Prepare for release v1.3.11 (#104)

Author: lcoombe

README.md

@@ -117,7 +117,7 @@ To only run the pairing stage of `ntLink` (the stage where the long reads are ma
 
  Installing from source code:
  ```
-curl -L --output ntLink-1.3.10.tar.gz https://github.com/bcgsc/ntLink/releases/download/v1.3.10/ntLink-1.3.10.tar.gz && tar xvzf ntLink-1.3.10.tar.gz 
+curl -L --output ntLink-1.3.11.tar.gz https://github.com/bcgsc/ntLink/releases/download/v1.3.11/ntLink-1.3.11.tar.gz && tar xvzf ntLink-1.3.11.tar.gz 
 ```
 
 #### Testing your installation

bin/ntlink_filter_sequences.py

@@ -51,7 +51,7 @@ def main():
     parser.add_argument("-f", help="Fudge factor for estimated overlap [0.5]", type=float, default=0.5)
     parser.add_argument("-g", help="Minimum gap size (bp) [20]", required=False, type=int, default=20)
     parser.add_argument("-t", help="Number of threads", default=8, type=int)
-    parser.add_argument("-v", "--version", action='version', version='ntLink v1.3.10')
+    parser.add_argument("-v", "--version", action='version', version='ntLink v1.3.11')
 
     args = parser.parse_args()
 

bin/ntlink_liftover_mappings.py

@@ -147,7 +147,7 @@ def main() -> None:
     parser.add_argument("-a", "--agp", help="Path to the AGP file", required=True)
     parser.add_argument("-o", "--output", help="Output file name", required=True)
     parser.add_argument("-k", "--kmer", help="Kmer size", required=True, type=int)
-    parser.add_argument("-v", "--version", action='version', version='ntLink v1.3.10')
+    parser.add_argument("-v", "--version", action='version', version='ntLink v1.3.11')
     args = parser.parse_args()
 
     # Read in the AGP file

bin/ntlink_overlap_sequences.py

@@ -563,7 +563,7 @@ def parse_arguments():
     parser.add_argument("-p", help="Output file prefix [ntlink_merge]", default="ntlink_merge", type=str)
     parser.add_argument("-v", help="Verbose output logging", action="store_true")
     parser.add_argument("--trim_info", help="Verbose log of trimming info", action="store_true")
-    parser.add_argument("--version", action='version', version='ntLink v1.3.10')
+    parser.add_argument("--version", action='version', version='ntLink v1.3.11')
 
     return parser.parse_args()
 

bin/ntlink_pair.py

@@ -530,7 +530,7 @@ def parse_arguments():
         parser.add_argument("--sensitive", help="Run more sensitive read mapping", action="store_true")
         parser.add_argument("--repeat-filter", help="Remove repetitive minimizers within a long read's sketch",
                             action="store_true")
-        parser.add_argument("-v", "--version", action='version', version='ntLink v1.3.10')
+        parser.add_argument("-v", "--version", action='version', version='ntLink v1.3.11')
         parser.add_argument("--verbose", help="Verbose output logging", action='store_true')
 
         return parser.parse_args()

bin/ntlink_patch_gaps.py

@@ -780,7 +780,7 @@ def main() -> None:
     parser.add_argument("--sensitive", help="Run more sensitive read mapping", action="store_true")
     parser.add_argument("--verbose", help="Verbose logging - print out trimmed scaffolds without gaps",
                         action="store_true")
-    parser.add_argument("-v", "--version", action='version', version='ntLink v1.3.10')
+    parser.add_argument("-v", "--version", action='version', version='ntLink v1.3.11')
     args = parser.parse_args()
 
     print_parameters(args)

bin/ntlink_stitch_paths.py

@@ -472,7 +472,7 @@ def parse_arguments():
         parser.add_argument("--transitive", help="Require transitive support for edges?", action="store_true")
         parser.add_argument("--conservative", help="Conservative mode - take optimal N50 paths, no stitching",
                             action="store_true")
-        parser.add_argument("-v", "--version", action='version', version='ntLink v1.3.10')
+        parser.add_argument("-v", "--version", action='version', version='ntLink v1.3.11')
 
         return parser.parse_args()
 

ntLink

@@ -2,7 +2,7 @@
 
 # ntLink: Scaffold assemblies using long reads and minimizers
 # Written by Lauren Coombe @lcoombe
-# ntLink v1.3.10
+# ntLink v1.3.11
 
 # Input files
 target=None
@@ -119,7 +119,7 @@ endif
 help:
 	@echo ""
 	@echo "ntLink: Scaffolding assemblies using long reads"
-	@echo "ntLink v1.3.10"
+	@echo "ntLink v1.3.11"
 	@echo "Usage: ntLink scaffold target=<target scaffolds> reads='List of long read files'"
 	@echo ""
 	@echo "To additionally run gap-filling (fill gap regions with raw read sequence):"
@@ -187,7 +187,7 @@ ifneq ($(shell command -v 'python3 -c "import btllib"'),)
 endif
 
 version:
-	@echo "ntLink v1.3.10"
+	@echo "ntLink v1.3.11"
 	@echo "Written by Lauren Coombe (lcoombe@bcgsc.ca)"
 
 

ntLink_rounds

@@ -2,7 +2,7 @@
 
 # ntLink: Scaffold assemblies using long reads and minimizers - launching ntLink rounds
 # Written by Lauren Coombe @lcoombe
-# ntLink v1.3.10
+# ntLink v1.3.11
 
 # Window size
 w=100
@@ -55,7 +55,7 @@ endif
 help:
 	@echo ""
 	@echo "ntLink: Scaffolding assemblies using long reads - running iterative rounds of ntLink"
-	@echo "ntLink v1.3.10"
+	@echo "ntLink v1.3.11"
 	@echo "Running rounds of ntLink - no gap-filling"
 	@echo "Usage: ntLink_rounds run_rounds target=<target scaffolds> reads='List of long read files' rounds=<Number>"
 	@echo ""

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="ntLink",
-    version="1.3.10",
+    version="1.3.11",
     author="Lauren Coombe",
     author_email="lcoombe@bcgsc.ca",
     description="Genome assembly scaffolder using long reads",