Re: [Seqan-dev] BZip2 not found

["Holtgrewe, Manuel" <manuel.holtgrewe@fu-berlin.de>]

You will not get a CMake message regarding libbzip2-dev.

However, I'm 99.999% sure that having bzip2 support or not is independent from anything seqan does with sam or bam.

*m
________________________________________
From: Bernd Jagla [bernd.jagla@pasteur.fr]
Sent: Friday, April 20, 2012 1:22 PM
To: seqan-dev@lists.fu-berlin.de
Subject: Re: [Seqan-dev] BZip2 not found

Hi,

after installing bzlib2 I cannot reproduce this problem anymore...

B

On 4/20/2012 10:21 AM, Bernd Jagla wrote:
> Hi,
>
> I get the following error message when executing bam_stats from the
> extras/demos...
>
> When I looked in the sources I saw that you are using Stream<Bgzf>
> bamStream; to open the stream... and with the BZlib2 not found can
> this be the reason for the problem?
>
> But if this is so, why is this not picked up  during compilation????
>
> Thanks for looking into this,
>
> Bernd
>
> bash-3.2$ ./bam_stats -B
> /pasteur/solexa2/solexa_travail/PF2/bowtie_genomes/af1163.fa
> /pasteur/hiseq/hiseq_travail/pf2/2011-Runs/111122_sn322_0173_BD0DY9ACXX/Gerald/L3_A
> F8/tophat-af1163/accepted_hits.bam
>
> /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/core/include/seqan/sequence/sequence_interface.h:804
> Assertion failed : pos <= static_cast<TPos>(length
> (me)) was: 1571263 > 1571256 (Trying to get an iterator behind a
> container through iter().)
>
> stack trace:
>   0          [0x4599ae]  seqan::ClassTest::fail() + 0xe
>   1          [0x45dc3d]
> seqan::Iterator<seqan::String<seqan::SimpleType<unsigned char,
> seqan::Dna5_>, seqan::Alloc<void> >, seqan::Tag<seqan::Rooted_>
> const>::Type seqan
> ::iter<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>,
> seqan::Alloc<void> >, unsigned long,
> seqan::Rooted_>(seqan::String<seqan::SimpleType<unsigned char, s
> eqan::Dna5_>, seqan::Alloc<void> >&, unsigned long,
> seqan::Tag<seqan::Rooted_>) + 0x6d
>   2          [0x45c924]
> seqan::Iterator<seqan::String<seqan::SimpleType<unsigned char,
> seqan::Dna5_>, seqan::Alloc<void> >,
> seqan::DefaultGetIteratorSpec<seqan::String<s
> eqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<void> >
> >::Type>::Type seqan::iter<seqan::String<seqan::SimpleType<unsigned
> char, seqan::Dna5_>, seqan::Alloc<
> void> >, unsigned long>(seqan::String<seqan::SimpleType<unsigned char,
> seqan::Dna5_>, seqan::Alloc<void> >&, unsigned long) + 0x24
>   3          [0x45c7fd]
> seqan::Iterator<seqan::Gaps<seqan::String<seqan::SimpleType<unsigned
> char, seqan::Dna5_>, seqan::Alloc<void> >, seqan::ArrayGaps>,
> seqan::Tag<seq
> an::Standard_> const>::Type
> seqan::_iteratorGapsArray<seqan::Gaps<seqan::String<seqan::SimpleType<unsigned
> char, seqan::Dna5_>, seqan::Alloc<void> >, seqan::ArrayGaps>, u
> nsigned long>(seqan::Gaps<seqan::String<seqan::SimpleType<unsigned
> char, seqan::Dna5_>, seqan::Alloc<void> >, seqan::ArrayGaps>&,
> unsigned long) + 0x1cd
>   4          [0x45c554]
> seqan::Iterator<seqan::Gaps<seqan::String<seqan::SimpleType<unsigned
> char, seqan::Dna5_>, seqan::Alloc<void> >, seqan::ArrayGaps>,
> seqan::Tag<seq
> an::Rooted_> const>::Type
> seqan::iter<seqan::String<seqan::SimpleType<unsigned char,
> seqan::Dna5_>, seqan::Alloc<void> >, unsigned long,
> seqan::Rooted_>(seqan::Gaps<seqan
> ::String<seqan::SimpleType<unsigned char, seqan::Dna5_>,
> seqan::Alloc<void> >, seqan::ArrayGaps>&, unsigned long,
> seqan::Tag<seqan::Rooted_>) + 0x24
>   5          [0x45c51b]
> seqan::Iterator<seqan::Gaps<seqan::String<seqan::SimpleType<unsigned
> char, seqan::Dna5_>, seqan::Alloc<void> >, seqan::ArrayGaps>,
> seqan::Tag<seq
> an::Rooted_> const>::Type
> seqan::begin<seqan::String<seqan::SimpleType<unsigned char,
