From 4b032cbb24ea7f7104f77156337706161b74de36 Mon Sep 17 00:00:00 2001 From: Lauren Coombe Date: Fri, 11 Oct 2024 16:14:16 -0700 Subject: [PATCH] Prepare for release v1.3.11 (#104) --- README.md | 2 +- bin/ntlink_filter_sequences.py | 2 +- bin/ntlink_liftover_mappings.py | 2 +- bin/ntlink_overlap_sequences.py | 2 +- bin/ntlink_pair.py | 2 +- bin/ntlink_patch_gaps.py | 2 +- bin/ntlink_stitch_paths.py | 2 +- ntLink | 6 +++--- ntLink_rounds | 4 ++-- setup.py | 2 +- 10 files changed, 13 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index d5e0650..cf78138 100644 --- a/README.md +++ b/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 diff --git a/bin/ntlink_filter_sequences.py b/bin/ntlink_filter_sequences.py index aa7a634..e4570ca 100755 --- a/bin/ntlink_filter_sequences.py +++ b/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() diff --git a/bin/ntlink_liftover_mappings.py b/bin/ntlink_liftover_mappings.py index 074bed2..6df924f 100755 --- a/bin/ntlink_liftover_mappings.py +++ b/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 diff --git a/bin/ntlink_overlap_sequences.py b/bin/ntlink_overlap_sequences.py index 87668e0..158a5b4 100755 --- a/bin/ntlink_overlap_sequences.py +++ b/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() diff --git a/bin/ntlink_pair.py b/bin/ntlink_pair.py index df0a0b0..a53c877 100755 --- a/bin/ntlink_pair.py +++ b/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() diff --git a/bin/ntlink_patch_gaps.py b/bin/ntlink_patch_gaps.py index 142b2bf..a867e29 100755 --- a/bin/ntlink_patch_gaps.py +++ b/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) diff --git a/bin/ntlink_stitch_paths.py b/bin/ntlink_stitch_paths.py index 1c9b18a..f72b911 100755 --- a/bin/ntlink_stitch_paths.py +++ b/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() diff --git a/ntLink b/ntLink index 79d2128..ea8bbf9 100755 --- a/ntLink +++ b/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= 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)" diff --git a/ntLink_rounds b/ntLink_rounds index 31486c7..ca1b15c 100755 --- 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 v1.3.10 +# 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= reads='List of long read files' rounds=" @echo "" diff --git a/setup.py b/setup.py index a84bb94..4db3f42 100644 --- a/setup.py +++ b/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",