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This tools requires samtools and zlib to compile. Please follow the link and install samtools first.
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Successful installation of samtools results in the following files (presumably in
/usr/local
):/usr/local/include/zlib.h /usr/local/include/bam.h /usr/local/include/htslib/*.h /usr/local/lib/libz.a /usr/local/lib/libbam.a /usr/local/lib/libhts.a
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Compile csam
run
make
orgcc -o csam csam.c -lhts -lbam -lz
or
gcc -I/usr/local/include -L/usr/local/lib -o csam csam.c -lhts -lbam -lz
incase
gcc
can't find the headers or libs
csam -i <bam> -r <ref> -p <prefix>
${prefix}.pre_adapter_detail_metrics.txt
${prefix}.bait_bias_detail_metrics.txt
CONTEXT_SIZEs other than 1 are not yet supported in this implementation.