Imported Upstream version 0.5

[pysam.git] / pysam / csamtools.pxd

diff --git a/pysam/csamtools.pxd b/pysam/csamtools.pxd
index 4ec74e3693c86aea8cc7052db6ace9a770c6bb6d..df3763802d7ee5742a5379acbfc43b4d052ddf6d 100644 (file)
--- a/pysam/csamtools.pxd
+++ b/pysam/csamtools.pxd
@@ -126,8 +126,7 @@ cdef extern from "bam.h":
      char *text
 
   ctypedef struct bam_index_t:
-      int32_t n
-      uint64_t n_no_coor
+      pass
 
   ctypedef struct bam_plbuf_t:
       pass
@@ -204,7 +203,6 @@ cdef extern from "bam.h":
   void bam_plp_set_mask(bam_plp_t iter, int mask)
   void bam_plp_reset(bam_plp_t iter)
   void bam_plp_destroy(bam_plp_t iter)
-  void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt)
 
   ##################################################
 
@@ -265,67 +263,67 @@ cdef extern from "sam.h":
   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
+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 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
+  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 * )
+  void bam_maqindel_ret_destroy( bam_maqindel_ret_t * )
 
-#  bam_maqindel_opt_t *bam_maqindel_opt_init()
+  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 )
+  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 )
                                                                
 
 cdef extern from "faidx.h":
@@ -377,13 +375,9 @@ cdef extern from "pysam_util.h":
 
     void pysam_set_stderr( FILE * file )
 
-    # return mapped/unmapped reads on tid
-    uint32_t pysam_get_mapped( bam_index_t *idx, int tid )
-    uint32_t pysam_get_unmapped( bam_index_t *idx, int tid )
-
-#    uint32_t pysam_glf_depth( glf1_t * g )
+    uint32_t pysam_glf_depth( glf1_t * g )
 
-#    void pysam_dump_glf( glf1_t * g, bam_maqcns_t * c )
+    void pysam_dump_glf( glf1_t * g, bam_maqcns_t * c )
 
 # need to declare all C fields and methods here
 cdef class AlignedRead:
@@ -399,8 +393,6 @@ cdef class Samfile:
     cdef bam_index_t *index
     # true if file is a bam file
     cdef int isbam
-    # true if not a file but a stream
-    cdef int isstream
     # true if file is not on the local filesystem
     cdef int isremote
     # current read within iteration
@@ -408,9 +400,6 @@ cdef class Samfile:
     # file opening mode
     cdef char * mode
 
-    # beginning of read section
-    cdef int64_t start_offset 
-
     cdef bam_header_t * _buildHeader( self, new_header )
     cdef bam1_t * getCurrent( self )
     cdef int cnext(self)
@@ -420,17 +409,3 @@ cdef class Samfile:
 
     cdef char * _getrname( self, int tid )
 
-cdef class IteratorRow:
-    pass
-
-cdef class IteratorRowAll(IteratorRow):
-    cdef bam1_t * b
-    cdef samfile_t * fp
-    # true if samfile belongs to this object
-    cdef int owns_samfile
-
-    cdef bam1_t * getCurrent( self )
-
-    cdef int cnext(self)
-
-