Skip to content

Commit

Permalink
Prepare for release v1.3.4 (#63)
Browse files Browse the repository at this point in the history
  • Loading branch information
lcoombe authored Jul 27, 2022
1 parent ab04a55 commit 7fa0077
Show file tree
Hide file tree
Showing 10 changed files with 13 additions and 13 deletions.
2 changes: 1 addition & 1 deletion README.md
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
2 changes: 1 addition & 1 deletion bin/ntlink_filter_sequences.py
Original file line number Diff line number Diff line change
Expand Up @@ -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()

Expand Down
2 changes: 1 addition & 1 deletion bin/ntlink_liftover_mappings.py
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
2 changes: 1 addition & 1 deletion bin/ntlink_overlap_sequences.py
Original file line number Diff line number Diff line change
Expand Up @@ -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()

Expand Down
2 changes: 1 addition & 1 deletion bin/ntlink_pair.py
Original file line number Diff line number Diff line change
Expand Up @@ -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()
Expand Down
2 changes: 1 addition & 1 deletion bin/ntlink_patch_gaps.py
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down
2 changes: 1 addition & 1 deletion bin/ntlink_stitch_paths.py
Original file line number Diff line number Diff line change
Expand Up @@ -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()

Expand Down
6 changes: 3 additions & 3 deletions ntLink
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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=<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 @@ -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 ([email protected])"


Expand Down
4 changes: 2 additions & 2 deletions ntLink_rounds
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

# ntLink: Scaffold assemblies using long reads and minimizers - launching ntLink rounds
# Written by Lauren Coombe @lcoombe
# ntLink v1.3.3
# ntLink v1.3.4

# Window size
w=100
Expand Down Expand Up @@ -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=<target scaffolds> reads='List of long read files' rounds=<Number>"
@echo ""
Expand Down
2 changes: 1 addition & 1 deletion setup.py
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@

setuptools.setup(
name="ntLink",
version="1.3.3",
version="1.3.4",
author="Lauren Coombe",
author_email="[email protected]",
description="Genome assembly scaffolder using long reads",
Expand Down

0 comments on commit 7fa0077

Please sign in to comment.