From 7fa007756f8286ba9a5545f610bc2e25547eee4f Mon Sep 17 00:00:00 2001 From: Lauren Coombe Date: Wed, 27 Jul 2022 15:14:43 -0700 Subject: [PATCH] Prepare for release v1.3.4 (#63) --- 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 b39d6f8..26a252f 100644 --- 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-1.3.3.tar.gz https://github.com/bcgsc/ntLink/releases/download/v1.3.3/ntLink-1.3.3.tar.gz && tar xvzf ntLink-1.3.3.tar.gz +curl -L --output ntLink-1.3.4.tar.gz https://github.com/bcgsc/ntLink/releases/download/v1.3.4/ntLink-1.3.4.tar.gz && tar xvzf ntLink-1.3.4.tar.gz ``` #### Testing your installation diff --git a/bin/ntlink_filter_sequences.py b/bin/ntlink_filter_sequences.py index 358fbb0..53af8ec 100755 --- 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 v1.3.3') + parser.add_argument("-v", "--version", action='version', version='ntLink v1.3.4') args = parser.parse_args() diff --git a/bin/ntlink_liftover_mappings.py b/bin/ntlink_liftover_mappings.py index 25d896d..84f3dcf 100755 --- 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 v1.3.3') + parser.add_argument("-v", "--version", action='version', version='ntLink v1.3.4') args = parser.parse_args() # Read in the AGP file diff --git a/bin/ntlink_overlap_sequences.py b/bin/ntlink_overlap_sequences.py index 3739512..7f25ef4 100755 --- 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 v1.3.3') + parser.add_argument("--version", action='version', version='ntLink v1.3.4') return parser.parse_args() diff --git a/bin/ntlink_pair.py b/bin/ntlink_pair.py index 28ca5e4..b3df388 100755 --- a/bin/ntlink_pair.py +++ b/bin/ntlink_pair.py @@ -495,7 +495,7 @@ def parse_arguments(): type=float, default=0) parser.add_argument("-c", "--checkpoint", help="Mappings checkpoint file", required=False) parser.add_argument("--pairs", help="Output pairs TSV file", action="store_true") - parser.add_argument("-v", "--version", action='version', version='ntLink v1.3.3') + parser.add_argument("-v", "--version", action='version', version='ntLink v1.3.4') 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 caa29d3..e4706d7 100755 --- 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 v1.3.3') + parser.add_argument("-v", "--version", action='version', version='ntLink v1.3.4') args = parser.parse_args() print_parameters(args) diff --git a/bin/ntlink_stitch_paths.py b/bin/ntlink_stitch_paths.py index 7f49ef3..00c71eb 100755 --- 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 v1.3.3') + parser.add_argument("-v", "--version", action='version', version='ntLink v1.3.4') return parser.parse_args() diff --git a/ntLink b/ntLink index c34fbdd..3b3cef0 100755 --- a/ntLink +++ b/ntLink @@ -2,7 +2,7 @@ # ntLink: Scaffold assemblies using long reads and minimizers # Written by Lauren Coombe @lcoombe -# ntLink v1.3.3 +# ntLink v1.3.4 # Input files target=None @@ -98,7 +98,7 @@ endif help: @echo "" @echo "ntLink: Scaffolding assemblies using long reads" - @echo "ntLink v1.3.3" + @echo "ntLink v1.3.4" @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):" @@ -164,7 +164,7 @@ ifneq ($(shell command -v 'python3 -c "import btllib"'),) endif version: - @echo "ntLink v1.3.3" + @echo "ntLink v1.3.4" @echo "Written by Lauren Coombe (lcoombe@bcgsc.ca)" diff --git a/ntLink_rounds b/ntLink_rounds index b1bb431..06b0b11 100755 --- a/ntLink_rounds +++ b/ntLink_rounds @@ -2,7 +2,7 @@ # ntLink: Scaffold assemblies using long reads and minimizers - launching ntLink rounds # Written by Lauren Coombe @lcoombe -# ntLink v1.3.3 +# ntLink v1.3.4 # Window size w=100 @@ -44,7 +44,7 @@ ntlink_path=$(shell dirname $(realpath $(MAKEFILE_LIST))) help: @echo "" @echo "ntLink: Scaffolding assemblies using long reads - running iterative rounds of ntLink" - @echo "ntLink v1.3.3" + @echo "ntLink v1.3.4" @echo "Running rounds of ntLink - no gap-filling" @echo "Usage: ntLink run_rounds target= reads='List of long read files' rounds=" @echo "" diff --git a/setup.py b/setup.py index d83000c..58a4bf5 100644 --- a/setup.py +++ b/setup.py @@ -5,7 +5,7 @@ setuptools.setup( name="ntLink", - version="1.3.3", + version="1.3.4", author="Lauren Coombe", author_email="lcoombe@bcgsc.ca", description="Genome assembly scaffolder using long reads",