#
# import is a python reserved word.
SAMTOOLS_DISPATCH = {
+ # samtools 'documented' commands
"view" : ( "view", None ),
"sort" : ( "sort", None),
- "samimport": ( "import", None),
- "pileup" : ( "pileup", ( (("-c",), Pileup.iterate ), ), ),
+ "mpileup" : ( "mpileup", None),
+ "depth" : ("depth", None),
"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) }
+ "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 ), ), ),
+
+ }
# instantiate samtools commands as python functions
for key, options in SAMTOOLS_DISPATCH.iteritems():