[med-svn] [bowtie2] branch master updated (5cc8fc5 -> b57d0e7)

[Alex Mestiashvili]

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

      from  5cc8fc5   updated changelog to reflect changes
       new  706918c   Imported Upstream version 2.2.0
       new  b3376d3   Merge tag 'upstream/2.2.0'
       new  e7790b2    - d/changelog: new upstream version 2.2.0  - d/bowtie2.install, d/rules:    new release introduces 2 new binaries: bowtie2-align-l and bowtie2-align-s    instead of bowtie2-align  - d/patches: refreshed
       new  b57d0e7   updated changelog

The 4 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 +-
 debian/bowtie2.install                             |   4 +-
 debian/changelog                                   |  11 +
 .../patches/fix_makefile_machine_detection.patch   |  21 +-
 debian/patches/hardening.patch                     |   2 +-
 debian/patches/series                              |   2 +-
 debian/rules                                       |   5 +-
 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 +-
 74 files changed, 4804 insertions(+), 2120 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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