countmut 0.2.4__tar.gz → 0.3.0__tar.gz

{countmut-0.2.4/countmut.egg-info → countmut-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: countmut
-Version: 0.2.4
+Version: 0.3.0
 Summary: Unified ultra-fast strand-aware mutation counter (C backend + samtools-style -e/-p filters)
 Author-email: Ye Chang <yech1990@gmail.com>
 License-Expression: MIT

countmut-0.3.0/backend/Makefile

@@ -0,0 +1,50 @@
+# Makefile for the countmut C core (links the full htslib vendored as a git
+# submodule, for BAM/CRAM support).
+#
+# Builds `countmut_core`, a binary that does all the counting.  Requires Lua 5.4.
+# The full htslib is built from the vendored submodule (../htslib) and linked.
+CC ?= cc
+LUA_CFLAGS := $(shell pkg-config --cflags lua5.4 2>/dev/null)
+ifeq ($(LUA_CFLAGS),)
+LUA_CFLAGS := $(shell pkg-config --cflags lua5.3 2>/dev/null)
+endif
+ifeq ($(LUA_CFLAGS),)
+LUA_CFLAGS := -I/usr/include/lua5.4
+endif
+LUA_LIBS := $(shell pkg-config --libs lua5.4 2>/dev/null)
+ifeq ($(LUA_LIBS),)
+LUA_LIBS := $(shell pkg-config --libs lua5.3 2>/dev/null)
+endif
+ifeq ($(LUA_LIBS),)
+LUA_LIBS := -llua5.4
+endif
+# Full htslib vendored as a git submodule (../htslib).  Override with HTSLIB_DIR.
+HTSLIB_DIR ?= ../htslib
+CFLAGS ?= -O3 -Wall -Wno-unused-result -pthread $(LUA_CFLAGS) -I$(HTSLIB_DIR) -I$(HTSLIB_DIR)/htslib
+OBJS	= bedidx.o countmut_expr.o countmut_core.o countmut_core_main.o
+# Statically link htslib (libhts.a) so the binary is self-contained (no runtime
+# libhts.so dependency) -- the PyPI wheel bundles the binary and it must run
+# without a separate htslib install.  libhts.a pulls in its own deps.
+LIBS	= $(HTSLIB_DIR)/libhts.a -lpthread -lz -lm -lbz2 -llzma -lcurl -lcrypto -ldeflate $(LUA_LIBS)
+PROG	= countmut_core
+
+.PHONY: all clean asan htslib
+
+all: htslib $(PROG)
+
+htslib:
+	$(MAKE) -C $(HTSLIB_DIR)
+
+$(PROG): $(OBJS)
+	$(CC) $(CFLAGS) -o $@ $^ $(LIBS)
+
+# AddressSanitizer build for leak/UB auditing
+asan:
+	$(MAKE) clean
+	$(MAKE) CFLAGS="-O1 -g -Wall -fsanitize=address -fno-omit-frame-pointer $(LUA_CFLAGS) -I$(HTSLIB_DIR) -I$(HTSLIB_DIR)/htslib" LIBS="-L$(HTSLIB_DIR) -lhts -lpthread -lz -lm -fsanitize=address $(LUA_LIBS)" $(PROG)
+
+.c.o:
+	$(CC) $(CFLAGS) -c $< -o $@
+
+clean:
+	rm -f $(PROG) *.o