# HG changeset patch
# User saskia-hiltemann
# Date 1457110570 18000
# Node ID f7ff063c738e7869f28dd524a1dfa0bdd968cbaa
# Parent  d6af2a78617fb4d411e7cb022af4d6e8b28dad8c
bugfix for COSMIC70 not giving output

diff -r d6af2a78617f -r f7ff063c738e tools/annovar/annovar.sh
--- a/tools/annovar/annovar.sh	Fri Mar 04 11:32:50 2016 -0500
+++ b/tools/annovar/annovar.sh	Fri Mar 04 11:56:10 2016 -0500
@@ -178,7 +178,7 @@
 #################################
 
 
-set -- `getopt -n$0 -u -a --longoptions="inputfile: buildver: humandb: varfile: VCF: chrcol: startcol: endcol: refcol: obscol: vartypecol: convertcoords: geneanno: hgvs: verdbsnp: tfbs: mce: cytoband: segdup: dgv: gwas: ver1000g: cg46: cg69: impactscores: newimpactscores: otherinfo: esp: exac03: exac03nonpsych: exac03nontcga: dbscsnv11: kaviar_20150923: hrcr1: mitimpact2: mitimpact24: dbnsfp30a: spidex: gonl: gerp: cosmic61: cosmic63: cosmic64: cosmic65: cosmic67: cosmic68: clinvar: nci60: outall: outfilt: outinvalid: scriptsdir: dorunannovar: dofilter: filt_dbsnp: filt1000GALL: filt1000GAFR: filt1000GAMR: filt1000GASN: filt1000GEUR: filtESP6500ALL: filtESP6500EA: filtESP6500AA: filtcg46: filtcg69: dummy:" "h:" "$@"` || usage
+set -- `getopt -n$0 -u -a --longoptions="inputfile: buildver: humandb: varfile: VCF: chrcol: startcol: endcol: refcol: obscol: vartypecol: convertcoords: geneanno: hgvs: verdbsnp: tfbs: mce: cytoband: segdup: dgv: gwas: ver1000g: cg46: cg69: impactscores: newimpactscores: otherinfo: esp: exac03: exac03nonpsych: exac03nontcga: dbscsnv11: kaviar_20150923: hrcr1: mitimpact2: mitimpact24: dbnsfp30a: spidex: gonl: gerp: cosmic61: cosmic63: cosmic64: cosmic65: cosmic67: cosmic68: cosmic70: clinvar: nci60: outall: outfilt: outinvalid: scriptsdir: dorunannovar: dofilter: filt_dbsnp: filt1000GALL: filt1000GAFR: filt1000GAMR: filt1000GASN: filt1000GEUR: filtESP6500ALL: filtESP6500EA: filtESP6500AA: filtcg46: filtcg69: dummy:" "h:" "$@"` || usage
 [ $# -eq 0 ] && usage
 
 
@@ -233,6 +233,7 @@
         --cosmic65)            cosmic65=$2;shift;;    # Y or N
         --cosmic67)            cosmic67=$2;shift;;    # Y or N
         --cosmic68)            cosmic68=$2;shift;;    # Y or N
+        --cosmic70)            cosmic70=$2;shift;;    # Y or N
         --nci60)               nci60=$2;shift;;       # Y or N
         --clinvar)             clinvar=$2;shift;;     # Y or N
         --filt_dbsnp)          filt_dbsnp=$2;shift;;  # Y or N
diff -r d6af2a78617f -r f7ff063c738e tools/annovar/annovar.xml
--- a/tools/annovar/annovar.xml	Fri Mar 04 11:32:50 2016 -0500
+++ b/tools/annovar/annovar.xml	Fri Mar 04 11:56:10 2016 -0500
@@ -20,6 +20,7 @@
         --cosmic65 "${cosmic65}"
         --cosmic67 "${cosmic67}"
         --cosmic68 "${cosmic68}"
+        --cosmic70 "${cosmic70}"
         --outall "${annotated}"
         --outinvalid "${invalid}"
         --dorunannovar "${dorun}"