[med-svn] [bowtie2] branch upstream updated (fa595da -> 706918c)

[Alex Mestiashvili]

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

      from  fa595da   Imported Upstream version 2.1.0
       new  706918c   Imported Upstream version 2.2.0

The 1 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                   | 124 +++++--
 MANUAL.markdown          | 108 ++++--
 Makefile                 | 163 ++++++--
 NEWS                     |  27 +-
 VERSION                  |   2 +-
 aligner_cache.cpp        |  16 +-
 aligner_cache.h          |  77 ++--
 aligner_driver.cpp       | 186 +++++++++-
 aligner_driver.h         |  84 ++++-
 aligner_result.cpp       |   6 +-
 aligner_result.h         |  56 +--
 aligner_seed.cpp         | 112 +++---
 aligner_seed.h           |  77 ++--
 aligner_seed2.cpp        | 355 +++++++++++++-----
 aligner_seed2.h          | 490 +++++++++++++-----------
 aligner_sw.cpp           |  47 ++-
 aligner_sw.h             |  21 +-
 aligner_sw_driver.cpp    | 119 +++---
 aligner_sw_driver.h      |  10 +-
 aln_sink.cpp             | 120 +++---
 aln_sink.h               |  25 +-
 binary_sa_search.h       |  30 +-
 blockwise_sa.h           | 206 +++++-----
 bowtie2                  | 183 ++++++---
 bowtie2-build            |  98 +++++
 bowtie2-inspect          |  74 ++++
 bt2_build.cpp            | 125 +++++--
 bt2_dp.cpp               | 788 +++++++++++++++++++++++++++++++++++++++
 bt2_idx.cpp              |  88 +++--
 bt2_idx.h                | 949 +++++++++++++++++++++++++++++------------------
 bt2_inspect.cpp          |  52 ++-
 bt2_io.cpp               | 401 ++++++++++----------
 bt2_search.cpp           | 120 +++---
 bt2_util.cpp             |  50 +--
 banded.h => btypes.h     |  57 ++-
 diff_sample.h            | 127 +++----
 doc/manual.html          |  34 +-
 dp_framer.h              |   6 +
 ds.h                     |  31 +-
 endian_swap.h            |  52 ++-
 fast_mutex.h             |   0
 filebuf.h                |   4 +-
 group_walk.h             | 230 ++++++------
 ls.h                     |   2 +-
 mm.h                     |   2 +
 multikey_qsort.cpp       |   2 +-
 multikey_qsort.h         |  85 ++---
 opts.h                   |   6 +-
 pat.cpp                  |   6 +
 pat.h                    |  11 +-
 processor_support.h      |  70 ++++
 random_source.h          |  17 +
 random_util.h            |   2 +-
 ref_read.cpp             |  36 +-
 ref_read.h               |  57 ++-
 reference.cpp            | 140 +++----
 reference.h              |  20 +-
 sam.cpp                  |  43 ++-
 sam.h                    |   3 +-
 scripts/infer_fraglen.pl |  29 +-
 scripts/make_e_coli.sh   |   4 +-
 shmem.h                  |   3 +
 sse_util.h               |   5 +
 third_party/cpuid.h      | 187 ++++++++++
 tinythread.cpp           |   0
 tinythread.h             |   0
 word_io.h                | 209 ++++++++---
 zbox.h                   |  10 +-
 68 files changed, 4780 insertions(+), 2099 deletions(-)
 create mode 100755 bowtie2-build
 create mode 100755 bowtie2-inspect
 create mode 100644 bt2_dp.cpp
 copy banded.h => btypes.h (57%)
 mode change 100755 => 100644 fast_mutex.h
 create mode 100644 processor_support.h
 create mode 100644 third_party/cpuid.h
 mode change 100755 => 100644 tinythread.cpp
 mode change 100755 => 100644 tinythread.h

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