[med-svn] [bowtie2] 02/06: Merge tag 'upstream/2.2.1'

[Alex Mestiashvili]

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malex-guest pushed a commit to branch master
in repository bowtie2.

commit c4f2041f12fc878f6e6ae83403abb1c1fefe01e8
Merge: fc494ca 89ac339
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Fri Mar 7 08:44:20 2014 +0100

    Merge tag 'upstream/2.2.1'
    
    Upstream version 2.2.1

 MANUAL          | 24 ++++++++++-------
 MANUAL.markdown | 32 +++++++++++++++-------
 NEWS            | 18 ++++++++++---
 VERSION         |  2 +-
 bowtie2         | 17 +++++++-----
 bt2_idx.h       | 12 ++++-----
 bt2_io.cpp      | 82 ++++++++++++++++++++-------------------------------------
 bt2_search.cpp  |  6 +++--
 doc/manual.html | 12 +++++++--
 mm.h            | 15 -----------
 ref_read.h      | 13 ---------
 reference.cpp   | 33 +++++++----------------
 word_io.h       | 72 --------------------------------------------------
 13 files changed, 120 insertions(+), 218 deletions(-)

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