Pulled down update to submodule_dir

snakecnv/common.smk

@@ -87,6 +87,18 @@ class Command(object):
     def wdir(self):
         return self._wdir
 
+    def get_param(self, key):
+        if key not in self.params:
+            print_error_exit("key %s absent from config file" % key)
+        return self.params[key]
+
+    def get_param_as_str(self, key):
+        param = self.get_param(key)
+        if isinstance(param, list):
+            return " ".join(map(str, param))
+        else:
+            return str(param)
+
     def get_sample_fastq(self, wildcards):
         pass
 
@@ -407,7 +419,8 @@ class MergeBatches(Detection):
                    svtype=[x for x in self.varianttypes if x != "mCNV"])
         return outputs
 
-class Popsim(Common):
+
+class Popsim(Command):
     def __init__(self, params):
         Command.__init__(self, params)
 
@@ -418,6 +431,34 @@ class Popsim(Common):
                    svtype=[x for x in self.varianttypes if x != "mCNV"])
         return outputs
 
+    def buildpop_inputs(self, wildcards):
+        inputs = {
+            "reference": self.reference
+        }
+        params = {
+            "nstretches": False,
+            "genotypes": False,
+            "sv_list": False
+        }
+        if NSTRETCHES is not None:
+            inputs["nstretches"] = NSTRETCHES
+            params["nstretches"] = True
+        if GENOTYPES is not None:
+            inputs["genotypes"] = GENOTYPES
+            params["genotypes"] = True
+        if SV_LIST is not None:
+            inputs["sv_list"] = SV_LIST
+            params["sv_list"] = True
+
+        return inputs, params
+
+    def buildpop_outputs(self):
+        outputs = []
+        for n in range(1, NB_INDS+1):
+            outputs += [os.path.abspath(os.path.join("pop", "indiv%d_1.fq.gz" % n)),
+                        os.path.abspath(os.path.join("pop", "indiv%d_2.fq.gz" % n))]
+        return outputs
+
 
 def set_absolute_path(params, key):
     params["_"+key] = params[key]