_MALLOC(dst, len + 1);
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memcpy(dst, src, len + 1);
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return dst;
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}
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char *gfa_strndup(const char *src, size_t n)
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{
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char *dst;
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GFA_MALLOC(dst, n + 1);
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strncpy(dst, src, n);
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dst[n] = 0;
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return dst;
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}
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char **gv_read_list(const char *o, int *n_)
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{
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int n = 0, m = 0;
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char **s = 0;
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*n_ = 0;
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if (*o != '@') {
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const char *q = o, *p;
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for (p = q;; ++p) {
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if (*p == ',' || *p == 0) {
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if (n == m) {
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m = m? m<<1 : 16;
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GFA_REALLOC(s, m);
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}
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s[n++] = gfa_strndup(q, p - q);
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if (*p == 0) break;
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q = p + 1;
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}
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}
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} else {
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gzFile fp;
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kstream_t *ks;
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kstring_t str = {0,0,0};
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int dret;
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fp = gzopen(o + 1, "r");
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if (fp == 0) return 0;
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ks = ks_init(fp);
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while (ks_getuntil(ks, KS_SEP_LINE, &str, &dret) >= 0) {
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char *p;
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for (p = str.s; *p && !isspace(*p); ++p);
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if (n == m) {
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m = m? m<<1 : 16;
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GFA_REALLOC(s, m);
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}
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s[n++] = gfa_strndup(str.s, p - str.s);
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}
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ks_destroy(ks);
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gzclose(fp);
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}
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if (s) s = (char**)realloc(s, n * sizeof(char*));
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*n_ = n;
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return s;
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}
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void ha_extract_print(const All_reads *rs, int n_rounds, int n, char **list)
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{
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strmap_t *h;
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khint_t k;
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int i, absent, m, l, max_len = 0;
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uint64_t j;
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char *s = 0;
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const ma_hit_t_alloc *ov[2] = { rs->paf, rs->reverse_paf };
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FILE *fp = stdout;
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for (j = 0; j < rs->total_reads; ++j) {
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if (max_len < (int)Get_NAME_LENGTH(*rs, j))
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max_len = Get_NAME_LENGTH(*rs, j);
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}
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GFA_MALLOC(s, max_len + 1);
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h = ss_init();
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for (i = 0; i < n; ++i) {
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k = ss_put(h, gfa_strdup(list[i]), &absent);
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kh_val(h, k) = -1;
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}
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for (m = 0; m < n_rounds; ++m) {
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for (j = 0; j < rs->total_reads; ++j) {
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for (l = 0; l < 2; ++l) {
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const ma_hit_t_alloc *o = &ov[l][j];
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for (i = 0; i < (int)o->length; ++i) {
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uint64_t q = Get_qn(o->buffer[i]);
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uint64_t t = Get_tn(o->buffer[i]);
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int q_hit = 0, t_hit = 0;
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strncpy(s, Get_NAME(*rs, q), Get_NAME_LENGTH(*rs, q)); s[Get_NAME_LENGTH(*rs, q)] = 0;
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k = ss_get(h, s);
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q_hit = (k < kh_end(h) && kh_val(h, k) < m);
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strncpy(s, Get_NAME(*rs, t), Get_NAME_LENGTH(*rs, t)); s[Get_NAME_LENGTH(*rs, t)] = 0;
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k = ss_get(h, s);
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t_hit = (k < kh_end(h) && kh_val(h, k) < m);
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if ((!q_hit && !t_hit) || (q_hit && t_hit)) continue;
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if (!q_hit) {
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char *tmp = gfa_strndup(Get_NAME(*rs, q), Get_NAME_LENGTH(*rs, q));
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k = ss_put(h, tmp, &absent);
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if (absent) kh_val(h, k) = m;
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else free(tmp);
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}
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if (!t_hit) {
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char *tmp = gfa_strndup(Get_NAME(*rs, t), Get_NAME_LENGTH(*rs, t));
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k = ss_put(h, tmp, &absent);
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if (absent) kh_val(h, k) = m;
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else free(tmp);
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}
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}
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}
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}
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}
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for (j = 0; j < rs->total_reads; ++j) {
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for (l = 0; l < 2; ++l) {
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const ma_hit_t_alloc *o = &ov[l][j];
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for (i = 0; i < (int)o->length; ++i) {
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uint64_t q = Get_qn(o->buffer[i]);
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uint64_t t = Get_tn(o->buffer[i]);
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int q_hit = 0, t_hit = 0;
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strncpy(s, Get_NAME(*rs, q), Get_NAME_LENGTH(*rs, q)); s[Get_NAME_LENGTH(*rs, q)] = 0;
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k = ss_get(h, s);
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q_hit = (k < kh_end(h));
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strncpy(s, Get_NAME(*rs, t), Get_NAME_LENGTH(*rs, t)); s[Get_NAME_LENGTH(*rs, t)] = 0;
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k = ss_get(h, s);
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t_hit = (k < kh_end(h));
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if (!q_hit && !t_hit) continue;
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fwrite(Get_NAME(*rs, q), 1, Get_NAME_LENGTH(*rs, q), fp);
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fwrite("\t", 1, 1, fp);
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fprintf(fp, "%lu\t", (unsigned long)Get_READ_LENGTH(*rs, q));
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fprintf(fp, "%d\t", Get_qs(o->buffer[i]));
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fprintf(fp, "%d\t", Get_qe(o->buffer[i]));
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fputs(o->buffer[i].rev? "-\t" : "+\t", fp);
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fwrite(Get_NAME(*rs, t), 1, Get_NAME_LENGTH(*rs, t), fp);
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fwrite("\t", 1, 1, fp);
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fprintf(fp, "%lu\t", (unsigned long)Get_READ_LENGTH(*rs, t));
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fprintf(fp, "%d\t", Get_ts(o->buffer[i]));
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fprintf(fp, "%d\t%d\t%d\t%d\n", Get_te(o->buffer[i]), o->buffer[i].ml, o->buffer[i].bl, !l);
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}
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}
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}
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for (k = 0; k != kh_end(h); ++k)
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if (kh_exist(h, k))
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free((char*)kh_key(h, k));
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ss_destroy(h);
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free(s);
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}
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void ha_extract_print_list(const All_reads *rs, int n_rounds, const char *o)
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{
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int i, n;
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char **list;
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list = gv_read_list(o, &n);
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ha_extract_print(rs, n_rounds, n, list);
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for (i = 0; i < n; ++i) free(list[i]);
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free(list);
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}
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