Integrate BKC (for 10X/Visium), add lookup table, bump version, make …

…some cleanups

.dockerignore

@@ -8,5 +8,4 @@
 !Makefile
 !download_kmc.py
 !hash.git
-
-
+!.git/

.gitignore

@@ -6,6 +6,7 @@ src/common/kmc_api/*.o
 src/satc_merge/*.o
 src/satc_dump/*.o
 src/compactors/*.o
+src/read_selector/*.o
 src/dsv_manip/*.o
 *.fastq
 *.fastq.gz

.gitmodules

@@ -1,6 +1,24 @@
-[submodule "libs/cloudflare-zlib"]
-	path = libs/cloudflare-zlib
-	url = https://github.com/refresh-bio/dependencies-zlib/
+[submodule "libs/mimalloc"]
+	path = libs/mimalloc
+	url = https://github.com/microsoft/mimalloc
 [submodule "libs/zstd"]
 	path = libs/zstd
-	url = https://github.com/refresh-bio/dependencies-zstd/
+	url = https://github.com/refresh-bio/dependencies-zstd
+[submodule "libs/SBWT"]
+	path = libs/SBWT
+	url = https://github.com/refresh-bio-dependencies/SBWT
+[submodule "libs/zlib-ng"]
+	path = libs/zlib-ng
+	url = https://github.com/refresh-bio-dependencies/zlib-ng.git
+[submodule "libs/isa-l"]
+	path = libs/isa-l
+	url = https://github.com/refresh-bio-dependencies/isa-l.git
+[submodule "build_tools/nasm"]
+	path = build_tools/nasm
+	url = https://github.com/netwide-assembler/nasm.git
+[submodule "libs/libdeflate"]
+	path = libs/libdeflate
+	url = https://github.com/refresh-bio-dependencies/libdeflate
+[submodule "libs/bkc"]
+	path = libs/bkc
+	url = https://github.com/refresh-bio/bkc

Dockerfile

@@ -6,14 +6,15 @@ WORKDIR /home/ubuntu
 COPY . src
 RUN  \
     apt-get update -y \
-    && apt-get install -y make python3 g++ wget time \
+    && apt-get install -y cmake make python3 g++ wget time git \
     && cp -r src build \ 
 	&& cd build \
 	&& make -j \
 	&& make install \
 	&& cd .. \
 	&& rm -rf build \
-	&& apt-get remove -y make git wget g++ \
+	&& apt-get remove -y cmake make wget g++ git \
 	&& apt-get autoremove -y \
 	&& apt-get clean \
+	&& rm -rf src/.git \
 	&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*