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r309: improved SAM header output

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Heng Li
2017-08-25 10:35:58 +08:00
parent 240f6caaff
commit 0fe1a224ab
9 changed files with 61 additions and 42 deletions
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map.c
+2 -1
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@@ -385,7 +385,8 @@ int mm_map_file(const mm_idx_t *idx, const char *fn, const mm_mapopt_t *opt, int
if (pl.fp == 0) return -1;
pl.opt = opt, pl.mi = idx;
pl.n_threads = n_threads, pl.mini_batch_size = mini_batch_size;
if (opt->flag & MM_F_OUT_SAM) sam_write_sam_header(idx);
if ((opt->flag & MM_F_OUT_SAM) && !(opt->flag & MM_F_NO_SAM_SQ))
mm_write_sam_SQ(idx);
kt_pipeline(n_threads == 1? 1 : 2, worker_pipeline, &pl, 3);
free(pl.str.s);
mm_bseq_close(pl.fp);