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Skip empty FASTA sequences, and allow to force taxids #27

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Skip empty FASTA sequences, and allow to force taxids #27

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Commits on Jul 10, 2015

  1. Added .gitignore files

    @fbreitwieser
    fbreitwieser committed Jul 10, 2015
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  2. Skip empty FASTA sequences instead of exiting the program

    @fbreitwieser
    fbreitwieser committed Jul 10, 2015
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  3. Added options -T to force taxid of the sequences, and -v for verbose … 

    …output

When -T is set, for each observed k-mer the taxid of the sequence is set - instead of the
lowest common ancestor of of the sequence taxid and the currently set taxid. This is useful
for setting the taxid of contaminant sequences, which may also be observed in database
genomes, to the contaminant taxid.

-v gives more verbose output
    @fbreitwieser
    fbreitwieser committed Jul 10, 2015
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  4. added comments

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    fbreitwieser committed Jul 10, 2015
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Commits on Sep 17, 2015

  1. update

    @fbreitwieser
    fbreitwieser committed Sep 17, 2015
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Commits on Dec 4, 2015

  1. Added '>kraken:taxid|' header parsing to set_lcas - makes it possible… 

    … to run set_lcas on sequences that were not in the DB build originally
    @fbreitwieser
    fbreitwieser committed Dec 4, 2015
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Commits on Dec 20, 2015

  1. Only report missing kmers when verbose

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    fbreitwieser committed Dec 20, 2015
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Commits on Dec 9, 2016

  1. Use 'find ... -exec cat' instead 'find .. -print0 | xargs -0 cat'

    @fbreitwieser
    fbreitwieser committed Dec 9, 2016
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  2. Allow multiple --db arguments

    @fbreitwieser
    fbreitwieser committed Dec 9, 2016
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Commits on Feb 9, 2017

  1. Count unique k-mers for each taxid

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    fbreitwieser committed Feb 9, 2017
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Commits on Feb 12, 2017

  1. Skip two gi2seqid and seqid2taxid map creation for now

    @fbreitwieser
    fbreitwieser committed Feb 12, 2017
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Commits on Feb 15, 2017

  1. Don't display counts

    @fbreitwieser
    fbreitwieser committed Feb 15, 2017
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  2. Fix Makefile

    @fbreitwieser
    fbreitwieser committed Feb 15, 2017
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  3. Added taxdb from k-SLAM for writing report after classification

    @fbreitwieser
    fbreitwieser committed Feb 15, 2017
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Commits on Feb 16, 2017

  1. Build report and taxDB in Kraken

    @fbreitwieser
    fbreitwieser committed Feb 16, 2017
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Commits on Feb 18, 2017

  1. Allow compressed output, and fix report file generation

    @fbreitwieser
    fbreitwieser committed Feb 18, 2017
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Commits on Feb 20, 2017

  1. Don't use nodes file in classify

    @fbreitwieser
    fbreitwieser committed Feb 20, 2017
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Commits on Feb 21, 2017

  1. Added generate-taxonomy-ids-for-sequences and typed TaxonomyDB

    @fbreitwieser
    fbreitwieser committed Feb 21, 2017
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  2. Use less critical pragma - better parallelization

    @fbreitwieser
    fbreitwieser committed Feb 21, 2017
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Commits on Feb 22, 2017

  1. Fix for using multiple databases for search

    @fbreitwieser
    fbreitwieser committed Feb 22, 2017
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  2. Update README.md

    @fbreitwieser
    fbreitwieser authored Feb 22, 2017
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Commits on Apr 12, 2017

  1. Do not need taxonomy nodes anymore

    @fbreitwieser
    fbreitwieser committed Apr 12, 2017
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  2. Check if there's a taxonomy entry

    @fbreitwieser
    fbreitwieser committed Apr 12, 2017
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  3. Merge branch 'taxid-bitmap' of https://github.com/fbreitwieser/kraken … 

    …into taxid-bitmap

Conflicts:
	src/taxdb.h
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    fbreitwieser committed Apr 12, 2017
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  4. Merge branch 'master' of https://github.com/fbreitwieser/kraken

    @fbreitwieser
    fbreitwieser committed Apr 12, 2017
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  5. Use template for ReadCounts

    @fbreitwieser
    fbreitwieser committed Apr 12, 2017
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  6. Merge branch 'taxid-bitmap'

    @fbreitwieser
    fbreitwieser committed Apr 12, 2017
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  7. Renamed to kraken_hll

