--- /dev/null
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <zlib.h>
+#include "kstring.h"
+#include "kseq.h"
+KSTREAM_INIT(gzFile, gzread, 16384)
+
+#define N_TMPSTR 5
+
+#define write_cigar(_c, _n, _m, _v) do { \
+ if (_n == _m) { \
+ _m = _m? _m<<1 : 4; \
+ _c = realloc(_c, _m * sizeof(unsigned)); \
+ } \
+ _c[_n++] = (_v); \
+ } while (0)
+
+int main(int argc, char *argv[])
+{
+ gzFile fp;
+ kstream_t *ks;
+ kstring_t s, t[N_TMPSTR];
+ int dret, i, af_n, af_max, af_i;
+ long n_ctgs = 0, n_reads = 0, m_cigar = 0, n_cigar = 0;
+ unsigned *af, *cigar = 0;
+
+ if (argc == 1) {
+ fprintf(stderr, "\nUsage: ace2sam <in.ace>\n\n");
+ fprintf(stderr, " ace2sam in.ace > a2s.out 2> a2s.err\n");
+ fprintf(stderr, " (grep ^H a2s.err | sed s,^..,,; cat a2s.out) > a2s.sam\n");
+ fprintf(stderr, " grep ^S a2s.err | sed s,^..,, > a2s.fa\n\n");
+ return 1;
+ }
+ s.l = s.m = 0; s.s = 0;
+ af_n = af_max = af_i = 0; af = 0;
+ for (i = 0; i < N_TMPSTR; ++i) t[i].l = t[i].m = 0, t[i].s = 0;
+ fp = strcmp(argv[1], "-")? gzopen(argv[1], "r") : gzdopen(fileno(stdin), "r");
+ ks = ks_init(fp);
+ while (ks_getuntil(ks, 0, &s, &dret) >= 0) {
+ if (strcmp(s.s, "AS") == 0) {
+ ks_getuntil(ks, 0, &s, &dret); n_ctgs = atol(s.s);
+ ks_getuntil(ks, 0, &s, &dret); n_reads = atol(s.s);
+ if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
+ } else if (strcmp(s.s, "CO") == 0) {
+ t[0].l = t[1].l = t[2].l = t[3].l = t[4].l = 0; // 0: name; 1: padded; 2: unpadded; 3: CIGAR/flat-cigar; 4: SAM line
+ af_n = af_i = 0;
+ ks_getuntil(ks, 0, &s, &dret); kputs(s.s, &t[0]);
+ ks_getuntil(ks, 0, &s, &dret);
+ ks_getuntil(ks, 0, &s, &dret); n_reads = atoi(s.s);
+ ks_getuntil(ks, '\n', &s, &dret);
+ fprintf(stderr, "S >%s\n", t[0].s);
+ while (ks_getuntil(ks, '\n', &s, &dret) >= 0 && s.l > 0) {
+ kputs(s.s, &t[1]);
+ fputs("S ", stderr); fputs(s.s, stderr); fputc('\n', stderr);
+ }
+
+#define __padded2cigar(sp, su) do { \
+ int i, l_M = 0, l_D = 0; \
+ kputsn(sp.s, sp.l, &su); su.l = 0; \
+ for (i = 0; i < sp.l; ++i) { \
+ if (sp.s[i] == '*') { \
+ if (l_M) write_cigar(cigar, n_cigar, m_cigar, l_M<<4); \
+ ++l_D; l_M = 0; \
+ } else { \
+ if (l_D) write_cigar(cigar, n_cigar, m_cigar, l_D<<4 | 2); \
+ ++l_M; l_D = 0; \
+ su.s[su.l++] = sp.s[i]; \
+ } \
+ } \
+ su.s[su.l] = 0; \
+ if (l_M) write_cigar(cigar, n_cigar, m_cigar, l_M<<4); \
+ else write_cigar(cigar, n_cigar, m_cigar, l_D<<4 | 2); \
+ } while (0)
+
+ n_cigar = 0;
+ __padded2cigar(t[1], t[2]);
+ for (i = 0; i < n_cigar; ++i) {
+ kputw(cigar[i]>>4, &t[3]); kputc("MIDNSHP=X"[cigar[i]&0xf], &t[3]);
+ }
+ kputsn(t[0].s, t[0].l, &t[4]); kputs("\t516\t", &t[4]); kputsn(t[0].s, t[0].l, &t[4]); kputs("\t1\t60\t", &t[4]);
