[Patchwork-commits] r146 - .git .git/logs .git/logs/refs/heads .git/logs/refs/remotes/origin .git/refs/heads .git/refs/remotes/origin pkg/patchwork/R pkg/patchworkData/data

[noreply at r-forge.r-project.org]

Author: sebastian_d
Date: 2012-07-10 10:38:08 +0200 (Tue, 10 Jul 2012)
New Revision: 146

Added:
   pkg/patchworkData/data/commonSnpsHG18.RData
Modified:
   .git/COMMIT_EDITMSG
   .git/index
   .git/logs/HEAD
   .git/logs/refs/heads/master
   .git/logs/refs/remotes/origin/master
   .git/refs/heads/master
   .git/refs/remotes/origin/master
   pkg/patchwork/R/patchwork.alleledata.r
Log:
adding support for hg18 snps

Modified: .git/COMMIT_EDITMSG
===================================================================
--- .git/COMMIT_EDITMSG	2012-06-29 14:21:47 UTC (rev 145)
+++ .git/COMMIT_EDITMSG	2012-07-10 08:38:08 UTC (rev 146)
@@ -1 +1 @@
-update changelog post recommit
+forgot this file =)

Modified: .git/index
===================================================================
(Binary files differ)

Modified: .git/logs/HEAD
===================================================================
--- .git/logs/HEAD	2012-06-29 14:21:47 UTC (rev 145)
+++ .git/logs/HEAD	2012-07-10 08:38:08 UTC (rev 146)
@@ -1,2 +1,4 @@
 0000000000000000000000000000000000000000 6980fef84a3043d074fe5e46a935b84815d90e03 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1340969996 +0200	commit (initial): recommitting project
 6980fef84a3043d074fe5e46a935b84815d90e03 693c0c176e7aaf19c80e78373ef88877e785cd91 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1340970681 +0200	commit: update changelog post recommit
+693c0c176e7aaf19c80e78373ef88877e785cd91 598eb7173584784980db9537d26490901a99827d Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1341908911 +0200	commit: Added snp data for hg18
+598eb7173584784980db9537d26490901a99827d f33a41d4b92635e2b52ac0bb8a49d6990ed7089c Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1341909020 +0200	commit: forgot this file =)

Modified: .git/logs/refs/heads/master
===================================================================
--- .git/logs/refs/heads/master	2012-06-29 14:21:47 UTC (rev 145)
+++ .git/logs/refs/heads/master	2012-07-10 08:38:08 UTC (rev 146)
@@ -1,2 +1,4 @@
 0000000000000000000000000000000000000000 6980fef84a3043d074fe5e46a935b84815d90e03 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1340969996 +0200	commit (initial): recommitting project
 6980fef84a3043d074fe5e46a935b84815d90e03 693c0c176e7aaf19c80e78373ef88877e785cd91 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1340970681 +0200	commit: update changelog post recommit
+693c0c176e7aaf19c80e78373ef88877e785cd91 598eb7173584784980db9537d26490901a99827d Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1341908911 +0200	commit: Added snp data for hg18
+598eb7173584784980db9537d26490901a99827d f33a41d4b92635e2b52ac0bb8a49d6990ed7089c Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1341909020 +0200	commit: forgot this file =)

Modified: .git/logs/refs/remotes/origin/master
===================================================================
--- .git/logs/refs/remotes/origin/master	2012-06-29 14:21:47 UTC (rev 145)
+++ .git/logs/refs/remotes/origin/master	2012-07-10 08:38:08 UTC (rev 146)
@@ -1,2 +1,4 @@
 0000000000000000000000000000000000000000 6980fef84a3043d074fe5e46a935b84815d90e03 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1340970343 +0200	update by push
 6980fef84a3043d074fe5e46a935b84815d90e03 693c0c176e7aaf19c80e78373ef88877e785cd91 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1340970693 +0200	update by push
+693c0c176e7aaf19c80e78373ef88877e785cd91 598eb7173584784980db9537d26490901a99827d Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1341908930 +0200	update by push
+598eb7173584784980db9537d26490901a99827d f33a41d4b92635e2b52ac0bb8a49d6990ed7089c Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1341909278 +0200	update by push

Modified: .git/refs/heads/master
===================================================================
--- .git/refs/heads/master	2012-06-29 14:21:47 UTC (rev 145)
+++ .git/refs/heads/master	2012-07-10 08:38:08 UTC (rev 146)
@@ -1 +1 @@
-693c0c176e7aaf19c80e78373ef88877e785cd91
+f33a41d4b92635e2b52ac0bb8a49d6990ed7089c

Modified: .git/refs/remotes/origin/master
===================================================================
--- .git/refs/remotes/origin/master	2012-06-29 14:21:47 UTC (rev 145)
+++ .git/refs/remotes/origin/master	2012-07-10 08:38:08 UTC (rev 146)
@@ -1 +1 @@
-693c0c176e7aaf19c80e78373ef88877e785cd91
+f33a41d4b92635e2b52ac0bb8a49d6990ed7089c

Modified: pkg/patchwork/R/patchwork.alleledata.r
===================================================================
--- pkg/patchwork/R/patchwork.alleledata.r	2012-06-29 14:21:47 UTC (rev 145)
+++ pkg/patchwork/R/patchwork.alleledata.r	2012-07-10 08:38:08 UTC (rev 146)
@@ -4,9 +4,9 @@
 	#Load data included in package
 	packagepath = system.file(package="patchwork")
 	#load(paste(packagepath,"/data/commonSnps132.RData",sep=""))
-	
-	data(commonSnps132,package="patchworkData")
 
+	#data(commonSnps132,package="patchworkData")
+
 	#if .perl folder exists, delete it.
 	#test = getwd()
 	#try( setwd(".perl"),silent=TRUE)
@@ -49,7 +49,21 @@
 		alf$achr[alf$achr == as.character(i)] = paste("chr",as.character(i),sep="")
 		}
 	
-	
+	#Check if HG18 or HG19 should be applied
+	con = file(Pileup,"rt")
+	firstline = readLines(con,1)
+	hgcheck = strsplit(firstline,"\t")
+
+
+	if (hgcheck[[1]][2] <= 10000)
+		{
+		data(commonSnpsHG18,package="patchworkData")
+		}
+	else
+		{
+		data(commonSnps132,package="patchworkData")
+		}
+
 	alf=merge(alf,dbSnp[,c(1,3)], all=F, by=1:2)
 
 	#Finally, if a matched normal was available, remove SNPs that were not (somewhat) heterozygous there.

Added: pkg/patchworkData/data/commonSnpsHG18.RData
===================================================================
(Binary files differ)


Property changes on: pkg/patchworkData/data/commonSnpsHG18.RData
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream