[med-svn] [kraken] branch master updated (0321be8 -> 154c9e1)

[Andreas Tille]

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tille pushed a change to branch master
in repository kraken.

      from  0321be8   Upload to unstable
       new  1e43ce8   New upstream version 1.0
       new  8c59a8d   Update upstream source from tag 'upstream/1.0'
       new  cee4a19   New upstream version
       new  65a107d   Adapt patches
       new  afed940   Standards-Version: 4.1.1
       new  154c9e1   Upload to unstable

The 6 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 ++
 debian/changelog                    |   7 ++
 debian/control                      |   2 +-
 debian/patches/kraken_tmp_dir.patch |   2 +-
 debian/patches/use_jellyfish1.patch |  14 ++--
 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 +++++--
 35 files changed, 777 insertions(+), 274 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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