Added compilation of examples and of the C++ version; output soft clipping in cigars; fixed cigar generation in C++ version; fixed memory leaks; fixed compilation warnings.

[ahippo]

There are significant changes to the Makefile in this pull request. I hope, you'll find them useful. There are also a change in cigar output, a change in fix of internal cigar representaion and memory leak fixes. The most of other changes are just whitespace changes (trailing whitespaces removed) and are purely cosmetic.

Please, merge the pull request. Thank you in advance!

[mengyao]

Dear Andrey,

Sorry for the late reply. I was very busy during my past two weeks.

Thank you very much for your contribution to the SSW library.

I appreciate your improvements to the codes. There is only one thing in this revision that I don’t agree: treat compilation warnings as errors.

From developers’ aspect this can help us to write cleaner codes, but it may cause problem at users’ side.

There are always unexpected running environments for SSW. Some gcc/g++ compiler can give more strict warning criterion, which we don’t expect. If a small problem causes the failure of the compile, some users may miss the opportunity to try out SSW.

If you would like to remove this revision, I will be very happy to merge your improvement.

Thanks again,

Mengyao

On Jan 20, 2014, at 12:53 PM, Andrey Mazo notifications@github.com wrote:

There are significant changes to the Makefile in this pull request. I hope, you'll find them useful. The most of other changes are just whitespace changes (trailing whitespaces removed) and are purely cosmetic.

Please, merge the pull request. Thank you in advance!

You can merge this Pull Request by running

git pull https://github.com/ahippo/Complete-Striped-Smith-Waterman-Library master Or view, comment on, or merge it at:

https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/pull/6

Commit Summary

strip trailing whitespaces Makefile tweaks treat compilation warnings as errors. ssw_test depends on kseq.h too. Added compilation of C++ version and example. Fixed compilation warnings in ssw_cpp.cpp File Changes

M src/Makefile (40) M src/example.c (32) M src/example.cpp (2) M src/main.c (108) M src/ssw.c (246) M src/ssw.h (72) M src/ssw_cpp.cpp (68) M src/ssw_cpp.h (40) Patch Links:

https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/pull/6.patch https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/pull/6.diff — Reply to this email directly or view it on GitHub.

[ahippo]

Dear Mengyao,

Thank you very much for your reply! It's great that almost all of the changes are fine with you! Ok, I see your point and agree with it, so I'm fine to drop the commit which adds -Werror. I see 2 possible ways to do that: 1) commit a new changeset which reverts -Werror changeset (via git revert) 2) rebase my branch to completely remove -Werror changeset from the history (via git rebase -i) Which way should I go?

Thank you!

Dear Andrey,

Sorry for the late reply. I was very busy during my past two weeks.

Thank you very much for your contribution to the SSW library.

I appreciate your improvements to the codes. There is only one thing in this revision that I don’t agree: treat compilation warnings as errors.

From developers’ aspect this can help us to write cleaner codes, but it may cause problem at users’ side.

There are always unexpected running environments for SSW. Some gcc/g++ compiler can give more strict warning criterion, which we don’t expect. If a small problem causes the failure of the compile, some users may miss the opportunity to try out SSW.

If you would like to remove this revision, I will be very happy to merge your improvement.

Thanks again,

Mengyao

[mengyao]

Dear Andrey,

I think it doesn’t matter.

Please just let me know after you revised.

Many thanks,

Mengyao

On Jan 29, 2014, at 1:54 PM, Andrey Mazo notifications@github.com wrote:

Dear Mengyao,

Thank you very much for your reply! It's great that almost all of the changes are fine with you! Ok, I see your point and agree with it, so I'm fine to drop the commit which adds -Werror. I see 2 possible ways to do that: 1) commit a new changeset which reverts -Werror changeset (via git revert) 2) rebase my branch to completely remove -Werror changeset from the history (via git rebase -i) Which way should I go?

Thank you!

Dear Andrey,

Sorry for the late reply. I was very busy during my past two weeks.

Thank you very much for your contribution to the SSW library.

I appreciate your improvements to the codes. There is only one thing in this revision that I don’t agree: treat compilation warnings as errors.

From developers’ aspect this can help us to write cleaner codes, but it may cause problem at users’ side.

There are always unexpected running environments for SSW. Some gcc/g++ compiler can give more strict warning criterion, which we don’t expect. If a small problem causes the failure of the compile, some users may miss the opportunity to try out SSW.

If you would like to remove this revision, I will be very happy to merge your improvement.

Thanks again,

Mengyao

— Reply to this email directly or view it on GitHub.

[ahippo]

I've just removed -Werror. (I did git revert for simplicity.)

Thank you!

[mengyao]

Thank you. I have merged.

[ahippo]

Thank you very much!