[med-svn] [bowtie2] 02/04: Merge tag 'upstream/2.2.0'

[Alex Mestiashvili]

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

commit b3376d3526fa92bb334c5bc966e377e0bc711d59
Merge: 5cc8fc5 706918c
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Thu Feb 20 12:17:27 2014 +0100

    Merge tag 'upstream/2.2.0'
    
    Upstream version 2.2.0

 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 +--
 multikey_qsort.cpp => btypes.h |  30 +-
 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, 4781 insertions(+), 2071 deletions(-)

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