Merge pull request #27 from smithlabcode/bam-format-output

Direct BAM format output

.github/workflows/c-cpp.yml

@@ -16,8 +16,12 @@ jobs:
     - uses: actions/checkout@v3
       with:
         submodules: recursive
+    - name: Update packages
+      run: sudo apt-get update
     - name: Install autotools
       run: sudo apt-get install -y autoconf automake libtool
+    - name: Install dependencies
+      run: sudo apt-get install -y libhts-dev
     - name: Generate configure script
       run: ./autogen.sh
     - name: configure

.gitmodules

@@ -1,3 +1,6 @@
 [submodule "src/smithlab_cpp"]
 	path = src/smithlab_cpp
 	url = ../smithlab_cpp.git
+[submodule "src/bamxx"]
+	path = src/bamxx
+	url = [email protected]:smithlabcode/bamxx.git

Makefile.am

@@ -34,7 +34,7 @@ ACLOCAL_AMFLAGS = -I m4
 
 SUBDIRS := src/smithlab_cpp
 install installdirs: SUBDIRS := $(filter-out src/smithlab_cpp, $(SUBDIRS))
-AM_CPPFLAGS = -I $(top_srcdir)/src/smithlab_cpp
+AM_CPPFLAGS = -I $(top_srcdir)/src/smithlab_cpp -I $(top_srcdir)/src/bamxx
 
 CXXFLAGS = -Wall -O3 $(OPENMP_CXXFLAGS) # default has optimization on
 
@@ -53,7 +53,9 @@ libabismal_a_SOURCES += \
 	src/AbismalAlign.hpp \
 	src/AbismalIndex.hpp \
 	src/dna_four_bit_bisulfite.hpp \
-	src/popcnt.hpp
+	src/popcnt.hpp \
+	src/abismal_cigar_utils.hpp \
+	src/bamxx/bamxx.hpp
 
 LDADD = libabismal.a src/smithlab_cpp/libsmithlab_cpp.a
 

configure.ac

@@ -33,6 +33,17 @@ AC_PROG_RANLIB
 
 AC_CONFIG_SUBDIRS([src/smithlab_cpp])
 
+dnl check for HTSLib if requested
+hts_fail_msg="
+Failed to locate HTSLib on your system. Please use the LDFLAGS and
+CPPFLAGS variables to specify the directories where the HTSLib library
+and headers can be found.
+"
+
+dnl check for required libraries
+AC_SEARCH_LIBS([hts_version], [hts], [], [AC_MSG_FAILURE([$hts_fail_msg])])
+
+
 dnl OpenMP happens here
 AC_OPENMP([C++])
 AS_VAR_IF(OPENMP_CXXFLAGS, [], [
@@ -43,10 +54,6 @@ dnl now we get setup for the right OpenMP flags
 ADS_OPENMP([], [AC_MSG_FAILURE([OpenMP must be installed to build abismal])])
 ])dnl end of OpenMP stuff
 
-dnl check for the Zlib library
-AC_CHECK_LIB([z], [zlibVersion], [],
-  [AC_MSG_FAILURE([Zlib must be installed to build abismal])], [])
-
 AC_CONFIG_FILES([
 Makefile
 ])