[med-svn] [bowtie2] branch upstream updated (706918c -> 2eb8a65)

[Alex Mestiashvili]

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malex-guest pushed a change to branch upstream
in repository bowtie2.

      from  706918c   Imported Upstream version 2.2.0
       new  89ac339   Imported Upstream version 2.2.1
       new  2eb8a65   Imported Upstream version 2.2.2

The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 MANUAL          | 29 ++++++++++++--------
 MANUAL.markdown | 37 +++++++++++++++++---------
 NEWS            | 22 +++++++++++++---
 VERSION         |  2 +-
 bowtie2         | 17 +++++++-----
 bt2_idx.h       | 12 ++++-----
 bt2_io.cpp      | 82 ++++++++++++++++++++-------------------------------------
 bt2_search.cpp  |  6 +++--
 doc/manual.html | 14 +++++++---
 mm.h            | 15 -----------
 ref_read.h      | 13 ---------
 reference.cpp   | 67 +++++++++++++++++++++++++---------------------
 reference.h     |  9 ++++---
 word_io.h       | 72 --------------------------------------------------
 14 files changed, 165 insertions(+), 232 deletions(-)

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