v1.2.3 release (#55)

* Tigmint v1.2.3

* Preparing for v1.2.3 release

* azure-pipelines.yml: Update environment

* Expected outputs: update molecule BED file (ubuntu-latest sort)

Author: lcoombe

azure-pipelines.yml

@@ -2,9 +2,9 @@
 
 jobs:
 - job:
-  displayName: ubuntu-16.04
+  displayName: ubuntu-latest
   pool:
-    vmImage: 'ubuntu-16.04'
+    vmImage: 'ubuntu-latest'
 
   steps:
   - script: echo "##vso[task.prependpath]$CONDA/bin"
@@ -16,9 +16,7 @@ jobs:
       curl https://apt.llvm.org/llvm-snapshot.gpg.key | sudo apt-key add -
       sudo apt-add-repository "deb http://apt.llvm.org/xenial/ llvm-toolchain-xenial-11 main"
       sudo apt-get update
-      sudo apt-get install -y --no-install-recommends clang-format-11 clang-tidy-11
-      sudo ln -sf clang-format-11 /usr/bin/clang-format
-      sudo ln -sf clang-tidy-11 /usr/bin/clang-tidy
+      sudo apt-get install -y --no-install-recommends clang-format clang-tidy
     displayName: Install clang-format and clang-tidy
   - script: make -C src all
     displayName: Compile C++ executables

bin/tigmint-cut

@@ -242,7 +242,7 @@ 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 1.2.2")
+    parser.add_argument("--version", action="version", version="tigmint-cut 1.2.3")
     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-make

@@ -123,7 +123,7 @@ help:
 	@echo 'For more information see https://bcgsc.github.io/tigmint/'
 
 version:
-	@echo "Tigmint 1.2.2"
+	@echo "Tigmint 1.2.3"
 	@echo "Written by Shaun Jackman @sjackman."
 
 all: tigmint arcs

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 1.2.2")
+                        version="tigmint_estimate_dist.py 1.2.3")
 
     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 1.2.2')
+            '--version', action='version', version='tigmint-molecule 1.2.3')
         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 1.2.2')
+        parser.add_argument('--version', action='version', version='tigmint_molecule_paf.py 1.2.3')
         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="1.2.2",
+    version="1.2.3",
     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 = "v1.0";
+const static std::string VERSION = "v1.2.3";
 const static size_t MAX_THREADS = 6;
 
 static void

tests/test_installation/expected_outputs/test_contig_long.test_longreads.cut500.molecule.size2000.bed

@@ -24,8 +24,8 @@ test_misassembly	2447	6369	18	8
 test_misassembly	2447	6499	41	9
 test_misassembly	2447	6542	100	9
 test_misassembly	2447	6551	101	9
-test_misassembly	2447	6551	72	9
 test_misassembly	2447	6551	7	9
+test_misassembly	2447	6551	72	9
 test_misassembly	2451	6527	87	9
 test_misassembly	2455	5626	14	7
 test_misassembly	2455	6523	73	9