Remove obsolete source files and unnecessary includes

c{sam,bcf}tools_util.h are long since replaced by {sam,bcf}tools.pysam.h.
Only this commented-out libctabix.pyx code used getline(), so remove its
fallback definition in pysam_utils.c and hence remove the now-empty
pysam_util.[ch]. Remove unused header inclusions from htslib_util.c.

Author: jmarshall

pysam/cbcftools_util.h

@@ -1,13 +1,8 @@
-#include <ctype.h>
 #include <assert.h>
 #include "htslib/khash.h"
-#include "htslib/ksort.h"
 #include "htslib/sam.h"
 #include "htslib/hts.h"
-#include "htslib/knetfile.h"
-#include "htslib/kseq.h"
 #include "htslib_util.h"
-#include <stdio.h>
 
 #ifndef inline
 #define inline __inline

pysam/csamtools_util.h

@@ -1012,70 +1012,6 @@ def tabix_index(filename,
 
     return filename
 
-# #########################################################
-# cdef class tabix_file_iterator_old:
-#     '''iterate over ``infile``.
-
-#     This iterator is not safe. If the :meth:`__next__()` method is called 
-#     after ``infile`` is closed, the result is undefined (see ``fclose()``).
-
-#     The iterator might either raise a StopIteration or segfault.
-#     '''
-
-
-#     def __cinit__(self, 
-#                   infile, 
-#                   Parser parser,
-#                   int buffer_size = 65536 ):
-
-#         cdef int fd = PyObject_AsFileDescriptor( infile )
-#         if fd == -1: raise ValueError( "I/O operation on closed file." )
-#         self.infile = fdopen( fd, 'r')
-
-#         if self.infile == NULL: raise ValueError( "I/O operation on closed file." )
-
-#         self.buffer = <char*>malloc( buffer_size )        
-#         self.size = buffer_size
-#         self.parser = parser
-
-#     def __iter__(self):
-#         return self
-
-#     cdef __cnext__(self):
-
-#         cdef char * b
-#         cdef size_t nbytes
-#         b = self.buffer
-
-#         while not feof( self.infile ):
-#             nbytes = getline( &b, &self.size, self.infile)
-
-#             # stop at first error or eof
-#             if (nbytes == -1): break
-#             # skip comments
-#             if (b[0] == '#'): continue
-
-#             # skip empty lines
-#             if b[0] == '\0' or b[0] == '\n' or b[0] == '\r': continue
-
-#             # make sure that entry is complete
-#             if b[nbytes-1] != '\n' and b[nbytes-1] != '\r':
-#                 result = b
-#                 raise ValueError( "incomplete line at %s" % result )
-
-#             # make sure that this goes fully through C
-#             # otherwise buffer is copied to/from a
-#             # Python object causing segfaults as
-#             # the wrong memory is freed
-#             return self.parser.parse( b, nbytes )
-
-#         raise StopIteration
-
-#     def __dealloc__(self):
-#         free(self.buffer)
-
-#     def __next__(self):
-#         return self.__cnext__()
 
 #########################################################
 #########################################################

pysam/htslib_util.c

@@ -630,7 +630,7 @@ def prebuild_libcsamtools(ext, force):
          extra_objects=separate_htslib_objects,
          libraries=external_htslib_libraries + internal_htslib_libraries),
     dict(name="pysam.libcutils",
-         sources=[source_pattern % "utils", "pysam/pysam_util.c"] + os_c_files,
+         sources=[source_pattern % "utils"] + os_c_files,
          extra_objects=separate_htslib_objects,
          libraries=external_htslib_libraries + internal_htslib_libraries + internal_samtools_libraries),
     dict(name="pysam.libcalignmentfile",