65 lines
1.8 KiB
C
65 lines
1.8 KiB
C
#ifndef MM_BSEQ_H
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#define MM_BSEQ_H
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#include <stdint.h>
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#include <string.h>
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#ifdef __cplusplus
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extern "C" {
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#endif
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struct mm_bseq_file_s;
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typedef struct mm_bseq_file_s mm_bseq_file_t;
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typedef struct {
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int l_seq, rid;
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char *name, *seq, *qual, *comment;
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} mm_bseq1_t;
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mm_bseq_file_t *mm_bseq_open(const char *fn);
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void mm_bseq_close(mm_bseq_file_t *fp);
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mm_bseq1_t *mm_bseq_read3(mm_bseq_file_t *fp, int64_t chunk_size, int with_qual, int with_comment, int frag_mode, int *n_);
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mm_bseq1_t *mm_bseq_read2(mm_bseq_file_t *fp, int64_t chunk_size, int with_qual, int frag_mode, int *n_);
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mm_bseq1_t *mm_bseq_read(mm_bseq_file_t *fp, int64_t chunk_size, int with_qual, int *n_);
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mm_bseq1_t *mm_bseq_read_frag2(int n_fp, mm_bseq_file_t **fp, int64_t chunk_size, int with_qual, int with_comment, int *n_);
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mm_bseq1_t *mm_bseq_read_frag(int n_fp, mm_bseq_file_t **fp, int64_t chunk_size, int with_qual, int *n_);
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int mm_bseq_eof(mm_bseq_file_t *fp);
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extern unsigned char seq_nt4_table[256];
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extern unsigned char seq_comp_table[256];
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static inline int mm_qname_len(const char *s)
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{
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int l;
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l = strlen(s);
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return l >= 3 && s[l-1] >= '0' && s[l-1] <= '9' && s[l-2] == '/'? l - 2 : l;
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}
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static inline int mm_qname_same(const char *s1, const char *s2)
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{
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int l1, l2;
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l1 = mm_qname_len(s1);
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l2 = mm_qname_len(s2);
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return (l1 == l2 && strncmp(s1, s2, l1) == 0);
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}
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static inline void mm_revcomp_bseq(mm_bseq1_t *s)
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{
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int i, t, l = s->l_seq;
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for (i = 0; i < l>>1; ++i) {
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t = s->seq[l - i - 1];
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s->seq[l - i - 1] = seq_comp_table[(uint8_t)s->seq[i]];
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s->seq[i] = seq_comp_table[t];
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}
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if (l&1) s->seq[l>>1] = seq_comp_table[(uint8_t)s->seq[l>>1]];
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if (s->qual)
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for (i = 0; i < l>>1; ++i)
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t = s->qual[l - i - 1], s->qual[l - i - 1] = s->qual[i], s->qual[i] = t;
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}
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#ifdef __cplusplus
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}
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#endif
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#endif
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