[med-svn] [kraken] branch upstream updated (54160fe -> 1e43ce8)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository kraken.

      from  54160fe   Imported Upstream version 0.10.5~beta
       new  1e43ce8   New upstream version 1.0

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:
 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(-)
 create mode 100755 scripts/convert_gb_to_fa.pl
 create mode 100755 scripts/lookup_accession_numbers.pl
 create mode 100755 scripts/rsync_from_ncbi.pl
 create mode 100755 scripts/scan_fasta_file.pl
 create mode 100644 src/kmer_estimator.cpp

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