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Prepare for release v1.3.11 (#104)
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lcoombe authored Oct 11, 2024
1 parent 6497852 commit 4b032cb
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion bin/ntlink_filter_sequences.py
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Expand Up @@ -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()

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2 changes: 1 addition & 1 deletion bin/ntlink_liftover_mappings.py
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion bin/ntlink_overlap_sequences.py
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Expand Up @@ -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()

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2 changes: 1 addition & 1 deletion bin/ntlink_pair.py
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Expand Up @@ -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()
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2 changes: 1 addition & 1 deletion bin/ntlink_patch_gaps.py
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Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion bin/ntlink_stitch_paths.py
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Expand Up @@ -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()

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6 changes: 3 additions & 3 deletions ntLink
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Expand Up @@ -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
Expand Down Expand Up @@ -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):"
Expand Down Expand Up @@ -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 ([email protected])"


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4 changes: 2 additions & 2 deletions ntLink_rounds
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Expand Up @@ -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
Expand Down Expand Up @@ -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 ""
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2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -5,7 +5,7 @@

setuptools.setup(
name="ntLink",
version="1.3.10",
version="1.3.11",
author="Lauren Coombe",
author_email="[email protected]",
description="Genome assembly scaffolder using long reads",
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