+ int bam_prob_realn(bam1_t *b, char *ref)
+ int bam_cap_mapQ(bam1_t *b, char *ref, int thres)
+
+
+cdef extern from "glf.h":
+ ctypedef struct glf1_t:
+ pass
+
+cdef extern from "bam_maqcns.h":
+
+ ctypedef struct bam_maqcns_t:
+ float het_rate, theta
+ int n_hap, cap_mapQ, errmod, min_baseQ
+ float eta, q_r
+ double *fk, *coef
+ double *lhet
+ void *aux
+
+ glf1_t *bam_maqcns_glfgen(int n,
+ bam_pileup1_t *pl,
+ uint8_t ref_base,
+ bam_maqcns_t *bm)
+
+ ctypedef struct bam_maqindel_opt_t:
+ int q_indel
+ float r_indel
+ float r_snp
+ int mm_penalty, indel_err, ambi_thres
+
+ uint32_t bam_maqcns_call(int n, bam_pileup1_t *pl, bam_maqcns_t *bm)
+ bam_maqcns_t * bam_maqcns_init()
+ void bam_maqcns_destroy(bam_maqcns_t *bm)
+ void bam_maqcns_prepare(bam_maqcns_t *bm)
+
+ uint32_t glf2cns(glf1_t *g, int q_r)
+
+ int BAM_ERRMOD_MAQ2
+ int BAM_ERRMOD_MAQ
+ int BAM_ERRMOD_SOAP
+
+ ctypedef struct bam_maqindel_ret_t:
+ int indel1
+ int indel2
+ int cnt1
+ int cnt2
+ int cnt_anti
+ int cnt_ref
+ int cnt_ambi
+ char *s[2]
+ int gt
+ int gl[2]
+ int q_cns
+ int q_ref
+
+ void bam_maqindel_ret_destroy( bam_maqindel_ret_t * )
+
+ bam_maqindel_opt_t *bam_maqindel_opt_init()
+
+ bam_maqindel_ret_t * bam_maqindel(int n,
+ int pos,
+ bam_maqindel_opt_t * mi,
+ bam_pileup1_t * pl,
+ char *ref,
+ int _n_types,
+ int * _types )
+
+