refactoring for htslib

.gitignore

@@ -3,7 +3,7 @@
 *#
 
 # test directory
-pysam/
+tests/pysam/
 tests/tmp*
 tests/*.bam
 tests/*.bai

MANIFEST.in

@@ -34,35 +34,37 @@ include pysam.py
 # pysam tests
 include tests/00README.txt
 include tests/Makefile
-include tests/ex1.fa
-include tests/ex1.sam.gz
-include tests/ex3.sam
-include tests/ex4.sam
-include tests/ex5.sam
-include tests/ex6.sam
-include tests/ex7.sam
-include tests/ex8.sam
-include tests/ex9_fail.bam
-include tests/ex9_nofail.bam
-include tests/ex10.sam
-include tests/example.py
-include tests/pysam_test.py
-include tests/segfault_tests.py
-include tests/example_*.sam
-include tests/example_btag.bam
-include tests/tag_bug.bam
-include tests/example.vcf40
-include tests/example_empty_header.bam
-include tests/test_unaligned.bam
-include tests/issue100.bam
+include tests/pysam_data
+include tests/tabix_data
+#ex1.fa
+#include tests/ex1.sam.gz
+#include tests/ex3.sam
+#include tests/ex4.sam
+#include tests/ex5.sam
+#include tests/ex6.sam
+#include tests/ex7.sam
+#include tests/ex8.sam
+#include tests/ex9_fail.bam
+#include tests/ex9_nofail.bam
+#include tests/ex10.sam
+#include tests/example.py
+#include tests/pysam_test.py
+#include tests/segfault_tests.py
+#include tests/example_*.sam
+#include tests/example_btag.bam
+#include tests/tag_bug.bam
+#include tests/example.vcf40
+#include tests/example_empty_header.bam
+#include tests/test_unaligned.bam
+#include tests/issue100.bam
 
 # tabix tests
-include tests/tabix_test.py
-include tests/example.gtf.gz
-include tests/example.gtf.gz.tbi
-include tests/example.bed.gz
-include tests/example.bed.gz.tbi
-include tests/vcf-examples/*.vcf
+#include tests/tabix_test.py
+#include tests/example.gtf.gz
+#include tests/example.gtf.gz.tbi
+#include tests/example.bed.gz
+#include tests/example.bed.gz.tbi
+#include tests/vcf-examples/*.vcf
 
 # documentation
 include doc/*

pysam/__init__.py

@@ -1,118 +1,130 @@
-from pysam.csamtools import *
+from pysam.chtslib import *
 from pysam.ctabix import *
 import pysam.csamtools as csamtools
 import pysam.ctabix as ctabix
 from pysam.cvcf import *
 import pysam.cvcf as cvcf
 import pysam.Pileup as Pileup
-import sys
 import os
 
-class SamtoolsError( Exception ):
-    '''exception raised in case of an error incurred in the samtools library.'''
+
+class SamtoolsError(Exception):
+    '''exception raised in case of an error incurred in the samtools
+    library.'''
 
     def __init__(self, value):
         self.value = value
+
     def __str__(self):
         return repr(self.value)
 
+
 class SamtoolsDispatcher(object):
-    '''samtools dispatcher. 
+    '''samtools dispatcher.
 
     Emulates the samtools command line as module calls.
     
-    Captures stdout and stderr. 
+    Captures stdout and stderr.
 
     Raises a :class:`pysam.SamtoolsError` exception in case
     samtools exits with an error code other than 0.
 
-    Some command line options are associated with parsers.
-    For example, the samtools command "pileup -c" creates
-    a tab-separated table on standard output. In order to 
-    associate parsers with options, an optional list of 
-    parsers can be supplied. The list will be processed
-    in order checking for the presence of each option.
+    Some command line options are associated with parsers.  For
+    example, the samtools command "pileup -c" creates a tab-separated
+    table on standard output. In order to associate parsers with
+    options, an optional list of parsers can be supplied. The list
+    will be processed in order checking for the presence of each
+    option.
+
+    If no parser is given or no appropriate parser is found, the
+    stdout output of samtools commands will be returned.
 
-    If no parser is given or no appropriate parser is found, 
-    the stdout output of samtools commands will be returned.
     '''
-    dispatch=None
-    parsers=None
 
-    def __init__(self,dispatch, parsers): 
+    dispatch = None
+    parsers = None
+
+    def __init__(self, dispatch, parsers):
         self.dispatch = dispatch
         self.parsers = parsers
         self.stderr = []
 
