// taken from bam_index.c
// The order of the following declarations is important.
// #######################################################
+#define BAM_MAX_BIN 37450 // =(8^6-1)/7+1
+// initialize hashes
typedef struct
{
uint64_t u, v;
#define pair64_lt(a,b) ((a).u < (b).u)
+KSORT_INIT(myoff, pair64_t, pair64_lt);
+
typedef struct {
uint32_t m, n;
pair64_t *list;
uint64_t *offset;
} bam_lidx_t;
-KSORT_INIT(my_off, pair64_t, pair64_lt);
-KHASH_MAP_INIT_INT(my_i, bam_binlist_t);
+
+// initialize hashes ('i' and 's' are idenditifiers)
+KHASH_MAP_INIT_INT(i, bam_binlist_t);
KHASH_MAP_INIT_STR(s, int)
struct __bam_index_t
{
int32_t n;
- khash_t(my_i) **index;
+ uint64_t n_no_coor; // unmapped reads without coordinate
+ khash_t(i) **index;
bam_lidx_t *index2;
};
bam_pileup1_t *pu;
int flag_mask;
};
-
+
static mempool_t *mp_init()
{
mempool_t *mp;
errmod_t *em;
} bmc_aux_t;
-uint32_t pysam_glf_depth( glf1_t * g )
+// Return number of mapped reads on tid.
+// If tid < 0, return mapped reads without a coordinate (0)
+uint32_t pysam_get_mapped( const bam_index_t *idx, const int tid )
{
- return g->depth;
-}
-
-void pysam_dump_glf( glf1_t * g, bam_maqcns_t * c )
-{
- int x = 0;
- fprintf(stderr,
- "glf: ref_base=%i, max_mapQ=%i, min_lk=%i, depth=%i",
- g->ref_base,
- g->max_mapQ,
- g->min_lk,
- g->depth );
-
- for (x = 0; x < 10; ++x)
- fprintf(stderr, ", lk%x=%i, ", x, g->lk[x]);
-
- fprintf(stderr,
- "maqcns: het_rate=%f, theta=%f, n_hap=%i, cap_mapQ=%i, errmod=%i, min_baseQ=%i, eta=%f, q_r=%f, aux_max=%i",
- c->het_rate,
- c->theta,
- c->n_hap,
- c->cap_mapQ,
- c->errmod,
- c->min_baseQ,
- c->eta,
- c->q_r,
- c->aux->max);
-
- for (x = 0; x < c->aux->max; ++x)
+ if (tid >= 0)
{
- fprintf(stderr, ", info-%i=%i ", x, c->aux->info[x]);
- if (c->aux->info[x] == 0) break;
+ khint_t k;
+ khash_t(i) *h = idx->index[tid];
+ k = kh_get(i, h, BAM_MAX_BIN);
+
+ if (k != kh_end(h))
+ return kh_val(h, k).list[1].u;
+ else
+ return 0;
}
-
- for (x = 0; x < c->aux->max; ++x)
+
+ return 0;
+}
+
+uint32_t pysam_get_unmapped( const bam_index_t *idx, const int tid )
+{
+
+ if (tid >= 0)
{
- fprintf(stderr, ", info16-%i=%i ", x, c->aux->info16[x]);
- if (c->aux->info16[x] == 0) break;
+ khint_t k;
+ khash_t(i) *h = idx->index[tid];
+ k = kh_get(i, h, BAM_MAX_BIN);
+
+ if (k != kh_end(h))
+ return kh_val(h, k).list[1].v;
+ else
+ return 0;
}
+
+ return idx->n_no_coor;
}
+/* uint32_t pysam_glf_depth( glf1_t * g ) */
+/* { */
+/* return g->depth; */
+/* } */
+
+
+/* void pysam_dump_glf( glf1_t * g, bam_maqcns_t * c ) */
+/* { */
+/* int x = 0; */
+/* fprintf(stderr, */
+/* "glf: ref_base=%i, max_mapQ=%i, min_lk=%i, depth=%i", */
+/* g->ref_base, */
+/* g->max_mapQ, */
+/* g->min_lk, */
+/* g->depth ); */
+
+/* for (x = 0; x < 10; ++x) */
+/* fprintf(stderr, ", lk%x=%i, ", x, g->lk[x]); */
+
+/* fprintf(stderr, */
+/* "maqcns: het_rate=%f, theta=%f, n_hap=%i, cap_mapQ=%i, errmod=%i, min_baseQ=%i, eta=%f, q_r=%f, aux_max=%i", */
+/* c->het_rate, */
+/* c->theta, */
+/* c->n_hap, */
+/* c->cap_mapQ, */
+/* c->errmod, */
+/* c->min_baseQ, */
+/* c->eta, */
+/* c->q_r, */
+/* c->aux->max); */
+
+/* for (x = 0; x < c->aux->max; ++x) */
+/* { */
+/* fprintf(stderr, ", info-%i=%i ", x, c->aux->info[x]); */
+/* if (c->aux->info[x] == 0) break; */
+/* } */
+
+/* for (x = 0; x < c->aux->max; ++x) */
+/* { */
+/* fprintf(stderr, ", info16-%i=%i ", x, c->aux->info16[x]); */
+/* if (c->aux->info16[x] == 0) break; */
+/* } */
+/* } */
+
// command line within python.
