|
| #define | _read_token(_p) (_p); for (; *(_p) && *(_p) != '\t'; ++(_p)); if (*(_p) != '\t') goto err_ret; *(_p)++ = 0 |
| |
| #define | _read_token_aux(_p) (_p); for (; *(_p) && *(_p) != '\t'; ++(_p)); *(_p)++ = 0 |
| |
| #define | _get_mem(type_t, _x, _s, _l) ks_resize((_s), (_s)->l + (_l)); *(_x) = (type_t*)((_s)->s + (_s)->l); (_s)->l += (_l) |
| |
| #define | _parse_err(cond, msg) do { if ((cond) && hts_verbose >= 1) { fprintf(stderr, "[E::%s] " msg "\n", __func__); goto err_ret; } } while (0) |
| |
| #define | _parse_warn(cond, msg) if ((cond) && hts_verbose >= 2) fprintf(stderr, "[W::%s] " msg "\n", __func__) |
| |
| #define | STRNCMP(a, b, n) (strncasecmp((a),(b),(n)) || strlen(a)!=(n)) |
| |
| #define | _cop(c) ((c)&BAM_CIGAR_MASK) |
| |
| #define | _cln(c) ((c)>>BAM_CIGAR_SHIFT) |
| |
|
| typedef | khash_t (s2i) |
| |
| void | bam_hdr_destroy (bam_hdr_t *h) |
| |
| bam_hdr_t * | bam_hdr_dup (const bam_hdr_t *h0) |
| |
| bam_hdr_t * | bam_hdr_read (BGZF *fp) |
| |
| int | bam_hdr_write (BGZF *fp, const bam_hdr_t *h) |
| |
| int | bam_name2id (bam_hdr_t *h, const char *ref) |
| |
| bam1_t * | bam_init1 () |
| |
| void | bam_destroy1 (bam1_t *b) |
| |
| bam1_t * | bam_copy1 (bam1_t *bdst, const bam1_t *bsrc) |
| |
| bam1_t * | bam_dup1 (const bam1_t *bsrc) |
| |
| int | bam_cigar2qlen (int n_cigar, const uint32_t *cigar) |
| |
| int | bam_cigar2rlen (int n_cigar, const uint32_t *cigar) |
| |
| int32_t | bam_endpos (const bam1_t *b) |
| |
| int | bam_read1 (BGZF *fp, bam1_t *b) |
| |
| int | bam_write1 (BGZF *fp, const bam1_t *b) |
| |
| int | bam_index_build (const char *fn, int min_shift) |
| |
| hts_idx_t * | sam_index_load (samFile *fp, const char *fn) |
| |
| hts_itr_t * | sam_itr_queryi (const hts_idx_t *idx, int tid, int beg, int end) |
| |
| hts_itr_t * | sam_itr_querys (const hts_idx_t *idx, bam_hdr_t *hdr, const char *region) |
| |
| bam_hdr_t * | sam_hdr_parse (int l_text, const char *text) |
| |
| bam_hdr_t * | sam_hdr_read (htsFile *fp) |
| |
| int | sam_hdr_write (htsFile *fp, const bam_hdr_t *h) |
| |
| int | sam_parse1 (kstring_t *s, bam_hdr_t *h, bam1_t *b) |
| |
| int | sam_read1 (htsFile *fp, bam_hdr_t *h, bam1_t *b) |
| |
| int | sam_format1 (const bam_hdr_t *h, const bam1_t *b, kstring_t *str) |
| |
| int | sam_write1 (htsFile *fp, const bam_hdr_t *h, const bam1_t *b) |
| |
| void | bam_aux_append (bam1_t *b, const char tag[2], char type, int len, uint8_t *data) |
| |
| uint8_t * | bam_aux_get (const bam1_t *b, const char tag[2]) |
| |
| int | bam_aux_del (bam1_t *b, uint8_t *s) |
| |
| int32_t | bam_aux2i (const uint8_t *s) |
| |
| double | bam_aux2f (const uint8_t *s) |
| |
| char | bam_aux2A (const uint8_t *s) |
| |
| char * | bam_aux2Z (const uint8_t *s) |
| |
| int | sam_open_mode (char *mode, const char *fn, const char *format) |
| |
| int | bam_str2flag (const char *str) |
| |
| char * | bam_flag2str (int flag) |
| |
| typedef | khash_t (olap_hash) |
| |
| bam_plp_t | bam_plp_init (bam_plp_auto_f func, void *data) |
| |
| void | bam_plp_init_overlaps (bam_plp_t iter) |
| |
| void | bam_plp_destroy (bam_plp_t iter) |
| |
| const bam_pileup1_t * | bam_plp_next (bam_plp_t iter, int *_tid, int *_pos, int *_n_plp) |
| |
| int | bam_plp_push (bam_plp_t iter, const bam1_t *b) |
| |
| const bam_pileup1_t * | bam_plp_auto (bam_plp_t iter, int *_tid, int *_pos, int *_n_plp) |
| |
| void | bam_plp_reset (bam_plp_t iter) |
| |
| void | bam_plp_set_maxcnt (bam_plp_t iter, int maxcnt) |
| |
| bam_mplp_t | bam_mplp_init (int n, bam_plp_auto_f func, void **data) |
| |
| void | bam_mplp_init_overlaps (bam_mplp_t iter) |
| |
| void | bam_mplp_set_maxcnt (bam_mplp_t iter, int maxcnt) |
| |
| void | bam_mplp_destroy (bam_mplp_t iter) |
| |
| int | bam_mplp_auto (bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp) |
| |
1.8.4