Imported Upstream version 0.6

[pysam.git] / pysam / csamtools.pxd

diff --git a/pysam/csamtools.pxd b/pysam/csamtools.pxd
index df3763802d7ee5742a5379acbfc43b4d052ddf6d..4ec74e3693c86aea8cc7052db6ace9a770c6bb6d 100644 (file)
--- a/pysam/csamtools.pxd
+++ b/pysam/csamtools.pxd
@@ -126,7 +126,8 @@ cdef extern from "bam.h":
      char *text
 
   ctypedef struct bam_index_t:
-      pass
+      int32_t n
+      uint64_t n_no_coor
 
   ctypedef struct bam_plbuf_t:
       pass
@@ -203,6 +204,7 @@ 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)
 
   ##################################################
 
@@ -263,67 +265,67 @@ 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":
@@ -375,9 +377,13 @@ cdef extern from "pysam_util.h":
 
     void pysam_set_stderr( FILE * file )
 
-    uint32_t pysam_glf_depth( glf1_t * g )
+    # 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 )
 
-    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:
@@ -393,6 +399,8 @@ 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
@@ -400,6 +408,9 @@ 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)
@@ -409,3 +420,17 @@ 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)
+
+