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genome / pindel

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.
GNU General Public License v3.0
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not compile with samtools 1.2 #10

Open boboppie opened 9 years ago

boboppie commented 9 years ago

Dear dev,

While runing the install script:

$ samtools_HOME=/scratch/modules/samtools/1.2/bin/
$ ./INSTALL ${samtools_HOME}/bin

I got an error:

pindel.h:34:19: error: khash.h: No such file or directory

It worked fine with samtools 0.1.19.

Best wishes, Fengyuan

liangkaiye commented 9 years ago

Indeed, this is the case. The bam handling functions have been changed in the recent samtools versions.

Sent from my iPhone

On Apr 28, 2015, at 06:22, Fengyuan Hu notifications@github.com wrote:

Dear dev,

While runing the install script:

$ samtools_HOME=/scratch/modules/samtools/1.2/bin/ $ ./INSTALL ${samtools_HOME}/bin I got an error:

pindel.h:34:19: error: khash.h: No such file or directory It worked fine with samtools 0.1.19.

Best wishes, Fengyuan

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