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Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
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pindel fails with error while loading shared libraries: libhts.so.3 #116

Open myourshaw opened 4 years ago

myourshaw commented 4 years ago

I had to compile pindel using the suggestions for htslib from the FAQ, and the patches mentioned in Issue 111 Problems in installing pindel, including correcting the #include misleading instruction. I got "Pindel successfully compiled." But when I ran pindel, I got this error:

./pindel: error while loading shared libraries: libhts.so.3: cannot open shared object file: No such file or directory

libhts.so.3 in fact exists in /usr/local/lib and also in the directory parallel to pindel, /home/myourshaw/apps/pindeltest/htslib.

myourshaw commented 4 years ago

pindel will work if I copy the library and symlink to the pindel directory

cp ../htslib/libhts.so .
ln -s libhts.so libhts.so.3