Merge pull request #29 from ekopylova/master

modify print_all_reads + documentation
Merge pull request #30 from ekopylova/master

updated doxygen
Merge pull request #31 from ekopylova/master

moved freeing of file pointer to end of last processed reads file sectio...
Merge pull request #32 from ekopylova/master

paired_in and paired_out tested
Merge pull request #33 from ekopylova/master

created build.sh to avoid timestamp issues
Merge branch 'master' of https://github.com/biocore/sortmerna

merge with upstream