Hello I try to analyse my CLIP-seq data and a corresponding control inform of a normal RNA-seq data set. I think Piranha should be designed to do exactly this. Unfortunately I can not manage to install piranha with the bam file read support. Therefore I have three question, with the hope that some of you can help me out there:

1/ does anyone know a better way to analyse this kind of data? 2/ if I can not use Piranha with bam read support (-bin_size and -bin_size_covars options), I can still provide binned read count data. What is the appropriate way to provide the covariates in this scenario? 3/ Can someone give me a hint how I can make Piranha install using the bam file read options via bamtools? I have installed bamtools 2.5.1. If I call the piranha 1.2.1 configure via:

./configure  --with-bam_tools_headers="${HOME}/.local/include/bamtools/"  --with-bam_tools_library="${HOME}/.local/lib64/"

I get:

configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
provided BAMTools headers directory is ${HOME}/.local/include/bamtools/
provided BAMTools library directory is ${HOME}/.local/lib64/
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether we're compiling on Darwin/MacOS... no
checking for cos in -lm... yes
checking for cblas_dgemm in -lgslcblas... yes
checking for gsl_blas_dgemm in -lgsl... yes
checking for linking against gsl matrix... yes
checking for BAMTools... no
configure: WARNING: could not find BAMTools, disabling BAM support
configure: creating ./config.status
config.status: creating Makefile
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/test/Makefile
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/test/Makefile
config.status: creating src/progs/Makefile
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/test/Makefile
config.status: creating src/progs/Makefile
config.status: creating src/common/Makefile
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/test/Makefile
config.status: creating src/progs/Makefile
config.status: creating src/common/Makefile
config.status: creating src/common/config.hpp
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/test/Makefile
config.status: creating src/progs/Makefile
config.status: creating src/common/Makefile
config.status: creating src/common/config.hpp
config.status: creating src/test/regressionTests.xml
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library

bamtools 2.5.1 is installed and the content of the lib and include directories are:

tree ${HOME}/.local/include/bamtools/
${HOME}/.local/include/bamtools/
├── api
│   ├── algorithms
│   │   └── Sort.h
│   ├── api_global.h
│   ├── BamAlgorithms.h
│   ├── BamAlignment.h
│   ├── BamAux.h
│   ├── BamConstants.h
│   ├── BamIndex.h
│   ├── BamMultiReader.h
│   ├── BamReader.h
│   ├── BamWriter.h
│   ├── IBamIODevice.h
│   ├── SamConstants.h
│   ├── SamHeader.h
│   ├── SamProgramChain.h
│   ├── SamProgram.h
│   ├── SamReadGroupDictionary.h
│   ├── SamReadGroup.h
│   ├── SamSequenceDictionary.h
│   └── SamSequence.h
└── shared
└── bamtools_global.h

tree ${HOME}/.local/lib64/
${HOME}/.local/lib64/
├── libbamtools.a
└── pkgconfig
└── bamtools-1.pc

I tried several other strategies and used hints I found online, without any improvment. Therefore I decided to contact you directly. Any help highly appreciated.

Thank you very in advance.