Question: Pindel during compile : pindel.h:35:24: error: htslib/sam.h: No such file or directory
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gravatar for johnnytam100
10 weeks ago by
johnnytam10020
johnnytam10020 wrote:

When I tried to compile Pindel using the following command :

./INSTALL /data/tam/script/samtools-1.5/

The following error (partially) appeared :

pindel.h:34:26: error: htslib/khash.h: No such file or directory
pindel.h:35:24: error: htslib/sam.h: No such file or directory
In file included from refreader.cpp:26:
pindel.h:34:26: error: htslib/khash.h: No such file or directory
pindel.h:35:24: error: htslib/sam.h: No such file or directory
In file included from searcher.cpp:22:
pindel.h:34:26: error: htslib/khash.h: No such file or directory
pindel.h:35:24: error: htslib/sam.h: No such file or directory
In file included from reporter.cpp:32:
pindel.h:34:26: error: htslib/khash.h: No such file or directory
pindel.h:35:24: error: htslib/sam.h: No such file or directory
reader.cpp:29:24: error: htslib/sam.h: No such file or directory
reader.cpp:30:28: error: htslib/kstring.h: No such file or directory
reader.cpp:31:25: error: htslib/kseq.h: No such file or directory
reader.cpp:32:26: error: htslib/khash.h: No such file or directory
reader.cpp:33:26: error: htslib/ksort.h: No such file or directory

Is it I have to add a path to the htslib directory? Use what command?

Thank you!

htslib pindel • 161 views
ADD COMMENTlink modified 18 days ago by Biostar ♦♦ 20 • written 10 weeks ago by johnnytam10020

Where and how did you get your samtools? There should be a htslib folder in /data/tam/script/samtools-1.5/. Is it not there?

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by genomax37k
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