> seqan::Dna5_>, seqan::Alloc<void> >, seqan::ArrayGaps,
> seqan::Rooted_>(seqan::Gaps<s
> eqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>,
> seqan::Alloc<void> >, seqan::ArrayGaps>&, seqan::Tag<seqan::Rooted_>)
> + 0x3b
>   6          [0x4576bc]
> seqan::Iterator<seqan::Gaps<seqan::String<seqan::SimpleType<unsigned
> char, seqan::Dna5_>, seqan::Alloc<void> >, seqan::ArrayGaps>,
> seqan::Default
> GetIteratorSpec<seqan::Gaps<seqan::String<seqan::SimpleType<unsigned
> char, seqan::Dna5_>, seqan::Alloc<void> >, seqan::ArrayGaps>
> >::Type>::Type seqan::begin<seqan::Gaps<
> seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>,
> seqan::Alloc<void> >, seqan::ArrayGaps>
> >(seqan::Gaps<seqan::String<seqan::SimpleType<unsigned char, seqan::
> Dna5_>, seqan::Alloc<void> >, seqan::ArrayGaps>&) + 0x1c
>   7          [0x460703]  unsigned int
> seqan::cigarToGapAnchorContig<seqan::String<seqan::CigarElement<char,
> unsigned int>, seqan::Alloc<void> >, seqan::Gaps<seqan::String
> <seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<void> >,
> seqan::ArrayGaps> >(seqan::String<seqan::CigarElement<char, unsigned
> int>, seqan::Alloc<void> > con
> st&, seqan::Gaps<seqan::String<seqan::SimpleType<unsigned char,
> seqan::Dna5_>, seqan::Alloc<void> >, seqan::ArrayGaps>&) + 0x23
>   8          [0x4575d6]  void
> seqan::bamRecordToAlignment<seqan::String<seqan::SimpleType<unsigned
> char, seqan::Dna5_>, seqan::Alloc<void> >, seqan::ArrayGaps, seqan::Str
> ing<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<void>
> > >(seqan::Align<seqan::String<seqan::SimpleType<unsigned char,
> seqan::Dna5_>, seqan::Alloc<void> >
> , seqan::ArrayGaps>&, seqan::String<seqan::SimpleType<unsigned char,
> seqan::Dna5_>, seqan::Alloc<void> >&, seqan::BamAlignmentRecord&) + 0xa6
>   9          [0x4543bb]  int
> doWork<seqan::Stream<seqan::Tag<seqan::Bgzf_> >,
> seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>,
> seqan::Alloc<void> >, seqan::O
> wner<seqan::Tag<seqan::Default_> >, seqan::Tag<seqan::Bam_>
> >(seqan::Stream<seqan::Tag<seqan::Bgzf_> >&,
> seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, s
> eqan::Dna5_>, seqan::Alloc<void> >,
> seqan::Owner<seqan::Tag<seqan::Default_> > >&, Options const&,
> seqan::Tag<seqan::Bam_> const&) + 0x41b
>  10          [0x45120f]  main + 0x8df
>  11      [0x3782c1d994]  __libc_start_main + 0xf4
>  12          [0x44fba9]  __gxx_personality_v0 + 0xe9
>
> Aborted
>
> On 4/20/2012 9:41 AM, Holtgrewe, Manuel wrote:
>> BZIP2 is not needed for BAM. You only need it for the BZ2Stream to
>> work, e.g. if your reads are bz2 compressed. BZ2 has good compression
>> at a trade-off of quite high running times so people in
>> Bioinformatics usually prefer zlib.
>>
>> On Debian/Ubuntu, you need libbz2-dev for BZip2 support.
>>
>> *m
>> ________________________________________
>> From: Bernd Jagla [bernd.jagla@pasteur.fr]
>> Sent: Friday, April 20, 2012 9:37 AM
>> To: seqan-dev@lists.fu-berlin.de
>> Subject: [Seqan-dev] BZip2 not found
>>
>> Hi,
>>
>> I get the following error message when executing cmake:
>>
>> BZip2 libraries could not be found!
>>
>> As I am not system administrator, which libraries do I have to ask for
>> to be installed on a Linux system?
>>
>> Does this affect reading / writing BAM files? (I was under the
>> impression that only Zlib is needed)
>>
>> When installing BZip2 locally how do I tell cmake about where to find
>> the library?
>>
>> Thanks a lot for your continued support,
>>
>> Bernd
>>
>>
>> _______________________________________________
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>> seqan-dev@lists.fu-berlin.de
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>>
>
>
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