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write hits to tmp files (unfinished)

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Heng Li
2018-07-14 12:15:10 -04:00
parent 5cfa621b2d
commit 1a55227d5a
8 changed files with 103 additions and 31 deletions
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minimap.h
+4 -1
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@@ -60,6 +60,7 @@ typedef struct {
typedef struct {
int32_t b, w, k, flag;
uint32_t n_seq; // number of reference sequences
int32_t index;
mm_idx_seq_t *seq; // sequence name, length and offset
uint32_t *S; // 4-bit packed sequence
struct mm_idx_bucket_s *B; // index (hidden)
@@ -136,6 +137,8 @@ typedef struct {
int32_t mid_occ; // ignore seeds with occurrences above this threshold
int32_t max_occ;
int mini_batch_size; // size of a batch of query bases to process in parallel
const char *split_prefix;
} mm_mapopt_t;
// index reader
@@ -318,7 +321,7 @@ void mm_tbuf_destroy(mm_tbuf_t *b);
*/
mm_reg1_t *mm_map(const mm_idx_t *mi, int l_seq, const char *seq, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *name);
void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **seqs, int *n_regs, mm_reg1_t **regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname);
int mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **seqs, int *n_regs, mm_reg1_t **regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname);
/**
* Align a fasta/fastq file and print alignments to stdout