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| #define | BAM_CMATCH 0 |
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| #define | BAM_CINS 1 |
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| #define | BAM_CDEL 2 |
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| #define | BAM_CREF_SKIP 3 |
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| #define | BAM_CSOFT_CLIP 4 |
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| #define | BAM_CHARD_CLIP 5 |
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| #define | BAM_CPAD 6 |
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| #define | BAM_CEQUAL 7 |
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| #define | BAM_CDIFF 8 |
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| #define | BAM_CBACK 9 |
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| #define | BAM_CIGAR_STR "MIDNSHP=XB" |
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| #define | BAM_CIGAR_SHIFT 4 |
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| #define | BAM_CIGAR_MASK 0xf |
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| #define | BAM_CIGAR_TYPE 0x3C1A7 |
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| #define | bam_cigar_op(c) ((c)&BAM_CIGAR_MASK) |
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| #define | bam_cigar_oplen(c) ((c)>>BAM_CIGAR_SHIFT) |
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| #define | bam_cigar_opchr(c) (BAM_CIGAR_STR[bam_cigar_op(c)]) |
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| #define | bam_cigar_gen(l, o) ((l)<<BAM_CIGAR_SHIFT|(o)) |
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| #define | bam_cigar_type(o) (BAM_CIGAR_TYPE>>((o)<<1)&3) |
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| #define | BAM_FPAIRED 1 |
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| #define | BAM_FPROPER_PAIR 2 |
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| #define | BAM_FUNMAP 4 |
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| #define | BAM_FMUNMAP 8 |
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| #define | BAM_FREVERSE 16 |
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| #define | BAM_FMREVERSE 32 |
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| #define | BAM_FREAD1 64 |
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| #define | BAM_FREAD2 128 |
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| #define | BAM_FSECONDARY 256 |
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| #define | BAM_FQCFAIL 512 |
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| #define | BAM_FDUP 1024 |
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| #define | BAM_FSUPPLEMENTARY 2048 |
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| #define | bam_is_rev(b) (((b)->core.flag&BAM_FREVERSE) != 0) |
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| #define | bam_is_mrev(b) (((b)->core.flag&BAM_FMREVERSE) != 0) |
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| #define | bam_get_qname(b) ((char*)(b)->data) |
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| #define | bam_get_cigar(b) ((uint32_t*)((b)->data + (b)->core.l_qname)) |
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| #define | bam_get_seq(b) ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname) |
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| #define | bam_get_qual(b) ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1)) |
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| #define | bam_get_aux(b) ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1) + (b)->core.l_qseq) |
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| #define | bam_get_l_aux(b) ((b)->l_data - ((b)->core.n_cigar<<2) - (b)->core.l_qname - (b)->core.l_qseq - (((b)->core.l_qseq + 1)>>1)) |
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| #define | bam_seqi(s, i) ((s)[(i)>>1] >> ((~(i)&1)<<2) & 0xf) |
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| #define | bam_itr_destroy(iter) hts_itr_destroy(iter) |
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| #define | bam_itr_queryi(idx, tid, beg, end) sam_itr_queryi(idx, tid, beg, end) |
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| #define | bam_itr_querys(idx, hdr, region) sam_itr_querys(idx, hdr, region) |
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| #define | bam_itr_next(htsfp, itr, r) hts_itr_next((htsfp)->fp.bgzf, (itr), (r), 0) |
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| #define | bam_index_load(fn) hts_idx_load((fn), HTS_FMT_BAI) |
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| #define | sam_itr_destroy(iter) hts_itr_destroy(iter) |
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| #define | sam_itr_next(htsfp, itr, r) hts_itr_next((htsfp)->fp.bgzf, (itr), (r), (htsfp)) |
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| #define | sam_open(fn, mode) (hts_open((fn), (mode))) |
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| #define | sam_close(fp) hts_close(fp) |
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| bam_hdr_t * | bam_hdr_init (void) |
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| bam_hdr_t * | bam_hdr_read (BGZF *fp) |
