[med-svn] [snp-sites] 01/04: New upstream version 2.3.3

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository snp-sites.

commit 298cfae1360903f9d56510eff595fb7a3b27ad4b
Author: Sascha Steinbiss <satta at debian.org>
Date:   Tue Jun 13 12:09:49 2017 +0200

    New upstream version 2.3.3
---
 AUTHORS              |  2 +-
 Dockerfile           | 19 +++++++++++++++++++
 LICENSE              |  4 ++++
 VERSION              |  2 +-
 src/alignment-file.c |  2 +-
 src/snp-sites.c      | 14 ++++++++------
 6 files changed, 34 insertions(+), 9 deletions(-)

diff --git a/AUTHORS b/AUTHORS
index 6d74363..bb6527c 100644
--- a/AUTHORS
+++ b/AUTHORS
@@ -1,3 +1,3 @@
 Andrew J. Page <ap13 at sanger.ac.uk>
-Ben Taylor <bt5 at sanger.ac.uk>
+Ben Taylor <path-help at sanger.ac.uk>
 Jorge Soares <path-help at sanger.ac.uk>
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..a1aeca3
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,19 @@
+#
+#  From this base-image / starting-point
+#
+FROM debian:testing
+
+#
+#  Authorship
+#
+MAINTAINER ap13 at sanger.ac.uk
+
+#
+# Pull in packages from testing
+#
+RUN apt-get update -qq
+
+#
+# Install Roary
+#
+RUN apt-get install snp-sites
diff --git a/LICENSE b/LICENSE
index c433dce..8050100 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,3 +1,7 @@
+Copyright (c) 2012 - 2016 by Genome Research Ltd.
+
+This is free software, licensed under:
+
                     GNU GENERAL PUBLIC LICENSE
                        Version 3, 29 June 2007
 
diff --git a/VERSION b/VERSION
index f90b1af..0bee604 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-2.3.2
+2.3.3
diff --git a/src/alignment-file.c b/src/alignment-file.c
index b1d83d7..01b73b6 100644
--- a/src/alignment-file.c
+++ b/src/alignment-file.c
@@ -184,7 +184,7 @@ void detect_snps(char filename[], int pure_mode, int output_monomorphic)
   }
 
   int current_snp_index = 0;
-  snp_locations = calloc(number_of_snps, sizeof(int));
+  snp_locations = calloc(number_of_snps +1, sizeof(int));
   for(i = 0; i < length_of_genome; i++)
   {
       if(first_sequence[i] == '>' || (output_monomorphic && first_sequence[i] != '#'))
diff --git a/src/snp-sites.c b/src/snp-sites.c
index 8ce28aa..0f56224 100644
--- a/src/snp-sites.c
+++ b/src/snp-sites.c
@@ -27,6 +27,8 @@
 #include "phylib-of-snp-sites.h"
 #include "fasta-of-snp-sites.h"
 
+char ** bases_for_snps;
+
 static int generate_snp_sites_generic(char filename[],
                                       int output_multi_fasta_file,
                                       int output_vcf_file,
@@ -37,20 +39,20 @@ static int generate_snp_sites_generic(char filename[],
 	int i;
 	detect_snps(filename, pure_mode, output_monomorphic);
 
-	char* bases_for_snps[get_number_of_snps()];
-	
+  bases_for_snps =  calloc(get_number_of_snps()+1, sizeof(char*));
+  
 	for(i = 0; i < get_number_of_snps(); i++)
 	{
-		bases_for_snps[i] = calloc(get_number_of_samples()+1 ,sizeof(char));
+		bases_for_snps[i] = calloc(get_number_of_samples()+1, sizeof(char));
 	}
-	
+  
 	get_bases_for_each_snp(filename, bases_for_snps);
-	
+  
 	char output_filename_base[FILENAME_MAX];
 	char filename_without_directory[FILENAME_MAX];
 	strip_directory_from_filename(filename, filename_without_directory);
 	strncpy(output_filename_base, filename_without_directory, FILENAME_MAX);
-	
+  
 	if(output_filename != NULL && *output_filename != '\0')
 	{
 		strncpy(output_filename_base, output_filename, FILENAME_MAX);

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