Prepare for release v1.2.9 (#114)

* Prepare for release v1.2.9

* bump version for long-to-linked-pe.cpp

* Remove tigmint-make-liftover

Author: lcoombe

README.md

@@ -54,7 +54,7 @@ make -C src
 ```
 or
 ```
-curl -L https://github.com/bcgsc/tigmint/releases/download/v1.2.8/tigmint-1.2.8.tar.gz | tar xz && cd tigmint-1.2.8
+curl -L https://github.com/bcgsc/tigmint/releases/download/v1.2.9/tigmint-1.2.9.tar.gz | tar xz && cd tigmint-1.2.9
 make -C src
 ```
 

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 1.2.8")
+    parser.add_argument("--version", action="version", version="tigmint-cut 1.2.9")
     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)

bin/tigmint-filter-paf

@@ -21,7 +21,7 @@ def main() -> None:
                                                  "output molecule extents BED")
     parser.add_argument("PAF", help="Input PAF file")
     parser.add_argument("-m", help="Minimum size of output extents (bp)", default=2000, type=int)
-    parser.add_argument('--version', action='version', version='tigmint-filter-paf 1.2.8')
+    parser.add_argument('--version', action='version', version='tigmint-filter-paf 1.2.9')
 
     args = parser.parse_args()
 

bin/tigmint-make

@@ -154,7 +154,7 @@ help:
 	@echo 'For more information see https://bcgsc.github.io/tigmint/'
 
 version:
-	@echo "Tigmint 1.2.8"
+	@echo "Tigmint 1.2.9"
 	@echo "Written by Shaun Jackman @sjackman."
 
 all: tigmint arcs

bin/tigmint-ntlink-map

@@ -49,7 +49,7 @@ def main():
                                        "if not in PATH", type=str)
     parser.add_argument("-m", help="Minimum size for mapping block (bp) [2000]", default=2000, type=int)
     parser.add_argument("--span", help="Span value specified for tigmint-cut", required=True)
-    parser.add_argument('--version', action='version', version='tigmint-ntlink-map 1.2.8')
+    parser.add_argument('--version', action='version', version='tigmint-ntlink-map 1.2.9')
 
     args = parser.parse_args()
 

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 1.2.8")
+                        version="tigmint_estimate_dist.py 1.2.9")
 
     args = parser.parse_args()
 

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 1.2.8')
+            '--version', action='version', version='tigmint-molecule 1.2.9')
         parser.add_argument(
             metavar="BAM", dest="in_bam_filename",
             help="Input BAM file sorted by BX tag then position, - for stdin")

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 1.2.8')
+        parser.add_argument('--version', action='version', version='tigmint_molecule_paf.py 1.2.9')
         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]",

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="tigmint",
-    version="1.2.8",
+    version="1.2.9",
     author="Shaun Jackman",
     author_email="[email protected]",
     description="Correct misassemblies using linked or long reads",

src/long-to-linked-pe.cpp

@@ -21,7 +21,7 @@
 #include <vector>
 
 const static std::string PROGNAME = "long-to-linked-pe";
-const static std::string VERSION = "v1.2.8";
+const static std::string VERSION = "v1.2.9";
 const static size_t MAX_THREADS = 6;
 
 static void