// taken from the main function in bamtk.c
// added code to reset getopt
-extern int main_samview(int argc, char *argv[]);
-extern int main_import(int argc, char *argv[]);
-extern int bam_pileup(int argc, char *argv[]);
-extern int bam_merge(int argc, char *argv[]);
-extern int bam_sort(int argc, char *argv[]);
-extern int bam_index(int argc, char *argv[]);
-extern int faidx_main(int argc, char *argv[]);
-extern int bam_mating(int argc, char *argv[]);
-extern int bam_rmdup(int argc, char *argv[]);
-extern int glf3_view_main(int argc, char *argv[]);
-extern int bam_flagstat(int argc, char *argv[]);
-extern int bam_fillmd(int argc, char *argv[]);
+int bam_taf2baf(int argc, char *argv[]);
+int bam_mpileup(int argc, char *argv[]);
+int bam_merge(int argc, char *argv[]);
+int bam_index(int argc, char *argv[]);
+int bam_sort(int argc, char *argv[]);
+int bam_tview_main(int argc, char *argv[]);
+int bam_mating(int argc, char *argv[]);
+int bam_rmdup(int argc, char *argv[]);
+int bam_flagstat(int argc, char *argv[]);
+int bam_fillmd(int argc, char *argv[]);
+int bam_idxstats(int argc, char *argv[]);
+int main_samview(int argc, char *argv[]);
+int main_import(int argc, char *argv[]);
+int main_reheader(int argc, char *argv[]);
+int main_cut_target(int argc, char *argv[]);
+int main_phase(int argc, char *argv[]);
+int main_cat(int argc, char *argv[]);
+int main_depth(int argc, char *argv[]);
+int main_bam2fq(int argc, char *argv[]);
+int faidx_main(int argc, char *argv[]);
int pysam_dispatch(int argc, char *argv[] )
{
#endif
#endif
- // reset getop
+ // reset getopt
optind = 1;
if (argc < 2) return 1;
if (strcmp(argv[1], "view") == 0) return main_samview(argc-1, argv+1);
else if (strcmp(argv[1], "import") == 0) return main_import(argc-1, argv+1);
- else if (strcmp(argv[1], "pileup") == 0) return bam_pileup(argc-1, argv+1);
+ else if (strcmp(argv[1], "mpileup") == 0) return bam_mpileup(argc-1, argv+1);
else if (strcmp(argv[1], "merge") == 0) return bam_merge(argc-1, argv+1);
else if (strcmp(argv[1], "sort") == 0) return bam_sort(argc-1, argv+1);
- else if (strcmp(argv[1], "index") == 0) return bam_index(argc-1, argv+1);
+ else if (strcmp(argv[1], "index") == 0) return bam_index(argc-1, argv+1);
else if (strcmp(argv[1], "faidx") == 0) return faidx_main(argc-1, argv+1);
+ else if (strcmp(argv[1], "idxstats") == 0) return bam_idxstats(argc-1, argv+1);
else if (strcmp(argv[1], "fixmate") == 0) return bam_mating(argc-1, argv+1);
else if (strcmp(argv[1], "rmdup") == 0) return bam_rmdup(argc-1, argv+1);
- else if (strcmp(argv[1], "glfview") == 0) return glf3_view_main(argc-1, argv+1);
else if (strcmp(argv[1], "flagstat") == 0) return bam_flagstat(argc-1, argv+1);
else if (strcmp(argv[1], "calmd") == 0) return bam_fillmd(argc-1, argv+1);
else if (strcmp(argv[1], "fillmd") == 0) return bam_fillmd(argc-1, argv+1);
-
+ else if (strcmp(argv[1], "reheader") == 0) return main_reheader(argc-1, argv+1);
+ else if (strcmp(argv[1], "cat") == 0) return main_cat(argc-1, argv+1);
+ else if (strcmp(argv[1], "targetcut") == 0) return main_cut_target(argc-1, argv+1);
+ else if (strcmp(argv[1], "phase") == 0) return main_phase(argc-1, argv+1);
+ else if (strcmp(argv[1], "depth") == 0) return main_depth(argc-1, argv+1);
+ else if (strcmp(argv[1], "bam2fq") == 0) return main_bam2fq(argc-1, argv+1);
+
#if _CURSES_LIB != 0
else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
#endif
projects / pysam.git / blobdiff