[med-svn] [gwama] 03/04: Update upstream.docs

[Dylan Aïssi]

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bob.dybian-guest pushed a commit to branch master
in repository gwama.

commit 72dd02e72e2cb10550eca6d9cc587659d23fd2a7
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date:   Fri Aug 26 07:57:57 2016 +0200

    Update upstream.docs
---
 debian/rules                                     | 2 +-
 debian/upstream.docs/R_scripts/MANH.R            | 4 ++--
 debian/upstream.docs/{log2.txt => gwama_log.txt} | 3 +++
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/debian/rules b/debian/rules
index 764d97b..e232612 100755
--- a/debian/rules
+++ b/debian/rules
@@ -13,5 +13,5 @@ override_dh_auto_build:
 
 override_dh_installchangelogs:
 	# Install upstream log2.txt file as changelog
-	dh_installchangelogs debian/upstream.docs/log2.txt
+	dh_installchangelogs debian/upstream.docs/gwama_log.txt
 
diff --git a/debian/upstream.docs/R_scripts/MANH.R b/debian/upstream.docs/R_scripts/MANH.R
index e613bf8..8d73628 100644
--- a/debian/upstream.docs/R_scripts/MANH.R
+++ b/debian/upstream.docs/R_scripts/MANH.R
@@ -21,8 +21,8 @@ data<-read.table(input,stringsAsFactors=FALSE,header=TRUE,sep = "\t",na.strings
 png(out,height=600,width=800)
 
 obspval <- (data$p.value)
-chr <- (data$chromosome)
-pos <- (data$position)
+chr <- (data$chr)
+pos <- (data$pos)
 obsmax <- trunc(max(-log10(obspval)))+1
 
 sort.ind <- order(chr, pos) 
diff --git a/debian/upstream.docs/log2.txt b/debian/upstream.docs/gwama_log.txt
similarity index 94%
rename from debian/upstream.docs/log2.txt
rename to debian/upstream.docs/gwama_log.txt
index 843bc96..52c33f7 100644
--- a/debian/upstream.docs/log2.txt
+++ b/debian/upstream.docs/gwama_log.txt
@@ -1,3 +1,6 @@
+v2.2.2
+*--indel_alleles option now will flip negative strand for SNPs
+
 v2.1
 *Added option "--indel_alleles" for using longer allele names than single character. Please note that enabling that option will remove strand flipping.
 *Added "Analysis finished." line to log file and standard output.

-- 
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