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/* The MIT License
Copyright (c) 2011 Heng Li <lh3@live.co.uk>
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
*/
#include <config.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include <zlib.h>
#include "htslib/kstring.h"
#include "htslib/kseq.h"
KSTREAM_INIT(gzFile, gzread, 16384)
#define N_TMPSTR 5
#define LINE_LEN 60
// append a CIGAR operation plus length
#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)
// a fatal error
static void fatal(const char *msg)
{
fprintf(stderr, "E %s\n", msg);
exit(1);
}
// remove pads
static void remove_pads(const kstring_t *src, kstring_t *dst)
{
int i, j;
dst->l = 0;
kputsn(src->s, src->l, dst);
for (i = j = 0; i < dst->l; ++i)
if (dst->s[i] != '*') dst->s[j++] = dst->s[i];
dst->s[j] = 0;
dst->l = j;
}
int main(int argc, char *argv[])
{
gzFile fp;
kstream_t *ks;
kstring_t s, t[N_TMPSTR];
int dret, i, k, af_n, af_max, af_i, c, is_padded = 0, write_cns = 0, *p2u = 0;
long m_cigar = 0, n_cigar = 0;
unsigned *af, *cigar = 0;
while ((c = getopt(argc, argv, "pc")) >= 0) {
switch (c) {
case 'p': is_padded = 1; break;
case 'c': write_cns = 1; break;
}
}
if (argc == optind) {
fprintf(stderr, "\nUsage: ace2sam [-pc] <in.ace>\n\n");
fprintf(stderr, "Options: -p output padded SAM\n");
fprintf(stderr, " -c write the contig sequence in SAM\n\n");
fprintf(stderr, "Notes: 1. Fields must appear in the following order: (CO->[BQ]->(AF)->(RD->QA))\n");
fprintf(stderr, " 2. The order of reads in AF and in RD must be identical\n");
fprintf(stderr, " 3. Except in BQ, words and numbers must be separated by a single SPACE or TAB\n");
fprintf(stderr, " 4. This program writes the headerless SAM to stdout and header to stderr\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[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r");
if (fp == NULL) fatal("can't open input file");
ks = ks_init(fp);
while (ks_getuntil(ks, 0, &s, &dret) >= 0) {
if (strcmp(s.s, "CO") == 0) { // contig sequence
kstring_t *cns;
t[0].l = t[1].l = t[2].l = t[3].l = t[4].l = 0; // 0: name; 1: padded ctg; 2: unpadded ctg/padded read; 3: unpadded read; 4: SAM line
af_n = af_i = 0; // reset the af array
ks_getuntil(ks, 0, &s, &dret); kputs(s.s, &t[0]); // contig name
ks_getuntil(ks, '\n', &s, &dret); // read the whole line
while (ks_getuntil(ks, '\n', &s, &dret) >= 0 && s.l > 0) kputsn(s.s, s.l, &t[1]); // read the padded consensus sequence
remove_pads(&t[1], &t[2]); // construct the unpadded sequence
// compute the array for mapping padded positions to unpadded positions
p2u = realloc(p2u, t[1].m * sizeof(int));
for (i = k = 0; i < t[1].l; ++i) {
p2u[i] = k;
if (t[1].s[i] != '*') ++k;
}
// write out the SAM header and contig sequences
fprintf(stderr, "H @SQ\tSN:%s\tLN:%llu\n", t[0].s, (unsigned long long)(t[is_padded?1:2].l)); // The SAM header line
cns = &t[is_padded?1:2];
fprintf(stderr, "S >%s\n", t[0].s);
for (i = 0; i < cns->l; i += LINE_LEN) {
fputs("S ", stderr);
for (k = 0; k < LINE_LEN && i + k < cns->l; ++k)
fputc(cns->s[i + k], stderr);
fputc('\n', stderr);
}
#define __padded2cigar(sp) do { \
int i, l_M = 0, l_D = 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; \
} \
} \
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)
if (write_cns) { // write the consensus SAM line (dummy read)
n_cigar = 0;
if (is_padded) __padded2cigar(t[1]);
else write_cigar(cigar, n_cigar, m_cigar, t[2].l<<4);
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]);
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[2].s, t[2].l, &t[4]); kputs("\t*", &t[4]);
}
} else if (strcmp(s.s, "BQ") == 0) { // contig quality
if (t[0].l == 0) fatal("come to 'BQ' before reading 'CO'");
if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret); // read the entire "BQ" line
if (write_cns) t[4].s[--t[4].l] = 0; // remove the trailing "*"
for (i = 0; i < t[2].l; ++i) { // read the consensus quality
