From noreply at r-forge.r-project.org  Mon Oct 19 13:55:17 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon, 19 Oct 2015 13:55:17 +0200 (CEST)
Subject: [Patchwork-commits] r218 - .git .git/logs .git/logs/refs/heads
	.git/logs/refs/remotes/origin .git/refs/heads
	.git/refs/remotes/origin pkg/TAPS/R
Message-ID: <20151019115517.57BFC187BC5@r-forge.r-project.org>

Author: sebastian_d
Date: 2015-10-19 13:55:17 +0200 (Mon, 19 Oct 2015)
New Revision: 218

Modified:
   .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/TAPS/R/TAPS.r
Log:
bjorn changes

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

Modified: .git/logs/HEAD
===================================================================
--- .git/logs/HEAD	2015-06-26 07:33:33 UTC (rev 217)
+++ .git/logs/HEAD	2015-10-19 11:55:17 UTC (rev 218)
@@ -100,3 +100,4 @@
 e8cc7370da527f1d46bb81720f663ceed281e07d b5798bb1874d9dc8e50fa5083961a8836d79f76c Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1411979666 +0200	pull: Fast-forward
 b5798bb1874d9dc8e50fa5083961a8836d79f76c 52402622419759bc3642b6f49dd0f4abd2003d38 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1434615906 +0200	pull: Fast-forward
 52402622419759bc3642b6f49dd0f4abd2003d38 4bbde19cc8582ba3fb6caf01b1b01165c5db15d6 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1435303966 +0200	pull: Fast-forward
+4bbde19cc8582ba3fb6caf01b1b01165c5db15d6 0a1de5c432ad323bbac1093425e9a939f351b50b Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1445255649 +0200	pull: Fast-forward

Modified: .git/logs/refs/heads/master
===================================================================
--- .git/logs/refs/heads/master	2015-06-26 07:33:33 UTC (rev 217)
+++ .git/logs/refs/heads/master	2015-10-19 11:55:17 UTC (rev 218)
@@ -100,3 +100,4 @@
 e8cc7370da527f1d46bb81720f663ceed281e07d b5798bb1874d9dc8e50fa5083961a8836d79f76c Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1411979666 +0200	pull: Fast-forward
 b5798bb1874d9dc8e50fa5083961a8836d79f76c 52402622419759bc3642b6f49dd0f4abd2003d38 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1434615906 +0200	pull: Fast-forward
 52402622419759bc3642b6f49dd0f4abd2003d38 4bbde19cc8582ba3fb6caf01b1b01165c5db15d6 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1435303966 +0200	pull: Fast-forward
+4bbde19cc8582ba3fb6caf01b1b01165c5db15d6 0a1de5c432ad323bbac1093425e9a939f351b50b Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1445255649 +0200	pull: Fast-forward

Modified: .git/logs/refs/remotes/origin/master
===================================================================
--- .git/logs/refs/remotes/origin/master	2015-06-26 07:33:33 UTC (rev 217)
+++ .git/logs/refs/remotes/origin/master	2015-10-19 11:55:17 UTC (rev 218)
@@ -97,3 +97,4 @@
 e8cc7370da527f1d46bb81720f663ceed281e07d b5798bb1874d9dc8e50fa5083961a8836d79f76c Sebastian DiLorenzo <S_D at array-47-13.medsci.uu.se> 1411979666 +0200	pull: fast-forward
 b5798bb1874d9dc8e50fa5083961a8836d79f76c 52402622419759bc3642b6f49dd0f4abd2003d38 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1434615905 +0200	pull: fast-forward
 52402622419759bc3642b6f49dd0f4abd2003d38 4bbde19cc8582ba3fb6caf01b1b01165c5db15d6 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1435303966 +0200	pull: fast-forward
+4bbde19cc8582ba3fb6caf01b1b01165c5db15d6 0a1de5c432ad323bbac1093425e9a939f351b50b Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1445255649 +0200	pull: fast-forward

Modified: .git/refs/heads/master
===================================================================
--- .git/refs/heads/master	2015-06-26 07:33:33 UTC (rev 217)
+++ .git/refs/heads/master	2015-10-19 11:55:17 UTC (rev 218)
@@ -1 +1 @@
-4bbde19cc8582ba3fb6caf01b1b01165c5db15d6
+0a1de5c432ad323bbac1093425e9a939f351b50b

Modified: .git/refs/remotes/origin/master
===================================================================
--- .git/refs/remotes/origin/master	2015-06-26 07:33:33 UTC (rev 217)
+++ .git/refs/remotes/origin/master	2015-10-19 11:55:17 UTC (rev 218)
@@ -1 +1 @@
-4bbde19cc8582ba3fb6caf01b1b01165c5db15d6
+0a1de5c432ad323bbac1093425e9a939f351b50b

Modified: pkg/TAPS/R/TAPS.r
===================================================================
--- pkg/TAPS/R/TAPS.r	2015-06-26 07:33:33 UTC (rev 217)
+++ pkg/TAPS/R/TAPS.r	2015-10-19 11:55:17 UTC (rev 218)
@@ -15,7 +15,7 @@
 TAPS_plot <- function(#samples='all',
                      directory=NULL,autoEstimate=FALSE,
                       bin=250,cores=1,matched=FALSE,allelePeaks=FALSE) {
-    cores=1
+    # cores=1
     #Automatically check, and if needed install, packages stats and fields
     
     #Load stats. It should be in all, at least semi-new, R distributions so we dont need to install.package it or
@@ -77,6 +77,7 @@
     
     # for (i in 1:length(subs)) {
     #junk only stores the list from foreach.
+    sampleData$MHOF <- sampleData$MAPD <- NA
     junk <- foreach (i = 1:length(subs)) %dopar% {
         setwd(paste(root,'/',subs[i],sep=''))
         name <- subs[i]
@@ -269,7 +270,7 @@
 
 ###
 TAPS_call <- function(samples='all',directory=getwd(),cores=1) {
-    cores=1
+    # cores=1
     minseg=1
     maxCn=12
     #suppressPackageStartupMessages(library(xlsx))    
@@ -4079,4 +4080,5 @@
     if (any(data$Chromosome=='1'))
         data$Chromosome=paste('chr',data$Chromosome,sep='')
     return(data)
-}
\ No newline at end of file
+}
+