+ kputsn(t[3].s, t[3].l, &t[4]); kputs("\t*\t0\t0\t", &t[4]); kputsn(t[2].s, t[2].l, &t[4]); kputs("\t*", &t[4]);
+ fprintf(stderr, "H @SQ\tSN:%s\tLN:%ld\n", t[0].s, t[1].l);
+ } else if (strcmp(s.s, "BQ") == 0) {
+ if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
+ t[4].s[--t[4].l] = 0;
+ for (i = 0; i < t[2].l; ++i) {
+ int q;
+ if (ks_getuntil(ks, 0, &s, &dret) < 0) fprintf(stderr, "E truncated contig quality\n");
+ q = atoi(s.s) + 33;
+ if (q > 126) q = 126;
+ kputc(q, &t[4]);
+ }
+ if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
+ ks_getuntil(ks, '\n', &s, &dret);
+ puts(t[4].s); t[4].l = 0;
+ } else if (strcmp(s.s, "AF") == 0) { // read coordinate
+ int reversed, neg, pos;
+ if (t[4].l) puts(t[4].s);
+ t[4].l = 0;
+ ks_getuntil(ks, 0, &s, &dret);
+ ks_getuntil(ks, 0, &s, &dret); reversed = s.s[0] == 'C'? 1 : 0;
+ ks_getuntil(ks, 0, &s, &dret); pos = atoi(s.s); neg = pos < 0? 1 : 0; pos = pos < 0? -pos : pos;
+ if (af_n == af_max) {
+ af_max = af_max? af_max<<1 : 4;
+ af = realloc(af, af_max * sizeof(unsigned));
+ }
+ af[af_n++] = pos << 2 | neg << 1 | reversed;
+ } else if (strcmp(s.s, "RD") == 0) { // read sequence
+ t[2].l = t[3].l = t[4].l = 0;
+ ks_getuntil(ks, 0, &t[4], &dret); kputc('\t', &t[4]); // read name
+ kputw((af[af_i]&1)? 16 : 0, &t[4]); kputc('\t', &t[4]);
+ kputsn(t[0].s, t[0].l, &t[4]); kputc('\t', &t[4]); // the SAM line stops at RNAME
+ if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
+ while (ks_getuntil(ks, '\n', &s, &dret) >= 0 && s.l > 0) kputs(s.s, &t[2]);
+ } else if (strcmp(s.s, "QA") == 0) { // clipping
+ int beg, end, pos;
+ ks_getuntil(ks, 0, &s, &dret); ks_getuntil(ks, 0, &s, &dret); // skip quality clipping
+ ks_getuntil(ks, 0, &s, &dret); beg = atoi(s.s) - 1; // align clipping start
+ ks_getuntil(ks, 0, &s, &dret); end = atoi(s.s);
+ pos = af[af_i]>>2;
+ if (af[af_i]>>1&1) pos = -pos;
+ pos += beg;
+ kputw(pos, &t[4]); kputs("\t60\t", &t[4]);
+ n_cigar = 0; // start to generate CIGAR
+ if (beg) write_cigar(cigar, n_cigar, m_cigar, beg<<4|4);
+ __padded2cigar(t[2], t[3]);
+ if (end < t[2].l) write_cigar(cigar, n_cigar, m_cigar, (t[2].l-end)<<4|4);
+ if (n_cigar > 1 && (cigar[0]&0xf) == 4) cigar[1] -= beg<<4;
+ if (n_cigar > 1 && (cigar[n_cigar-1]&0xf) == 4) cigar[n_cigar-2] -= cigar[n_cigar-1]>>4<<4;
+ for (i = 0; i < n_cigar; ++i) {
+ kputw(cigar[i]>>4, &t[4]); kputc("MIDNSHP=X"[cigar[i]&0xf], &t[4]);
+ }
+ kputs("\t*\t0\t0\t", &t[4]);
+ kputsn(t[3].s, t[3].l, &t[4]); kputs("\t*", &t[4]);
+ puts(t[4].s);
+ ++af_i;
+ } else if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
+ }
+ ks_destroy(ks);
+ gzclose(fp);
+ free(af); free(s.s); free(cigar);
+ for (i = 0; i < N_TMPSTR; ++i) free(t[i].s);
+ return 0;
+}
projects / samtools.git / commitdiff