Author: Michael R. Crusoe <crusoe@debian.org>
Description: Use the libbwa-dev package
Forwarded: not-needed
--- uncalled.orig/Makefile
+++ uncalled/Makefile
@@ -5,9 +5,9 @@
 HDF5_LIB=$(shell pkg-config  --libs hdf5-serial)
 HDF5_INCLUDE=$(shell pkg-config  --cflags hdf5-serial)
 
-LIBBWA=./submods/bwa/libbwa.a
-BWA_LIB=-L./submods/bwa $(LIBBWA)
-BWA_INCLUDE=-I./submods/bwa
+LIBBWA=/usr/lib/libbwa.a
+BWA_LIB=$(LIBBWA)
+BWA_INCLUDE=-I/usr/include/bwa
 
 LIBS=$(HDF5_LIB) $(BWA_LIB) -lstdc++ -lz -ldl -pthread -lm 
 INCLUDE=-I submods/ -I submods/toml11 -I submods/fast5/include -I submods/pybind11/include -I submods/pdqsort $(HDF5_INCLUDE) $(BWA_INCLUDE)
--- uncalled.orig/setup.py
+++ uncalled/setup.py
@@ -44,7 +44,7 @@
         else:
             sys.stderr.write("All submodules present\n")
 
-        if os.path.exists("./submods/bwa/libbwa.a"):
+        if os.path.exists("/usr/lib/libbwa.a"):
             sys.stderr.write("Found libbwa.a\n")
         else:
             sys.stderr.write("building libbwa\n")
