add external_db

pathogenprofiler/bam.py

@@ -47,9 +47,12 @@ def call_variants(self,caller="GATK",gff_file=None,bed_file=None,call_method="op
 			return bcf(self.variant_bcf_file,prefix=self.prefix)
 	def gatk_gvcf(self,bed_file=None,low_dp_as_missing=False,max_dp=None,min_dp=10):
 		add_arguments_to_self(self,locals())
-		dict_file = self.ref_file.replace(".fasta","").replace(".fa","")
-		if nofile(dict_file+".dict"):
+		dict_file = self.ref_file.replace(".fasta","").replace(".fa","")+".dict"
+		if nofile(dict_file):
 			run_cmd("gatk CreateSequenceDictionary -R %(ref_file)s" % vars(self))
+		if nofile(self.ref_file+".fai"):
+			run_cmd("samtools faidx %(ref_file)s" % vars(self))
+
 		self.gvcf_file = "%s.gvcf.gz" % self.prefix
 		self.tmp_gvcf_file = "%s.tmp.gvcf.gz" % self.prefix
 		self.bed_option = "-L %s " % self.bed_file if self.bed_file else ""

setup.py

@@ -4,7 +4,7 @@
 setuptools.setup(
 
 	name="pathogen-profiler",
-	version="1.5.0",
+	version="1.6.0",
 	packages=["pathogenprofiler",],
 	license="GPL3",
 	long_description="Pathogen profiling tool",