36 fix threading memory leak (#41)

Fix the memory leak issue in the bam module and refactor the project for Bioconda submission.

Makefile

@@ -3,10 +3,8 @@ SRC_DIR := $(CURDIR)/src
 LIB_DIR := $(CURDIR)/lib
 
 all:
-    # Generate the SWIG python <-> C++ wrappers (Both ways)
-    # The Python wrapper is stored in the main directory, while the C++ wrapper code is stored in /src
+    # Generate the SWIG Python/C++ wrappers
 	swig -c++ -python -outdir $(LIB_DIR) -I$(INCL_DIR) -o $(SRC_DIR)/lrst_wrap.cpp $(SRC_DIR)/lrst.i
 
-	# Compile the C++ shared libraries
-	# The C++ wrapper binary _lrst is generated in the /src directory
+	# Compile the C++ shared libraries into lib/
 	python setup.py build_ext --build-lib $(LIB_DIR)

conda/build.sh

@@ -1,5 +1,7 @@
 #!/bin/bash
 
+# Build the C++ library
+
 # Add the library path to the LD_LIBRARY_PATH
 export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${PREFIX}/lib
 
@@ -13,11 +15,11 @@ $PYTHON setup.py -I"${PREFIX}"/include -L"${PREFIX}"/lib install
 cp "${SRC_DIR}"/longreadsum "${PREFIX}"/bin
 
 # Create the src directory
-mkdir -p "${PREFIX}"/src
+#mkdir -p "${PREFIX}"/lib
 
-# Copy the lib files to the src directory
-cp -r "${SRC_DIR}"/src/*.py "${PREFIX}"/src
+# Copy the lib files to the build directory
+cp -r "${SRC_DIR}"/src/*.py "${PREFIX}"/lib
 
 # Copy the SWIG generated library to the lib directory
-cp -r "${SRC_DIR}"/lib/*.py "${PREFIX}"/src
+cp -r "${SRC_DIR}"/lib/*.py "${PREFIX}"/lib
 cp -r "${SRC_DIR}"/lib/*.so "${PREFIX}"/lib

environment.yml

@@ -6,17 +6,15 @@ channels:
   - defaults
 dependencies:
   - python
-  - setuptools
-  - conda-build
   - hdf5
   - htslib
-  - samtools
   - swig
   - matplotlib
   - plotly=4.14
   - pytest
-  - pytest-dependency
   - pip
+  - pip:
+    - kaleido
 
 # conda env create --file=environment.yml
-# conda activate lrst_py36
+# conda activate lrst_py39

include/ComStruct.h

@@ -4,7 +4,7 @@
 #include <string>
 #include <map>
 #include <vector>
-
+#include <stdint.h>
 
 /////////////////////////////////
 #define MAX_F5EVENT_SIZE   3000000