Corrects CMakeLists.txt for location of pthreads library. Also update…

…s __main__.py, to opt-out of FMindexing rather than opt-in using --not-ref.

Former-commit-id: 9519fa7

CMakeLists.txt

@@ -5,26 +5,34 @@ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fconcepts -march=native")
 
 set(CMAKE_VERBOSE_MAKEFILE ON)
 
-find_package(OpenMP)
-find_library(pthread REQUIRED)
-find_library(z REQUIRED)
-find_library(bifrost REQUIRED)
+# find pthreads
+set(THREADS_PREFER_PTHREAD_FLAG ON)
+find_package(Threads REQUIRED)
 
+# find pybind and create python module
 find_package(pybind11 REQUIRED)
 pybind11_add_module(ggCaller_cpp src/call_ORFs.cpp src/ggCaller_bindings.cpp src/indexing.cpp src/match_string.cpp src/traversal.cpp src/unitigDict.cpp)
 
+# check for conda environment
 IF( DEFINED ENV{CONDA_PREFIX} )
+  # set conda directory
   SET(CONDA_DIR "$ENV{CONDA_PREFIX}")
+  # find Seqan3 packages
   find_path(SEQAN3_CLONE_DIR name bin PATHS ${CONDA_DIR} NO_DEFAULT_PATH)
   find_path(SEQAN3_INCLUDE_DIR name seqan PATHS "${SEQAN3_CLONE_DIR}/include" NO_DEFAULT_PATH)
   find_path(SEQAN3_SUBMODULES_DIR name submodules PATHS "${SEQAN3_INCLUDE_DIR}/seqan3" NO_DEFAULT_PATH)
   find_package(SeqAn3 REQUIRED HINT "${CONDA_PREFIX}/share/cmake/seqan3")
+  # link bifrost, zlib, seqan and pthreads
+  target_link_libraries(ggCaller_cpp PRIVATE seqan3::seqan3 ${CONDA_DIR}/lib/libbifrost.so ${CONDA_DIR}/lib/libz.so ${CONDA_DIR}/lib/libomp.so Threads::Threads)
 ELSE()
+  # find packages if conda not used
   find_package(SeqAn3 REQUIRED)
-ENDIF()
-
-target_link_libraries(ggCaller_cpp PRIVATE seqan3::seqan3 pthread z bifrost)
-
-if(OpenMP_CXX_FOUND)
+  find_library(z REQUIRED)
+  find_library(bifrost REQUIRED)
+  find_package(OpenMP)
+  target_link_libraries(ggCaller_cpp PRIVATE seqan3::seqan3 bifrost z pthread)
+  # link OpenMP if found
+  if(OpenMP_CXX_FOUND)
     target_link_libraries(ggCaller_cpp PRIVATE OpenMP::OpenMP_CXX)
-endif()
+  endif()
+ENDIF()

README.md

@@ -52,8 +52,8 @@ To run ggCaller using an existing Bifrost GFA file and Colours file, specify BOT
 - ```--graph <graph.gfa>``` Input GFA
 - ```--colours <colours.bfg_colors>``` Input colours file
 
-To enable filtering of artificially generated sequences via FMindexing (if sequences used to generate the GFA and Colours files were exclusively assembled genomes), additionally specify:
-- ```--is-ref```
+To disable filtering of artificially generated sequences via FMindexing (if sequences used to generate the GFA and Colours files are not exclusively assembled genomes), additionally specify:
+- ```--not-ref```
 
 Note: Ensure the sequences used to build the graph are in the same directories as when the graph was built.
 
@@ -92,11 +92,11 @@ argument. Bifrost uses kmer coverage filtering for read files to remove read err
 
 - Use existing graph which was built using assembled genomes only.
 
-```ggcaller --graph graph.gfa --colours colours.bfg_colours --is-ref --out calls.fasta```
+```ggcaller --graph graph.gfa --colours colours.bfg_colours --out calls.fasta```
 
 - Use existing graph which was built using reads or assembled genomes and reads.
 
-```ggcaller --graph graph.gfa --colours colours.bfg_colours --out calls.fasta```
+```ggcaller --graph graph.gfa --colours colours.bfg_colours --not-ref --out calls.fasta```
 
 Test data is available in the ```data``` directory.
 

ggCaller/__init__.py

@@ -2,4 +2,4 @@
 
 '''ggCaller: a gene caller for Bifrost graphs'''
 
-__version__ = '1.1.0'
+__version__ = '1.1.1'

ggCaller/__main__.py

@@ -18,10 +18,11 @@ def get_options():
     IO.add_argument('--colours',
                     default=None,
                     help='Bifrost colours file generated by Bifrost build.  ')
-    IO.add_argument('--is-ref',
-                    action="store_true",
-                    default=False,
-                    help='If using existing graph, was graph built with references or reads.  ')
+    IO.add_argument('--not-ref',
+                    action="store_false",
+                    default=True,
+                    help='If using existing graph, was not graph built exclusively with assembled genomes.  '
+                         '[Default = False] ')
     IO.add_argument('--refs',
                     default=None,
                     help='List of reference genomes (one file path per line). ')
@@ -73,7 +74,7 @@ def main():
     # parse command line arguments
     graph_file = options.graph
     colours_file = options.colours
-    is_ref = bool(options.is_ref)
+    is_ref = bool(options.not_ref)
     refs_file = options.refs
     reads_file = options.reads
     codons = options.codons