Hi SAM tools team, I have no problem building Cufflinks from source using samtools 0.1.17 on a Linux Redhat 64-bit system with user privileges. However, the configure step doesn't work for me with version 1.1. I copy libbam.a into ~/bin/lib/, copy header files into ~/bin/include/bam/, and copy samtools into ~/bin/. I set BAM_ROOT to $HOME/bin. Then I configure Cufflinks with --with-bam=$HOME/bin. However, with samtools 1.1, Cufflinks cannot detect the bam libraries. I haven't tried other versions. I'm fine with using version 0.1.17, but have you heard of anyone else having my problem or possible know why? Thanks. --Ben Ernest.
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