    @fbreitwieser
    fbreitwieser committed Apr 12, 2017
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  8. Fixed building of kraken_hll

    @fbreitwieser
    fbreitwieser committed Apr 12, 2017
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  9. Update README.md

    @fbreitwieser
    fbreitwieser authored Apr 12, 2017
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  10. Show numer of unique k-mers

    @fbreitwieser
    fbreitwieser committed Apr 12, 2017
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Commits on May 4, 2017

  1. Start all scripts with kraken_hll

    @fbreitwieser
    fbreitwieser committed May 4, 2017
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  2. Refactor TaxonomyDB constructor

    @fbreitwieser
    fbreitwieser committed May 4, 2017
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  3. Build taxdb in the end

    @fbreitwieser
    fbreitwieser committed May 4, 2017
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  4. Update build_taxdb.cpp

    @fbreitwieser
    fbreitwieser committed May 4, 2017
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Commits on May 5, 2017

  1. Include number of k-mers in database in taxDB

    @fbreitwieser
    fbreitwieser committed May 5, 2017
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Commits on May 7, 2017

  1. Update to read columns

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    fbreitwieser committed May 7, 2017
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Commits on Aug 13, 2017

  1. Added taxdb.cpp

    @fbreitwieser
    fbreitwieser committed Aug 13, 2017
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Commits on Aug 25, 2017

  1. Add UID mapping to Kraken-HLL

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    fbreitwieser committed Aug 25, 2017
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Commits on Aug 28, 2017

  1. Renamed to KrakenU

    @fbreitwieser
    fbreitwieser committed Aug 28, 2017
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Commits on Aug 31, 2017

  1. Put version string in separate file

    @fbreitwieser
    fbreitwieser committed Aug 31, 2017
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  2. Fixed script paths

    @fbreitwieser
    fbreitwieser committed Aug 31, 2017
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Commits on Sep 22, 2017

  1. Major update for UID mapping and having taxon entries for assemblies

    @fbreitwieser
    fbreitwieser committed Sep 22, 2017
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Commits on Sep 25, 2017

  1. Updated build script, and add some info when loading database

    @fbreitwieser
    fbreitwieser committed Sep 25, 2017
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  2. Added jellyfish submodule

    @fbreitwieser
    fbreitwieser committed Sep 25, 2017
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  3. specify branch for jellyfish

    @fbreitwieser
    fbreitwieser committed Sep 25, 2017
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  4. Instal jellyfish from code archive

    @fbreitwieser
    fbreitwieser committed Sep 25, 2017
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  5. Update .gitignore

    @fbreitwieser
    fbreitwieser committed Sep 25, 2017
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  6. Use /usr/bin/env

    @fbreitwieser
    fbreitwieser committed Sep 25, 2017
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  7. Much faster krakenu-download using forks and LWP

    @fbreitwieser
    fbreitwieser committed Sep 25, 2017
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  8. Add test files

    @fbreitwieser
    fbreitwieser committed Sep 25, 2017
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Commits on Sep 28, 2017

  1. Added files for automated tests

    @fbreitwieser
    fbreitwieser committed Sep 28, 2017
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  2. Added OSX files

    @fbreitwieser
    fbreitwieser committed Sep 28, 2017
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  3. Fix jellyfish installation - don't use make install

    @fbreitwieser
    fbreitwieser committed Sep 28, 2017
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  4. Add parameters --library-dir and --taxonomy-dir

    @fbreitwieser
    fbreitwieser committed Sep 28, 2017
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  5. Look for locally installed jellyfish, first

    @fbreitwieser
    fbreitwieser committed Sep 28, 2017
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  6. Add slurp_file for file reading - fix for OSX

    @fbreitwieser
    fbreitwieser committed Sep 28, 2017
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  7. Added classification rater (not working yet)

    @fbreitwieser
    fbreitwieser committed Sep 28, 2017
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Commits on Sep 30, 2017

  1. Allow multiple library directories on command line

    @fbreitwieser
    fbreitwieser committed Sep 30, 2017
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  2. Update on tests

    @fbreitwieser
    fbreitwieser committed Sep 30, 2017
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Commits on Oct 1, 2017

  1. Added script to dump taxDB to NCBI dump format

    @fbreitwieser
    fbreitwieser committed Oct 1, 2017
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  2. Added dusting and 'standard' db to testing

    @fbreitwieser
    fbreitwieser committed Oct 1, 2017
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  3. Make building work for OSX and Linux