int q;
if (ks_getuntil(ks, 0, &s, &dret) < 0) fprintf(stderr, "E truncated contig quality\n");
if (s.l) {
q = atoi(s.s) + 33;
if (q > 126) q = 126;
if (write_cns) kputc(q, &t[4]);
} else --i;
}
if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
ks_getuntil(ks, '\n', &s, &dret); // skip the empty line
if (write_cns) {
if (t[4].l) puts(t[4].s);
t[4].l = 0;
}
} else if (strcmp(s.s, "AF") == 0) { // padded read position
int reversed, neg, pos;
if (t[0].l == 0) fatal("come to 'AF' before reading 'CO'");
if (write_cns) {
if (t[4].l) puts(t[4].s);
t[4].l = 0;
}
ks_getuntil(ks, 0, &s, &dret); // read name
ks_getuntil(ks, 0, &s, &dret); reversed = s.s[0] == 'C'? 1 : 0; // strand
ks_getuntil(ks, 0, &s, &dret); pos = atoi(s.s); neg = pos < 0? 1 : 0; pos = pos < 0? -pos : pos; // position
if (af_n == af_max) { // double the af array
af_max = af_max? af_max<<1 : 4;
af = realloc(af, af_max * sizeof(unsigned));
}
af[af_n++] = pos << 2 | neg << 1 | reversed; // keep the placement information
} else if (strcmp(s.s, "RD") == 0) { // read sequence
if (af_i >= af_n) fatal("more 'RD' records than 'AF'");
t[2].l = t[3].l = t[4].l = 0;
ks_getuntil(ks, 0, &t[4], &dret); // QNAME
if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret); // read the entire RD line
while (ks_getuntil(ks, '\n', &s, &dret) >= 0 && s.l > 0) kputs(s.s, &t[2]); // read the read sequence
} else if (strcmp(s.s, "QA") == 0) { // clipping
if (af_i >= af_n) fatal("more 'QA' records than 'AF'");
int beg, end, pos, op;
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); // clipping end
if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
// compute 1-based POS
pos = af[af_i]>>2; // retrieve the position information
if (af[af_i]>>1&1) pos = -pos;
pos += beg; // now pos is the true padded position
// generate CIGAR
remove_pads(&t[2], &t[3]); // backup the unpadded read sequence
n_cigar = 0;
if (beg) write_cigar(cigar, n_cigar, m_cigar, beg<<4|4);
if (is_padded) {
__padded2cigar(t[2]);
if (beg && n_cigar > 1) cigar[1] -= beg<<4; // fix the left-hand CIGAR
if (end < t[2].l && n_cigar) cigar[n_cigar-1] -= (t[2].l - end)<<4; // fix the right-hand CIGAR
} else {
// generate flattened CIGAR string
for (i = beg, k = pos - 1; i < end; ++i, ++k)
t[2].s[i] = t[2].s[i] != '*'? (t[1].s[k] != '*'? 0 : 1) : (t[1].s[k] != '*'? 2 : 6);
// generate the proper CIGAR
for (i = beg + 1, k = 1, op = t[2].s[beg]; i < end; ++i) {
if (op != t[2].s[i]) {
write_cigar(cigar, n_cigar, m_cigar, k<<4|op);
op = t[2].s[i]; k = 1;
} else ++k;
}
write_cigar(cigar, n_cigar, m_cigar, k<<4|op);
// remove unnecessary "P" and possibly merge adjacent operations
for (i = 2; i < n_cigar; ++i) {
if ((cigar[i]&0xf) != 1 && (cigar[i-1]&0xf) == 6 && (cigar[i-2]&0xf) != 1) {
cigar[i-1] = 0;
if ((cigar[i]&0xf) == (cigar[i-2]&0xf)) // merge operations
cigar[i] += cigar[i-2], cigar[i-2] = 0;
}
}
for (i = k = 0; i < n_cigar; ++i) // squeeze out dumb operations
if (cigar[i]) cigar[k++] = cigar[i];
n_cigar = k;
}
if (end < t[2].l) write_cigar(cigar, n_cigar, m_cigar, (t[2].l - end)<<4|4);
// write the SAM line for the read
kputc('\t', &t[4]); // QNAME has already been written
kputw((af[af_i]&1)? 16 : 0, &t[4]); kputc('\t', &t[4]); // FLAG
kputsn(t[0].s, t[0].l, &t[4]); kputc('\t', &t[4]); // RNAME
kputw(is_padded? pos : p2u[pos-1]+1, &t[4]); // POS
kputs("\t60\t", &t[4]); // MAPQ
for (i = 0; i < n_cigar; ++i) { // CIGAR
kputw(cigar[i]>>4, &t[4]); kputc("MIDNSHP=X"[cigar[i]&0xf], &t[4]);
}
kputs("\t*\t0\t0\t", &t[4]); // empty MRNM, MPOS and TLEN
kputsn(t[3].s, t[3].l, &t[4]); // unpadded SEQ
kputs("\t*", &t[4]); // QUAL
puts(t[4].s); // print to stdout
++af_i;
} else if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
}
ks_destroy(ks);
gzclose(fp);
free(af); free(s.s); free(cigar); free(p2u);
for (i = 0; i < N_TMPSTR; ++i) free(t[i].s);
return 0;
}
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