Prepare for release v1.1.0 (#89)

README.md

@@ -118,6 +118,9 @@ ntJoin assemble target=my_scaffolds.fa target_weight=1 reference_config=config_f
 * We recommend setting the reference weight(s) to be higher than the target weight
 * If you are using a reference-grade assembly as the reference, set `n=2`, otherwise use the default `n=1`
 
+### Overlap feature
+* As of version 1.1.0, ntJoin can detect and trim overlaps between joined sequences. This feature is controlled by the `overlap` parameter, and is on `overlap=True` by default. To turn this behaviour off, specify `overlap=False`
+
 ## Installation Instructions
 #### Installing ntJoin using Brew
 ntJoin can be installed using [Homebrew](https://brew.sh) on macOS or [Linuxbrew](http://linuxbrew.sh) on Linux:

bin/ntjoin_assemble.py

@@ -983,7 +983,7 @@ def parse_arguments():
                                        "increasing/decreasing to assign contig orientation [90]\n "
                                        "Note: Only used with --mkt is NOT specified", default=90, type=int)
         parser.add_argument('-t', help="Number of threads for multiprocessing [1]", default=1, type=int)
-        parser.add_argument("-v", "--version", action='version', version='ntJoin v1.0.8')
+        parser.add_argument("-v", "--version", action='version', version='ntJoin v1.1.0')
         parser.add_argument("--agp", help="Output AGP file describing scaffolds", action="store_true")
         parser.add_argument("--no_cut", help="Do not cut input contigs, place in most representative path",
                             action="store_true")
@@ -1030,7 +1030,7 @@ def print_parameters(self):
 
     def main(self):
         "Run ntJoin graph stage"
-        print("Running ntJoin v1.0.8 ...\n")
+        print("Running ntJoin v1.1.0 ...\n")
         self.print_parameters()
 
         # Parse the weights of each input reference assembly

ntJoin

@@ -2,7 +2,7 @@
 
 # ntJoin: Scaffold assemblies using reference assemblies and minimizer graphs
 # Written by Lauren Coombe @lcoombe
-# ntJoin v1.0.8
+# ntJoin v1.1.0
 
 # Input files
 target=None
@@ -118,7 +118,7 @@ PYTHONPATH=$(assemble_path)/src/btllib/install/lib/btllib/python
 help:
 	@echo ""
 	@echo "ntJoin: Scaffolding assemblies using reference assemblies and minimizer graphs"
-	@echo "ntJoin v1.0.8"
+	@echo "ntJoin v1.1.0"
 	@echo "Usage: ntJoin assemble target=<target scaffolds> references='List of reference assemblies' reference_weights='List of weights per reference assembly'"
 	@echo ""
 	@echo "Options:"
@@ -186,7 +186,7 @@ ifeq ($(ref), None)
 endif
 
 version:
-	@echo "ntJoin v1.0.8"
+	@echo "ntJoin v1.1.0"
 	@echo "Written by Lauren Coombe (lcoombe@bcgsc.ca)"
 
 .PHONY: help all version analysis assemble check_params jupiter

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="ntJoin",
-    version="1.0.8",
+    version="1.1.0",
     author="Lauren Coombe",
     author_email="lcoombe@bcgsc.ca",
     description="Genome assembly scaffolder using minimizer graphs",