Prepare for release v1.3.2 (#58)

bcgsc · Jul 6, 2022 · 01e6899 · 01e6899
1 parent d2897ae
commit 01e6899
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Showing 10 changed files with 17 additions and 14 deletions.
diff --git a/README.md b/README.md
@@ -106,7 +106,7 @@ See the wiki page for more details.
 
  Installing from source code:
  ```
-curl -L --output ntLink-1.3.1.tar.gz https://github.com/bcgsc/ntLink/releases/download/v1.3.1/ntLink-1.3.1.tar.gz && tar xvzf ntLink-1.3.1.tar.gz 
+curl -L --output ntLink-1.3.2.tar.gz https://github.com/bcgsc/ntLink/releases/download/v1.3.2/ntLink-1.3.2.tar.gz && tar xvzf ntLink-1.3.2.tar.gz 
 ```
 
 #### Testing your installation

diff --git a/bin/ntlink_filter_sequences.py b/bin/ntlink_filter_sequences.py
@@ -27,7 +27,7 @@ def main():
     parser.add_argument("-k", help="K-mer size (bp)", required=True, type=int)
     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("-v", "--version", action='version', version='ntLink v1.3.1')
+    parser.add_argument("-v", "--version", action='version', version='ntLink v1.3.2')
 
     args = parser.parse_args()
 

diff --git a/bin/ntlink_liftover_mappings.py b/bin/ntlink_liftover_mappings.py
@@ -143,7 +143,7 @@ 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 v1.3.1')
+    parser.add_argument("-v", "--version", action='version', version='ntLink v1.3.2')
     args = parser.parse_args()
 
     # Read in the AGP file

diff --git a/bin/ntlink_overlap_sequences.py b/bin/ntlink_overlap_sequences.py
@@ -482,7 +482,7 @@ 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 v1.3.1')
+    parser.add_argument("--version", action='version', version='ntLink v1.3.2')
 
     return parser.parse_args()
 

diff --git a/bin/ntlink_pair.py b/bin/ntlink_pair.py
@@ -494,7 +494,7 @@ def parse_arguments():
                                        "Set to 0 to allow mapping block to be up to read length",
                             type=float, default=0)
         parser.add_argument("-c", "--checkpoint", help="Mappings checkpoint file", required=False)
-        parser.add_argument("-v", "--version", action='version', version='ntLink v1.3.1')
+        parser.add_argument("-v", "--version", action='version', version='ntLink v1.3.2')
         parser.add_argument("--verbose", help="Verbose output logging", action='store_true')
 
         return parser.parse_args()

diff --git a/bin/ntlink_patch_gaps.py b/bin/ntlink_patch_gaps.py
@@ -773,7 +773,7 @@ def main() -> None:
     parser.add_argument("--soft_mask", help="If specified, will soft mask the filled gap", 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 v1.3.1')
+    parser.add_argument("-v", "--version", action='version', version='ntLink v1.3.2')
     args = parser.parse_args()
 
     print_parameters(args)

diff --git a/bin/ntlink_stitch_paths.py b/bin/ntlink_stitch_paths.py
@@ -469,7 +469,7 @@ 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 v1.3.1')
+        parser.add_argument("-v", "--version", action='version', version='ntLink v1.3.2')
 
         return parser.parse_args()
 

diff --git a/ntLink b/ntLink
@@ -2,7 +2,7 @@
 
 # ntLink: Scaffold assemblies using long reads and minimizers
 # Written by Lauren Coombe @lcoombe
-# ntLink v1.3.1
+# ntLink v1.3.2
 
 # Input files
 target=None
@@ -95,7 +95,7 @@ endif
 help:
 	@echo ""
 	@echo "ntLink: Scaffolding assemblies using long reads"
-	@echo "ntLink v1.3.1"
+	@echo "ntLink v1.3.2"
 	@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):"
@@ -161,7 +161,7 @@ ifneq ($(shell command -v 'python3 -c "import btllib"'),)
 endif
 
 version:
-	@echo "ntLink v1.3.1"
+	@echo "ntLink v1.3.2"
 	@echo "Written by Lauren Coombe ([email protected])"
 
 

diff --git a/ntLink_rounds b/ntLink_rounds
@@ -2,7 +2,7 @@
 
 # ntLink: Scaffold assemblies using long reads and minimizers - launching ntLink rounds
 # Written by Lauren Coombe @lcoombe
-# ntLink v1.3.1
+# ntLink v1.3.2
 
 # Window size
 w=100
@@ -47,7 +47,7 @@ PYTHONPATH=$(ntlink_path)/src/btllib/install/lib/btllib/python
 help:
 	@echo ""
 	@echo "ntLink: Scaffolding assemblies using long reads - running iterative rounds of ntLink"
-	@echo "ntLink v1.3.1"
+	@echo "ntLink v1.3.2"
 	@echo "Running rounds of ntLink - no gap-filling"
 	@echo "Usage: ntLink run_rounds target=<target scaffolds> reads='List of long read files' rounds=<Number>"
 	@echo ""

diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="ntLink",
-    version="1.3.1",
+    version="1.3.2",
     author="Lauren Coombe",
     author_email="[email protected]",
     description="Genome assembly scaffolder using long reads",
@@ -15,7 +15,10 @@
     license="GPLv3",
     python_requires=">=3",
     install_requires=["python-igraph", "numpy"],
-    scripts = ["bin/ntlink_pair.py", "bin/read_fasta.py", "bin/ntlink_utils.py"],
+    scripts = ["bin/ntlink_pair.py", "bin/read_fasta.py", "bin/ntlink_utils.py",
+               "bin/ntlink_filter_sequences.py", "bin/ntlink_liftover_mappings.py",
+               "bin/ntlink_overlap_sequences.py", "bin/ntlink_patch_gaps.py",
+               "bin/ntlink_stitch_paths.py", "bin/ntjoin_utils.py"],
     classifiers=[
         "Programming Language :: Python :: 3",
         "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",