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#include <stdio.h>
#include <stdlib.h>
#include <assert.h>
#include <unistd.h>
#include "const.h"
#include "maqmap.h"
maqmap_t *maq_new_maqmap()
{
maqmap_t *mm = (maqmap_t*)calloc(1, sizeof(maqmap_t));
mm->format = MAQMAP_FORMAT_NEW;
return mm;
}
void maq_delete_maqmap(maqmap_t *mm)
{
int i;
if (mm == 0) return;
for (i = 0; i < mm->n_ref; ++i)
free(mm->ref_name[i]);
free(mm->ref_name);
free(mm->mapped_reads);
free(mm);
}
void maqmap_write_header(gzFile fp, const maqmap_t *mm)
{
int i, len;
gzwrite(fp, &mm->format, sizeof(int));
gzwrite(fp, &mm->n_ref, sizeof(int));
for (i = 0; i != mm->n_ref; ++i) {
len = strlen(mm->ref_name[i]) + 1;
gzwrite(fp, &len, sizeof(int));
gzwrite(fp, mm->ref_name[i], len);
}
gzwrite(fp, &mm->n_mapped_reads, sizeof(bit64_t));
}
maqmap_t *maqmap_read_header(gzFile fp)
{
maqmap_t *mm;
int k, len;
mm = maq_new_maqmap();
gzread(fp, &mm->format, sizeof(int));
if (mm->format != MAQMAP_FORMAT_NEW) {
if (mm->format > 0) {
fprintf(stderr, "** Obsolete map format is detected. Please use 'mapass2maq' command to convert the format.\n");
exit(3);
}
assert(mm->format == MAQMAP_FORMAT_NEW);
}
gzread(fp, &mm->n_ref, sizeof(int));
mm->ref_name = (char**)calloc(mm->n_ref, sizeof(char*));
for (k = 0; k != mm->n_ref; ++k) {
gzread(fp, &len, sizeof(int));
mm->ref_name[k] = (char*)malloc(len * sizeof(char));
gzread(fp, mm->ref_name[k], len);
}
/* read number of mapped reads */
gzread(fp, &mm->n_mapped_reads, sizeof(bit64_t));
return mm;
}
/* mapvalidate */
static void mapvalidate_core(gzFile fpin)
{
maqmap_t *m = maqmap_read_header(fpin);
maqmap1_t *m1, mm1;
bit64_t n = 0;
int i, l;
bit64_t *cnt;
m1 = &mm1;
cnt = (bit64_t*)calloc(m->n_ref, 8);
printf("[message] number of reference sequences: %d\n", m->n_ref);
while ((l = maqmap_read1(fpin, m1)) != 0) {
if (l != sizeof(maqmap1_t)) {
printf("[fatal error] truncated map file.\n");
break;
}
++n;
if ((int)m1->seqid >= m->n_ref) {
printf("[fatal error] maqmap1_t::seqid is invalid (%d >= %d).\n", m1->seqid, m->n_ref);
break;
}
++cnt[m1->seqid];
if (m1->size >= MAX_READLEN - 1) {
printf("[faltal error] maqmap1_t::size is invalid (%d >= %d).\n", m1->size, MAX_READLEN - 1);
break;
}
}
if (m->n_mapped_reads != 0) {
if (m->n_mapped_reads != n) {
printf("[warning] maqmap1_t::n_mapped_reads is set, but not equals the real number (%llu != %llu).\n",
m->n_mapped_reads, n);
}
}
for (i = 0; i != m->n_ref; ++i)
printf("[message] %s : %llu\n", m->ref_name[i], cnt[i]);
free(cnt);
maq_delete_maqmap(m);
}
/* mapview */
static void mapview_core(FILE *fpout, gzFile fpin, int is_verbose, int is_mm)
{
bit32_t j;
maqmap_t *m = maqmap_read_header(fpin);
maqmap1_t *m1, mm1;
m1 = &mm1;
while (maqmap_read1(fpin, m1)) {
fprintf(fpout, "%s\t%s\t%d\t%c\t%d\t%u\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d",
m1->name, m->ref_name[m1->seqid], (m1->pos>>1) + 1,
(m1->pos&1)? '-' : '+', m1->dist, m1->flag, m1->map_qual, (signed char)m1->seq[MAX_READLEN-1],
m1->alt_qual, m1->info1&0xf, m1->info2, m1->c[0], m1->c[1], m1->size);
if (is_verbose) {
fputc('\t', fpout);
for (j = 0; j != m1->size; ++j) {
if (m1->seq[j] == 0) fputc('n', fpout);
else if ((m1->seq[j]&0x3f) < 27) fputc("acgt"[m1->seq[j]>>6&3], fpout);
else fputc("ACGT"[m1->seq[j]>>6&3], fpout);
}
fputc('\t', fpout);
for (j = 0; j != m1->size; ++j)
fputc((m1->seq[j]&0x3f) + 33, fpout);
}
if (is_mm) {
bit64_t *p = (bit64_t*)(m1->seq + 55);
fprintf(fpout, "\t%llx", *p);
}
fputc('\n', fpout);
}
maq_delete_maqmap(m);
}
int ma_mapview(int argc, char *argv[])
{
int c, is_verbose = 1, is_mm = 0;
while ((c = getopt(argc, argv, "bN")) >= 0) {
switch (c) {
case 'b': is_verbose = 0; break;
case 'N': is_mm = 1; break;
}
}
if (argc == optind) {
fprintf(stderr, "Usage: maq mapview [-bN] <in.map>\n");
return 1;
}
gzFile fp = (strcmp(argv[optind], "-") == 0)? gzdopen(STDIN_FILENO, "r") : gzopen(argv[optind], "r");
mapview_core(stdout, fp, is_verbose, is_mm);
gzclose(fp);
return 0;
}
int ma_mapvalidate(int argc, char *argv[])
{
gzFile fp;
if (argc < 2) {
fprintf(stderr, "Usage: maq mapvalidate <in.map>\n");
return 1;
}
fp = (strcmp(argv[optind], "-") == 0)? gzdopen(STDIN_FILENO, "r") : gzopen(argv[1], "r");
mapvalidate_core(fp);
gzclose(fp);
return 0;
}
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