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print SAM header; remove tmp files

This commit is contained in:
Heng Li 2018-07-15 11:03:18 -04:00
parent 4b707aac92
commit a655cbef86
4 changed files with 20 additions and 4 deletions
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2
main.c
View File

@ -329,7 +329,7 @@ int main(int argc, char *argv[])
mm_write_sam_hdr(mi, rg, MM_VERSION, argc, argv); mm_write_sam_hdr(mi, rg, MM_VERSION, argc, argv);
} else { } else {
mm_write_sam_hdr(0, rg, MM_VERSION, argc, argv); mm_write_sam_hdr(0, rg, MM_VERSION, argc, argv);
if (mm_verbose >= 2) if (opt.split_prefix == 0 && mm_verbose >= 2)
fprintf(stderr, "[WARNING]\033[1;31m For a multi-part index, no @SQ lines will be outputted.\033[0m\n"); fprintf(stderr, "[WARNING]\033[1;31m For a multi-part index, no @SQ lines will be outputted.\033[0m\n");
} }
} }

5
map.c
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@ -659,7 +659,6 @@ int mm_split_merge(int n_segs, const char **fn, const mm_mapopt_t *opt, int n_sp
{ {
int i; int i;
pipeline_t pl; pipeline_t pl;
mm_idx_t *mi;
if (n_segs < 1 || n_split_idx < 1) return -1; if (n_segs < 1 || n_split_idx < 1) return -1;
memset(&pl, 0, sizeof(pipeline_t)); memset(&pl, 0, sizeof(pipeline_t));
pl.n_fp = n_segs; pl.n_fp = n_segs;
@ -681,6 +680,9 @@ int mm_split_merge(int n_segs, const char **fn, const mm_mapopt_t *opt, int n_sp
pl.rid_shift[i] = pl.rid_shift[i - 1]; pl.rid_shift[i] = pl.rid_shift[i - 1];
for (pl.rid_shift[0] = 0, i = 1; i < n_split_idx; ++i) for (pl.rid_shift[0] = 0, i = 1; i < n_split_idx; ++i)
pl.rid_shift[i] += pl.rid_shift[i - 1]; pl.rid_shift[i] += pl.rid_shift[i - 1];
if (opt->flag & MM_F_OUT_SAM)
for (i = 0; i < pl.mi->n_seq; ++i)
printf("@SQ\tSN:%s\tLN:%d\n", pl.mi->seq[i].name, pl.mi->seq[i].len);
kt_pipeline(2, worker_pipeline, &pl, 3); kt_pipeline(2, worker_pipeline, &pl, 3);
@ -692,5 +694,6 @@ int mm_split_merge(int n_segs, const char **fn, const mm_mapopt_t *opt, int n_sp
for (i = 0; i < pl.n_fp; ++i) for (i = 0; i < pl.n_fp; ++i)
mm_bseq_close(pl.fp[i]); mm_bseq_close(pl.fp[i]);
free(pl.fp); free(pl.fp);
mm_split_rm_tmp(opt->split_prefix, n_split_idx);
return 0; return 0;
} }

1
mmpriv.h
View File

@ -92,6 +92,7 @@ void mm_pair(void *km, int max_gap_ref, int dp_bonus, int sub_diff, int match_sc
FILE *mm_split_init(const char *prefix, const mm_idx_t *mi); FILE *mm_split_init(const char *prefix, const mm_idx_t *mi);
mm_idx_t *mm_split_merge_prep(const char *prefix, int n_splits, FILE **fp, uint32_t *n_seq_part); mm_idx_t *mm_split_merge_prep(const char *prefix, int n_splits, FILE **fp, uint32_t *n_seq_part);
int mm_split_merge(int n_segs, const char **fn, const mm_mapopt_t *opt, int n_split_idx); int mm_split_merge(int n_segs, const char **fn, const mm_mapopt_t *opt, int n_split_idx);
void mm_split_rm_tmp(const char *prefix, int n_splits);
void mm_err_puts(const char *str); void mm_err_puts(const char *str);
void mm_err_fwrite(const void *p, size_t size, size_t nitems, FILE *fp); void mm_err_fwrite(const void *p, size_t size, size_t nitems, FILE *fp);

16
splitidx.c
View File

@ -33,7 +33,7 @@ mm_idx_t *mm_split_merge_prep(const char *prefix, int n_splits, FILE **fp, uint3
int i, j; int i, j;
if (n_splits < 1) return 0; if (n_splits < 1) return 0;
fn = (char*)calloc(strlen(prefix) + 10, 1); fn = CALLOC(char, strlen(prefix) + 10);
for (i = 0; i < n_splits; ++i) { for (i = 0; i < n_splits; ++i) {
sprintf(fn, "%s.%.4d.tmp", prefix, i); sprintf(fn, "%s.%.4d.tmp", prefix, i);
if ((fp[i] = fopen(fn, "rb")) == 0) { if ((fp[i] = fopen(fn, "rb")) == 0) {
@ -47,7 +47,7 @@ mm_idx_t *mm_split_merge_prep(const char *prefix, int n_splits, FILE **fp, uint3
} }
free(fn); free(fn);
mi = (mm_idx_t*)calloc(1, sizeof(mm_idx_t)); mi = CALLOC(mm_idx_t, 1);
for (i = 0; i < n_splits; ++i) { for (i = 0; i < n_splits; ++i) {
mm_err_fread(&mi->k, 4, 1, fp[i]); // TODO: check if k is all the same mm_err_fread(&mi->k, 4, 1, fp[i]); // TODO: check if k is all the same
mm_err_fread(&n_seq_part[i], 4, 1, fp[i]); mm_err_fread(&n_seq_part[i], 4, 1, fp[i]);
@ -66,3 +66,15 @@ mm_idx_t *mm_split_merge_prep(const char *prefix, int n_splits, FILE **fp, uint3
} }
return mi; return mi;
} }
void mm_split_rm_tmp(const char *prefix, int n_splits)
{
int i;
char *fn;
fn = CALLOC(char, strlen(prefix) + 10);
for (i = 0; i < n_splits; ++i) {
sprintf(fn, "%s.%.4d.tmp", prefix, i);
remove(fn);
}
free(fn);
}