[med-svn] [bowtie2] branch master updated (fc494ca -> a07c983)

[Alex Mestiashvili]

This is an automated email from the git hooks/post-receive script.

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

      from  fc494ca   UNRELEASED->unstable
       new  89ac339   Imported Upstream version 2.2.1
       new  c4f2041   Merge tag 'upstream/2.2.1'
       new  f27a14e   d/changelog: new upstream version, push to unstable d/copyright: updated Copyright years
       new  2eb8a65   Imported Upstream version 2.2.2
       new  9f72f42   Merge tag 'upstream/2.2.2'
       new  a07c983   d/changelog: Imported Upstream version 2.2.2, upload to unstable

The 6 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 +++--
 debian/changelog | 13 +++++++++
 debian/copyright |  4 +--
 doc/manual.html  | 14 +++++++---
 mm.h             | 15 -----------
 ref_read.h       | 13 ---------
 reference.cpp    | 67 ++++++++++++++++++++++++---------------------
 reference.h      |  9 ++++---
 word_io.h        | 72 -------------------------------------------------
 16 files changed, 180 insertions(+), 234 deletions(-)

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