Merge branch 'master' of https://github.com/medvedevgroup/BubbZ

BubbZ/blocksfinder.cpp

@@ -43,7 +43,7 @@ namespace Sibelia
 	}
 
 	JunctionStorage * JunctionStorage::this_;
-	extern const std::string VERSION = "1.1.0";
+	extern const std::string VERSION = "1.1.1";
 
 	int64_t BlockInstance::GetSignedBlockId() const
 	{

BubbZ/bubbz

@@ -70,7 +70,7 @@ min() {
    [ "$1" -lt "$2" ] && echo $1 || echo $2
 }
 
-infile=$1
+infile="$@"
 twopaco_threads=$( min $threads 16 )
 dbg_file=$outdir/de_bruijn_graph.dbg
 

BubbZ/bubbz.cpp

@@ -119,7 +119,7 @@ int main(int argc, char * argv[])
 			threads.getValue(),
 			abundanceThreshold.getValue(),
 			0);
-		
+
 		std::cout << "Analyzing the graph..." << std::endl;
 		Sibelia::BlocksFinder finder(storage, kvalue.getValue());
 		finder.FindBlocks(minBlockSize.getValue(),

LICENSE.txt

@@ -1,3 +1,6 @@
+Copyright (c) 2020 I. Minkin and P. Medvedev.
+All rights reserved.
+
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions
 are met:

NEWS.md

@@ -1,3 +1,7 @@
+BubbZ 1.1.1
+===========
+* Bug fixes
+
 BubbZ 1.1.0
 ==============
 * Replaced the heuristic algorithm with the exact version

README.md

@@ -1,7 +1,7 @@
-BubbZ 1.1.0
+BubbZ 1.1.1
 ===============
 
-Release date: 12th April 2020
+Release date: 8th August 2020
 =================
 
 Authors
@@ -175,9 +175,9 @@ Citation
 ========
 If you use SibeliaZ in your research, please cite:
 
-	Scalable pairwise whole-genome homology mapping of largegenomes with BubbZ
+	Scalable pairwise whole-genome homology mapping of large genomes with BubbZ
 	Ilia Minkin, Paul Medvedev
-	Under review
+	iScience, 2020: https://doi.org/10.1016/j.isci.2020.101224
 
 License
 =======
@@ -190,4 +190,5 @@ E-mail your feedback at [email protected].
 Datasets used of analyses in the paper
 ======================================
 Mice and simulated genomes: https://github.com/medvedevgroup/SibeliaZ/blob/master/DATA.txt
-Salmonella RefSeq genomes accession numbers: https://github.com/medvedevgroup/SibeliaZ/blob/master/DATA.txt
+
+Salmonella RefSeq genomes accession numbers: https://github.com/medvedevgroup/BubbZ/blob/master/salmonella_refseq.txt