[med-svn] [kraken] 02/06: Update upstream source from tag 'upstream/1.0'

[Andreas Tille]

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tille pushed a commit to branch master
in repository kraken.

commit 8c59a8d60a1799dad9124291d16168f5bd767ea0
Merge: 0321be8 1e43ce8
Author: Andreas Tille <tille at debian.org>
Date:   Mon Nov 13 16:33:31 2017 +0100

    Update upstream source from tag 'upstream/1.0'
    
    Update to upstream version '1.0'
    with Debian dir 56229c2206797bd9bd81aaa95fad4c630a757db6

 CHANGELOG                           |   5 ++
 docs/MANUAL.html                    | 116 ++++++++++++++---------------
 docs/MANUAL.markdown                |  60 ++++++++-------
 docs/top.html                       |   2 +-
 install_kraken.sh                   |   7 +-
 scripts/add_to_library.sh           |  34 ++++++---
 scripts/build_kraken_db.sh          |  49 +++++++------
 scripts/convert_gb_to_fa.pl         |  58 +++++++++++++++
 scripts/cp_into_tempfile.pl         |   2 +-
 scripts/download_genomic_library.sh | 120 +++++++++++-------------------
 scripts/download_taxonomy.sh        |  46 +++++-------
 scripts/kraken                      |   2 +-
 scripts/kraken-build                |  10 +--
 scripts/kraken-filter               |   2 +-
 scripts/kraken-mpa-report           |   2 +-
 scripts/kraken-report               |   9 ++-
 scripts/kraken-translate            |   2 +-
 scripts/krakenlib.pm                |  29 +++++++-
 scripts/lookup_accession_numbers.pl |  65 +++++++++++++++++
 scripts/read_merger.pl              |   2 +-
 scripts/report_gi_numbers.pl        |   2 +-
 scripts/rsync_from_ncbi.pl          | 134 ++++++++++++++++++++++++++++++++++
 scripts/scan_fasta_file.pl          |  50 +++++++++++++
 scripts/standard_installation.sh    |   5 +-
 scripts/verify_gi_numbers.pl        |   2 +-
 src/Makefile                        |   4 +-
 src/classify.cpp                    |  22 ++++--
 src/db_shrink.cpp                   |   8 +-
 src/db_sort.cpp                     |   8 +-
 src/kmer_estimator.cpp              | 141 ++++++++++++++++++++++++++++++++++++
 src/set_lcas.cpp                    |  28 +++++--
 31 files changed, 761 insertions(+), 265 deletions(-)

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