version upd

Author: Michele Berselli

README.md

@@ -11,7 +11,7 @@ For more details, see granite [*documentation*](https://granite-suite.readthedoc
 ## Availability and requirements
 A ready-to-use docker image is available to download.
 
-    docker pull b3rse/granite:v0.1.12
+    docker pull b3rse/granite:v0.1.13
 
 To run locally, install the following libraries:
 

docs/conf.py

@@ -22,7 +22,7 @@
 author = 'Michele Berselli'
 
 # The full version, including alpha/beta/rc tags
-release = '0.1.12'
+release = '0.1.13'
 
 
 # -- General configuration ---------------------------------------------------

docs/install.md

@@ -2,7 +2,7 @@
 
 A ready-to-use docker image is available to download.
 
-    docker pull b3rse/granite:v0.1.12
+    docker pull b3rse/granite:v0.1.13
 
 To run locally, Python 3.6+ is required together with the following libraries:
 

granite/_version.py

@@ -1,4 +1,4 @@
 """Version information."""
 
 # The following line *must* be the last in the module, exactly as formatted:
-__version__ = "0.1.12"
+__version__ = "0.1.13"

granite/lib/shared_functions.py

@@ -271,7 +271,8 @@ def variant_type_sv(vnt_obj):
         SVTYPE = vnt_obj.get_tag_value("SVTYPE")
     except Exception:
         raise ValueError('\nERROR in parsing vcf, variant at position {0} does not contain SVTYPE in INFO\n'
-                .format(vnt_obj.CHROM+":"+str(vnt_obj.POS)))
+                .format(vnt_obj.CHROM + ":" + str(vnt_obj.POS)))
+    #end try
     if SVTYPE == 'DEL':
         return 'del'
     elif SVTYPE == 'DUP':
@@ -286,7 +287,9 @@ def variant_type_sv(vnt_obj):
         return 'cnv'
     else:
         raise ValueError('\nERROR in parsing vcf, variant at position {0} contains unexpected SVTYPE "{1}" in INFO\n'
-                .format(vnt_obj.CHROM+":"+str(vnt_obj.POS),SVTYPE))
+                .format(vnt_obj.CHROM + ":" + str(vnt_obj.POS), SVTYPE))
+    #end if
+#end def
 
 def allele_frequency(vnt_obj, aftag, idx=0):
     ''' return allele frequency for variant from aftag in INFO,

tests/files/SVqcVCF_oneSample.json

@@ -7,4 +7,4 @@
       "DUP": 1
     }
   ]
-}
+}

tests/files/SVqcVCF_twoSamples.json

@@ -13,4 +13,4 @@
       "DUP": 2
     }
   ]
-}
+}

tests/files/variant_type_sv_fail1.vcf

@@ -3,4 +3,4 @@
 ##reference=GCF_000001405.26
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
 1	46000	.	T	<CNV>	.	.	DBVARID;SVTYPE=CNV;END=111250
-1	46000	.	T	<CNV>	.	.	DBVARID;END=111250
+1	46000	.	T	<CNV>	.	.	DBVARID;END=111250