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| int | bam_hdr_write (BGZF *fp, const bam_hdr_t *h) |
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| void | bam_hdr_destroy (bam_hdr_t *h) |
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| int | bam_name2id (bam_hdr_t *h, const char *ref) |
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| bam_hdr_t * | bam_hdr_dup (const bam_hdr_t *h0) |
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| bam1_t * | bam_init1 (void) |
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| void | bam_destroy1 (bam1_t *b) |
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| int | bam_read1 (BGZF *fp, bam1_t *b) |
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| int | bam_write1 (BGZF *fp, const bam1_t *b) |
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| bam1_t * | bam_copy1 (bam1_t *bdst, const bam1_t *bsrc) |
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| bam1_t * | bam_dup1 (const bam1_t *bsrc) |
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| int | bam_cigar2qlen (int n_cigar, const uint32_t *cigar) |
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| int | bam_cigar2rlen (int n_cigar, const uint32_t *cigar) |
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| int32_t | bam_endpos (const bam1_t *b) |
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| int | bam_str2flag (const char *str) |
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| char * | bam_flag2str (int flag) |
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| int | bam_index_build (const char *fn, int min_shift) |
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| hts_idx_t * | sam_index_load (htsFile *fp, const char *fn) |
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| hts_itr_t * | sam_itr_queryi (const hts_idx_t *idx, int tid, int beg, int end) |
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| hts_itr_t * | sam_itr_querys (const hts_idx_t *idx, bam_hdr_t *hdr, const char *region) |
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| int | sam_open_mode (char *mode, const char *fn, const char *format) |
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| bam_hdr_t * | sam_hdr_parse (int l_text, const char *text) |
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| bam_hdr_t * | sam_hdr_read (samFile *fp) |
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| int | sam_hdr_write (samFile *fp, const bam_hdr_t *h) |
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| int | sam_parse1 (kstring_t *s, bam_hdr_t *h, bam1_t *b) |
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| int | sam_format1 (const bam_hdr_t *h, const bam1_t *b, kstring_t *str) |
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| int | sam_read1 (samFile *fp, bam_hdr_t *h, bam1_t *b) |
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| int | sam_write1 (samFile *fp, const bam_hdr_t *h, const bam1_t *b) |
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| uint8_t * | bam_aux_get (const bam1_t *b, const char tag[2]) |
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| int32_t | bam_aux2i (const uint8_t *s) |
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| double | bam_aux2f (const uint8_t *s) |
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| char | bam_aux2A (const uint8_t *s) |
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| char * | bam_aux2Z (const uint8_t *s) |
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| void | bam_aux_append (bam1_t *b, const char tag[2], char type, int len, uint8_t *data) |
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| int | bam_aux_del (bam1_t *b, uint8_t *s) |
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| bam_plp_t | bam_plp_init (bam_plp_auto_f func, void *data) |
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| void | bam_plp_destroy (bam_plp_t iter) |
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| int | bam_plp_push (bam_plp_t iter, const bam1_t *b) |
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| const bam_pileup1_t * | bam_plp_next (bam_plp_t iter, int *_tid, int *_pos, int *_n_plp) |
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| const bam_pileup1_t * | bam_plp_auto (bam_plp_t iter, int *_tid, int *_pos, int *_n_plp) |
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| void | bam_plp_set_maxcnt (bam_plp_t iter, int maxcnt) |
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| void | bam_plp_reset (bam_plp_t iter) |
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| bam_mplp_t | bam_mplp_init (int n, bam_plp_auto_f func, void **data) |
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| void | bam_mplp_init_overlaps (bam_mplp_t iter) |
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| void | bam_mplp_destroy (bam_mplp_t iter) |
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| void | bam_mplp_set_maxcnt (bam_mplp_t iter, int maxcnt) |
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| int | bam_mplp_auto (bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp) |
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1.8.4