#include "bam_endian.h"
#include "knetfile.h"
#include "pysam_util.h"
+#include "errmod.h" // for pysam_dump
+
+#ifndef inline
+#define inline __inline
+#endif
+
+// Definition of pysamerr
+#include "stdio.h"
+FILE * pysamerr = NULL;
+
+FILE * pysam_set_stderr(int fd)
+{
+ if (pysamerr != NULL)
+ fclose(pysamerr);
+ pysamerr = fdopen(fd, "w");
+ return pysamerr;
+}
+
+void pysam_unset_stderr()
+{
+ if (pysamerr != NULL)
+ fclose(pysamerr);
+ pysamerr = fopen("/dev/null", "w");
+}
// #######################################################
// utility routines to avoid using callbacks in bam_fetch
// 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;
return 1;
}
+typedef struct __bmc_aux_t {
+ int max;
+ uint32_t *info;
+ uint16_t *info16;
+ errmod_t *em;
+} bmc_aux_t;
+
+// 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 )
+{
+
+ if (tid >= 0)
+ {
+ 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;
+ }
+
+ return 0;
+}
+
+uint32_t pysam_get_unmapped( const bam_index_t *idx, const int tid )
+{
+
+ if (tid >= 0)
+ {
+ 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; */
+/* } */
+/* } */
+
+
+
+
// pysam dispatch function to emulate the samtools
// 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[] )
{
-
+ extern int optind;
#ifdef _WIN32
setmode(fileno(stdout), O_BINARY);
setmode(fileno(stdin), O_BINARY);
#endif
#endif
- extern int optind;
-
- // 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], "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], "faidx") == 0) return faidx_main(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);
-
+ int retval = 0;
+
+ if (strcmp(argv[1], "view") == 0) retval = main_samview(argc-1, argv+1);
+ else if (strcmp(argv[1], "import") == 0) retval = main_import(argc-1, argv+1);
+ else if (strcmp(argv[1], "mpileup") == 0) retval = bam_mpileup(argc-1, argv+1);
+ else if (strcmp(argv[1], "merge") == 0) retval = bam_merge(argc-1, argv+1);
+ else if (strcmp(argv[1], "sort") == 0) retval = bam_sort(argc-1, argv+1);
+ else if (strcmp(argv[1], "index") == 0) retval = bam_index(argc-1, argv+1);
+ else if (strcmp(argv[1], "faidx") == 0) retval = faidx_main(argc-1, argv+1);
+ else if (strcmp(argv[1], "idxstats") == 0) retval = bam_idxstats(argc-1, argv+1);
+ else if (strcmp(argv[1], "fixmate") == 0) retval = bam_mating(argc-1, argv+1);
+ else if (strcmp(argv[1], "rmdup") == 0) retval = bam_rmdup(argc-1, argv+1);
+ else if (strcmp(argv[1], "flagstat") == 0) retval = bam_flagstat(argc-1, argv+1);
+ else if (strcmp(argv[1], "calmd") == 0) retval = bam_fillmd(argc-1, argv+1);
+ else if (strcmp(argv[1], "fillmd") == 0) retval = bam_fillmd(argc-1, argv+1);
+ else if (strcmp(argv[1], "reheader") == 0) retval = main_reheader(argc-1, argv+1);
+ else if (strcmp(argv[1], "cat") == 0) retval = main_cat(argc-1, argv+1);
+ else if (strcmp(argv[1], "targetcut") == 0) retval = main_cut_target(argc-1, argv+1);
+ else if (strcmp(argv[1], "phase") == 0) retval = main_phase(argc-1, argv+1);
+ else if (strcmp(argv[1], "depth") == 0)
+ {
+ retval = main_depth(argc-1, argv+1);
+ }
+
+ else if (strcmp(argv[1], "bam2fq") == 0) retval = 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);
+ else if (strcmp(argv[1], "tview") == 0) retval = bam_tview_main(argc-1, argv+1);
#endif
else
{
fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
return 1;
}
- return 0;
+ fflush( stdout );
+
+ return retval;
}
// taken from samtools/bam_import.c
uint8_t * pos )
{
int d = nbytes_new-nbytes_old;
+ int new_size;
+ size_t offset;
// no change
if (d == 0) return b;
- int new_size = d + b->data_len;
- size_t offset = pos - b->data;
+ new_size = d + b->data_len;
+ offset = pos - b->data;
//printf("d=%i, old=%i, new=%i, old_size=%i, new_size=%i\n",
// d, nbytes_old, nbytes_new, b->data_len, new_size);
}
+void bam_init_header_hash(bam_header_t *header);
+
+// translate a reference string *s* to a tid
+// code taken from bam_parse_region
+int pysam_reference2tid( bam_header_t *header, const char * s )
+{
+
+ khiter_t iter;
+ khash_t(s) *h;
+
+ bam_init_header_hash(header);
+ h = (khash_t(s)*)header->hash;
+
+ iter = kh_get(s, h, s); /* get the ref_id */
+ if (iter == kh_end(h)) { // name not found
+ return -1;
+ }
+
+ return kh_value(h, iter);
+}
+
+// Auxiliary functions for B support
+void bam_aux_appendB(bam1_t *b, const char tag[2], char type, char subtype, int len, uint8_t *data)
+{
+
+ int ori_len;
+
+ int data_len;
+
+ // check that type is 'B'
+ if('B' != type) return;
+
+ ori_len = b->data_len;
+
+ data_len = len * bam_aux_type2size(subtype);
+ // infer the data length from the sub-type
+ b->data_len += 8 + data_len;
+
+ b->l_aux += 8 + data_len;
+
+ if (b->m_data < b->data_len)
+ {
+
+ b->m_data = b->data_len;
+
+ kroundup32(b->m_data);
+
+ b->data = (uint8_t*)realloc(b->data, b->m_data);
+
+ }
+
+ b->data[ori_len] = tag[0];
+ b->data[ori_len + 1] = tag[1];
+ // tag
+ b->data[ori_len + 2] = type;
+ // type
+ b->data[ori_len + 3] = subtype;
+ // subtype
+ (*(int32_t*)(b->data + ori_len + 4)) = len;
+ // size
+ memcpy(b->data + ori_len + 8, data, data_len);
+ // data
+}
+
+/*
+// return size of auxiliary type
+int bam_aux_type2size(int x)
+{
+ if (x == 'C' || x == 'c' || x == 'A') return 1;
+ else if (x == 'S' || x == 's') return 2;
+ else if (x == 'I' || x == 'i' || x == 'f') return 4;
+ else return 0;
+}
+*/
+
+
+
projects / pysam.git / blobdiff