Imported Upstream version 0.5

[pysam.git] / pysam / __init__.py

diff --git a/pysam/__init__.py b/pysam/__init__.py
index 8454f8e4b0739581a463484d1799ba2b2a43a1ad..ec0439f17290876217c610355072aa4f4d074efa 100644 (file)
--- a/pysam/__init__.py
+++ b/pysam/__init__.py
@@ -86,31 +86,19 @@ class SamtoolsDispatcher(object):
 #
 # import is a python reserved word.
 SAMTOOLS_DISPATCH = { 
-    # samtools 'documented' commands
     "view" : ( "view", None ),
     "sort" : ( "sort", None),
-    "mpileup" : ( "mpileup", None),
-    "depth" : ("depth", None),
+    "samimport": ( "import", None),
+    "pileup" : ( "pileup", ( (("-c",), Pileup.iterate ), ), ),
     "faidx" : ("faidx", None),
     "tview" : ("tview", None),
     "index" : ("index", None),
-    "idxstats" : ("idxstats", None),
     "fixmate" : ("fixmate", None),
+    "glfview" : ("glfview", 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),
-    # obsolete
-    # "pileup" : ( "pileup", ( (("-c",), Pileup.iterate ), ), ),
-
- }
+    "rmdup" : ("rmdup", None) }
 
 # instantiate samtools commands as python functions
 for key, options in SAMTOOLS_DISPATCH.iteritems():