Please install Boost and zlib.
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Download source from github
git clone https://github.com/PacificBiosciences/bam2fastx && cd bam2fastx
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Sync your code with the latest git code base:
git pull --rebase origin master && git submodule update --init
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Create build directory
mkdir build && cd build
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Invoke cmake with Boost and zlib as system libraries
cmake ..
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Or with user-specific paths
cmake -DBoost_INCLUDE_DIRS=/path/to/boost/include -DZLIB_INCLUDE_DIRS=/path/to/zlib/include -DZLIB_LIBRARIES=/path/to/zlib/lib ..
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Build
make
Both tools have an identical interface and take BAM and/or DataSet files as input. Examples:
bam2fasta -o projectName m54008_160330_053509.subreads.bam
bam2fastq -o myEcoliRuns m54008_160330_053509.subreads.bam m54008_160331_235636.subreads.bam
bam2fasta -o myHumanGenome m54012_160401_000001.subreadset.xml
Futher help can be requested with -h
. Issues? Problem? Please create a github issue.