A C++ toolchain
cmake
make
On a Debian Linux-based system such as Ubuntu
apt install build-essential cmake
will install the required software.
Builds are currently failing under OS X.
All required libraries are included in the repository under vendor/.
See vendor/README.md for more information.
Make a build directory
mkdir build
Run CMake from inside it
cd build
cmake ..
Run Make
make
This will build all the vendored libraries as well as bam-readcount.
The final binary, which can be moved anywhere, is
bin/bam-readcount
Try it on a test CRAM
cd ../test-data
../build/bin/bam-readcount -f rand1k.fa twolib.sorted.cram
There is a small two-library test CRAM file
test-data/twolib.sorted.cram
with associated reference
test-data/rand1k.fa
The reference is encoded in the CRAM as
@SQ SN:rand1k LN:1000 M5:11e5d1f36a8e123feb3dd934cc05569a UR:rand1k.fa
so bam-readcount should be run inside the test-data directory to
find the reference.