README_INSTALL

Dear Pindel users, we have updated Pindel install to compile with the latest samtools-1.2. Here is the instruction on how to install.

step 1
download samtools-1.2 and unzip the package. You should expect samtools folder as well as htslib folder inside samtools folder

step 2
compile samtools-1.2 and htslib using make

step 3
use the provided INSTALL script to compile pindel

./INSTALL /path/to/folder/samtools-1.2/htslib-1.2.1

then you should be good to use pindel.

If you encountered error while loading shared libraries: libhts.so.1:cannot open shared object file: No such file or directory, you should update library path or run pindel like
LD_LIBRARY_PATH=/path/to/samtools-1.2/htslib-1.2.1 ./pindel