     def __call__(self, *args, **kwargs):
         '''execute a samtools command
         '''
-        retval, stderr, stdout = csamtools._samtools_dispatch( self.dispatch, args )
-        if retval: raise SamtoolsError( 'csamtools returned with error %i: %s' % (retval, "\n".join( stderr ) ))
+        retval, stderr, stdout = csamtools._samtools_dispatch(
+            self.dispatch, args)
+        if retval:
+            raise SamtoolsError(
+                'csamtools returned with error %i: %s' %
+                (retval, "\n".join(stderr)))
         self.stderr = stderr
         # samtools commands do not propagate the return code correctly.
         # I have thus added this patch to throw if there is output on stderr.
         # Note that there is sometimes output on stderr that is not an error,
         # for example: [sam_header_read2] 2 sequences loaded.
         # Ignore messages like these
-        stderr = [ x for x in stderr \
-                       if not (x.startswith( "[sam_header_read2]" ) or \
-                                   x.startswith("[bam_index_load]") or \
-                                   x.startswith("[bam_sort_core]") or \
-                                   x.startswith("[samopen] SAM header is present") )
-                   ]
-        if stderr: raise SamtoolsError( "\n".join( stderr ) )
+        stderr = [x for x in stderr
+                  if not (x.startswith("[sam_header_read2]") or
+                          x.startswith("[bam_index_load]") or
+                          x.startswith("[bam_sort_core]") or
+                          x.startswith("[samopen] SAM header is present"))
+              ]
+        if stderr:
+            raise SamtoolsError("\n".join(stderr))
 
         # call parser for stdout:
         if not kwargs.get("raw") and stdout and self.parsers:
             for options, parser in self.parsers:
-                for option in options: 
-                    if option not in args: break
+                for option in options:
+                    if option not in args:
+                        break
                 else:
                     return parser(stdout)
 
         return stdout
 
-    def getMessages( self ):
+    def getMessages(self):
         return self.stderr
 
     def usage(self):
         '''return the samtools usage information for this command'''
-        retval, stderr, stdout = csamtools._samtools_dispatch( self.dispatch )
+        retval, stderr, stdout = csamtools._samtools_dispatch(
+            self.dispatch)
         return "".join(stderr)
 
 #
 # samtools command line options to export in python
 #
 # import is a python reserved word.
-SAMTOOLS_DISPATCH = { 
+SAMTOOLS_DISPATCH = {
     # samtools 'documented' commands
-    "view" : ( "view", None ),
-    "sort" : ( "sort", None),
-    "mpileup" : ( "mpileup", None),
-    "depth" : ("depth", None),
-    "faidx" : ("faidx", None),
-    "tview" : ("tview", None),
-    "index" : ("index", None),
-    "idxstats" : ("idxstats", None),
-    "fixmate" : ("fixmate", None),
-    "flagstat" : ("flagstat", None),
-    "calmd" : ("calmd", None),
-    "merge" : ("merge", None),  
-    "rmdup" : ("rmdup", None),
-    "reheader" : ("reheader", None),
-    "cat" : ("cat", None),
-    "targetcut" : ("targetcut", None),
-    "phase" : ("phase", None),
+    "view": ("view", None),
+    "sort": ("sort", None),
+    "mpileup": ("mpileup", None),
+    "depth": ("depth", None),
+    "faidx": ("faidx", None),
+    "tview": ("tview", None),
+    "index": ("index", None),
+    "idxstats": ("idxstats", None),
+    "fixmate": ("fixmate", None),
+    "flagstat": ("flagstat", None),
+    "calmd": ("calmd", None),
+    "merge": ("merge", None),
+    "rmdup": ("rmdup", None),
+    "reheader": ("reheader", None),
+    "cat": ("cat", None),
+    "targetcut": ("targetcut", None),
+    "phase": ("phase", None),
     # others
-    "samimport": ( "import", None),
-    "bam2fq" : ("bam2fq", None),
-    "pad2unpad" : ("pad2unpad", None),
-    "depad" : ("pad2unpad", None),
-    "bedcov" : ("bedcov", None),
-    "bamshuf" : ("bamshuf", None),
+    "samimport": ("import", None),
+    "bam2fq": ("bam2fq", None),
+    "pad2unpad": ("pad2unpad", None),
+    "depad": ("pad2unpad", None),
+    "bedcov": ("bedcov", None),
+    "bamshuf": ("bamshuf", None),
     # obsolete
-    # "pileup" : ( "pileup", ( (("-c",), Pileup.iterate ), ), ),
+    # "pileup": "pileup", ( (("-c",), Pileup.iterate),),),
 
  }
 
@@ -123,23 +135,25 @@ def usage(self):
 
 # hack to export all the symbols from csamtools
 __all__ = \
-    csamtools.__all__ + \
+    chtslib.__all__ + \
     ctabix.__all__ + \
     cvcf.__all__ +\
-    [ "SamtoolsError", "SamtoolsDispatcher" ] + list(SAMTOOLS_DISPATCH) +\
-    ["Pileup" ] 
+    ["SamtoolsError", "SamtoolsDispatcher"] +\
+    list(SAMTOOLS_DISPATCH) +\
+    ["Pileup"]
 
 from pysam.version import __version__, __samtools_version__
 
-###########################################################
-# Utility functions for compilation
+
 def get_include():
     '''return a list of include directories.'''
     dirname = os.path.abspath(os.path.join(os.path.dirname(__file__)))
-    return [ dirname,
-             os.path.join(dirname, 'include', 'samtools'),
-             os.path.join(dirname, 'include', 'tabix') ]
+    return [dirname,
+            os.path.join(dirname, 'include', 'samtools'),
+            os.path.join(dirname, 'include', 'tabix')]
+
 
 def get_defines():
     '''return a list of defined compilation parameters.'''
-    return [('_FILE_OFFSET_BITS','64'), ('_USE_KNETFILE','')]
+    return [('_FILE_OFFSET_BITS', '64'),
+            ('_USE_KNETFILE', '')]