From 028b0d77023adacf6ab0a57684b29b952ea7cd30 Mon Sep 17 00:00:00 2001 From: PuneetSS <55728708+PuneetSS@users.noreply.github.com> Date: Tue, 9 Nov 2021 15:33:35 -0800 Subject: [PATCH] Preparing for v1.2.5 release (#71) Co-authored-by: Puneet Sidhu --- bin/tigmint-cut | 2 +- bin/tigmint-make | 2 +- bin/tigmint_estimate_dist.py | 2 +- bin/tigmint_molecule.py | 2 +- bin/tigmint_molecule_paf.py | 2 +- setup.py | 2 +- src/long-to-linked-pe.cpp | 2 +- 7 files changed, 7 insertions(+), 7 deletions(-) diff --git a/bin/tigmint-cut b/bin/tigmint-cut index 8eb06b8..21c634f 100755 --- a/bin/tigmint-cut +++ b/bin/tigmint-cut @@ -258,7 +258,7 @@ def get_span(filename): def main(): parser = argparse.ArgumentParser(description="Find misassembled regions in assembly using Chromium molecule extents") - parser.add_argument("--version", action="version", version="tigmint-cut 1.2.4") + parser.add_argument("--version", action="version", version="tigmint-cut 1.2.5") parser.add_argument("fasta", type=str, help="Reference genome fasta file (must have FAI index generated)") parser.add_argument("bed", type=str, help="Sorted bed file of molecule extents") parser.add_argument("-o", "--fastaout", type=str, help="The output FASTA file.", required=True) diff --git a/bin/tigmint-make b/bin/tigmint-make index 788a78f..ec99d4e 100755 --- a/bin/tigmint-make +++ b/bin/tigmint-make @@ -126,7 +126,7 @@ help: @echo 'For more information see https://bcgsc.github.io/tigmint/' version: - @echo "Tigmint 1.2.4" + @echo "Tigmint 1.2.5" @echo "Written by Shaun Jackman @sjackman." all: tigmint arcs diff --git a/bin/tigmint_estimate_dist.py b/bin/tigmint_estimate_dist.py index 80625dc..dbda7cc 100755 --- a/bin/tigmint_estimate_dist.py +++ b/bin/tigmint_estimate_dist.py @@ -44,7 +44,7 @@ def main(): required=False) parser.add_argument("-v", "--version", action="version", - version="tigmint_estimate_dist.py 1.2.4") + version="tigmint_estimate_dist.py 1.2.5") args = parser.parse_args() diff --git a/bin/tigmint_molecule.py b/bin/tigmint_molecule.py index 75acde7..7f982f7 100755 --- a/bin/tigmint_molecule.py +++ b/bin/tigmint_molecule.py @@ -243,7 +243,7 @@ def parse_arguments(self): "Read a SAM/BAM file and output a TSV file. " "The SAM/BAM file must be sorted by BX tag and then by position.") parser.add_argument( - '--version', action='version', version='tigmint-molecule 1.2.4') + '--version', action='version', version='tigmint-molecule 1.2.5') parser.add_argument( metavar="BAM", dest="in_bam_filename", help="Input BAM file sorted by BX tag then position, - for stdin") diff --git a/bin/tigmint_molecule_paf.py b/bin/tigmint_molecule_paf.py index ccb7276..b29ce86 100755 --- a/bin/tigmint_molecule_paf.py +++ b/bin/tigmint_molecule_paf.py @@ -102,7 +102,7 @@ def parse_arguments(self): parser = argparse.ArgumentParser( description="Group linked reads simulated from long reads into molecules. " "Read a PAF file and output a BED file.") - parser.add_argument('--version', action='version', version='tigmint_molecule_paf.py 1.2.4') + parser.add_argument('--version', action='version', version='tigmint_molecule_paf.py 1.2.5') parser.add_argument(metavar="PAF", dest="PAF", help="Input PAF file, - for stdin") parser.add_argument("-o", "--output", dest="out_molecules_filename", help="Output molecule BED file [stdout]", diff --git a/setup.py b/setup.py index b802924..ad75573 100644 --- a/setup.py +++ b/setup.py @@ -5,7 +5,7 @@ setuptools.setup( name="tigmint", - version="1.2.4", + version="1.2.5", author="Shaun Jackman", author_email="sjackman@gmail.com", description="Correct misassemblies using linked or long reads", diff --git a/src/long-to-linked-pe.cpp b/src/long-to-linked-pe.cpp index 7d9e55f..4ef9858 100644 --- a/src/long-to-linked-pe.cpp +++ b/src/long-to-linked-pe.cpp @@ -21,7 +21,7 @@ #include const static std::string PROGNAME = "long-to-linked-pe"; -const static std::string VERSION = "v1.2.4"; +const static std::string VERSION = "v1.2.5"; const static size_t MAX_THREADS = 6; static void