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BenLangmead / bowtie

An ultrafast memory-efficient short read aligner
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Update to seqan 1.4.2 #105

Closed junaruga closed 3 years ago

junaruga commented 4 years ago

This PR is working in progress.

Right now bowtie is using seqan 1.1. And the seqan 1.X's latest version is 1.4.2 according to the downloading side (GitHub).

And actually in both Debian and Fedora, we need to build bowtie with the system seqan deb or RPM package (both package's versions are 1.4.2) patching the some files.

I would like to suggest to use seqan 1.4.2 for this repository.

Let me explain some commits for this PR.

First 3 commits are for the preparation.

1st commit is same with https://github.com/BenLangmead/bowtie/pull/102 . I expect the PR is merged at first to verify the bowtie. 2nd commit is a backport from bowtie2, that is related to https://github.com/BenLangmead/bowtie/pull/95#issuecomment-592657903 . Maybe this issue appears running bowtie with gcc-N high version and non-x86_64 architecture. 3rd commit is to run simple-test on s390x. simple-test works with the number of thread: 1 on s390x.

From 4th commit, I used Deiban's patch files. Thank you, Debian people for that.

seqan-library-1.4.2 directory is created like this steps.

$ wget http://packages.seqan.de/seqan-library/seqan-library-1.4.2.tar.bz2
$ tar xvf seqan-library-1.4.2.tar.bz2
$ mv seqan-library-1.4.2 third_party/
$ rm -rf third_party/seqan-library-1.4.2/share

Right now there is one CPU architecture common error like this.

/bowtie-build  --threads 2 --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie --debug   --trim3 4 -S --quiet -a .simple_tests.tmp --12 .simple_tests.tab
./third_party/seqan-library-1.4.2/include/seqan/sequence/string_base.h:498 Assertion failed : static_cast<TStringPos>(pos) < static_cast<TStringPos>(length(me)) was: 0 >= 0 (Trying to access an element behind the last one!)
bowtie aborted with exitlevel 134

See https://travis-ci.org/junaruga/bowtie/jobs/656448871#L1388

Maintainers or Debian people, do you have any idea to fix this? How do you think to update seqan ?

Thank you.

junaruga commented 4 years ago

Maintainers or Debian people, do you have any idea to fix this?

@mr-c do you have any idea for that? Could you invite the maintainer of bowtie here?

junaruga commented 4 years ago

Perhaps, it might be better to manage using https://github.com/seqan/seqan/tree/seqan-v1.4.2 as this repository's git submodule rather than using seqan-library-1.4.2.tar.bz2 . It 's like bowtie2 simde.

junaruga commented 3 years ago

I would close this PR, as it seems seqan dependency was dropped by the commit: https://github.com/BenLangmead/bowtie/commit/3945d8c7856286813cf7422c871e97db95908e29 on Bowtie 1.3.0.