Question: Breakdancer Compile Error: Regionlimitedbamreader.Hpp:23:5: Error: ‘Bam_Iter_T’ Does Not Name A Type
gravatar for William
5.9 years ago by
William4.4k wrote:

I tried to get the latest version from github and release 1.4.1 of breakdancer to run but all my attempts failed with this compile error:

I followed the file. Make of samtools works. cmake of breakdancer works. Make of breakdancer gives the following error:

/home/william/Downloads/breakdancer-1.4.1/src/lib/breakdancer/RegionLimitedBamReader.hpp:23:5: error: ‘bam_iter_t’ does not name a type

It seems like the a iterator variable is used of type ‘bam_iter_t' which is not a known type. See the part of code below. bam_iter_t is also not defined in the object that are included.

\#include "IBamReader.hpp"
\#include "BamReader.hpp"

\#include <boost/format.hpp>
\#include <stdexcept>
\#include <string>

template<typename Filter>
class RegionLimitedBamReader : public BamReader<Filter> {
RegionLimitedBamReader(std::string const& path, char const* region);

int next(bam1_t* entry);

int tid() const { return _tid; }
int beg() const { return _beg; }
int end() const { return _end; }

std::string _region;
bam_index_t* _index;
bam_iter_t _iter;
int _tid;
int _beg;
int _end;
breakdancer • 2.5k views
ADD COMMENTlink modified 5.8 years ago • written 5.9 years ago by William4.4k

Which version of Samtools are you compiling against?

ADD REPLYlink written 5.8 years ago by ernfrid380

I followed the file and downloaded samtools-0.1.6 from the given link, untarred it, build it, and exported it as the samtools root. RegionLimitedBamReader.hpp is not including anything from samtools so I don't expect the error to be related with samtools ?

ADD REPLYlink written 5.8 years ago by William4.4k

Can you try linking to a newer samtools like 0.1.19? I believe even though this file isn't linking to samtools explicitly, that type is only present in newer versions.

ADD REPLYlink written 5.8 years ago by ernfrid380
gravatar for William
5.8 years ago by
William4.4k wrote:

The file of breakdancer is out of date.

Instead of downloading samtools-0.1.6.tar.bz2 you should download samtools-0.1.19.tar.bz2 .

The rest of the installation worked for me after changing this.

ADD COMMENTlink written 5.8 years ago by William4.4k
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