    @fbreitwieser
    fbreitwieser committed Oct 1, 2017
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  4. Fixes for building and downloading

    @fbreitwieser
    fbreitwieser committed Oct 1, 2017
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  5. Fixed contaminants download

    @fbreitwieser
    fbreitwieser committed Oct 1, 2017
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  6. Fix for Linux/OSX building

    @fbreitwieser
    fbreitwieser committed Oct 1, 2017
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  7. Minor speed improvements in classify

    @fbreitwieser
    fbreitwieser committed Oct 1, 2017
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  8. Correct number of arguments

    @fbreitwieser
    fbreitwieser committed Oct 1, 2017
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  9. Ignore taxa not in taxonomy DB

    @fbreitwieser
    fbreitwieser committed Oct 1, 2017
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  10. Add comments

    @fbreitwieser
    fbreitwieser committed Oct 1, 2017
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  11. Update to read sim

    @fbreitwieser
    fbreitwieser committed Oct 1, 2017
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  12. Update to read sim

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    fbreitwieser committed Oct 1, 2017
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  13. Merge branch 'master' of https://github.com/fbreitwieser/kraken-hll 

    * 'master' of https://github.com/fbreitwieser/kraken-hll:
  Update to read sim
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Commits on Oct 2, 2017

  1. Various improvements and fixes for building and classification

    @fbreitwieser
    fbreitwieser committed Oct 2, 2017
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  2. Special treatment for host and conaminant taxids

    @fbreitwieser
    fbreitwieser committed Oct 2, 2017
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  3. Added build

    @fbreitwieser
    fbreitwieser committed Oct 2, 2017
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  4. Add new columns

    @fbreitwieser
    fbreitwieser committed Oct 2, 2017
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  5. Up default precision to 12

    @fbreitwieser
    fbreitwieser committed Oct 2, 2017
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  6. use unordered maps

    @fbreitwieser
    fbreitwieser committed Oct 2, 2017
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  7. Merge branch 'master' of https://github.com/fbreitwieser/kraken-hll 

    * 'master' of https://github.com/fbreitwieser/kraken-hll:
  Various improvements and fixes for building and classification
  Update to read sim
  Update to read sim
  Add comments
  Ignore taxa not in taxonomy DB
  Correct number of arguments
  Minor speed improvements in classify
  Fix for Linux/OSX building

Conflicts:
	src/set_lcas.cpp
	tests/build-dbs.sh
    @fbreitwieser
    fbreitwieser committed Oct 2, 2017
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  8. Check library directories exist

    @fbreitwieser
    fbreitwieser committed Oct 2, 2017
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  9. Merge branch 'master' of https://github.com/fbreitwieser/kraken-hll 

    * 'master' of https://github.com/fbreitwieser/kraken-hll:
  use unordered maps
  Up default precision to 12
  Add new columns
    @fbreitwieser
    fbreitwieser committed Oct 2, 2017
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  10. Use uid_mapping headers

    @fbreitwieser
    fbreitwieser committed Oct 2, 2017
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  11. Merge branch 'master' of https://github.com/fbreitwieser/kraken-hll 

    * 'master' of https://github.com/fbreitwieser/kraken-hll:
  Use uid_mapping headers
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    fbreitwieser committed Oct 2, 2017
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  12. update init.sh

    @fbreitwieser
    fbreitwieser committed Oct 2, 2017
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  13. Fix bug in reading names and nodes

    @fbreitwieser
    fbreitwieser committed Oct 2, 2017
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Commits on Oct 18, 2017

  1. Dump taxdb without ending separators (for kraken-report)

    @fbreitwieser
    fbreitwieser committed Oct 18, 2017
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  2. Allow to run build_taxdb with a taxdb as consistency check

    @fbreitwieser
    fbreitwieser committed Oct 18, 2017
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  3. Update to classification grading

    @fbreitwieser
    fbreitwieser committed Oct 18, 2017
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  4. Do not give separate taxids for human sequences (fixed now)

    @fbreitwieser
    fbreitwieser committed Oct 18, 2017
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  5. Add species subgroup and group ranks

    @fbreitwieser
    fbreitwieser committed Oct 18, 2017
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  6. Don't use .at() for vector access

    @fbreitwieser
    fbreitwieser committed Oct 18, 2017
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  7. Test modification of lca

    @fbreitwieser
    fbreitwieser committed Oct 18, 2017
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  8. Merge branch 'master' of https://github.com/fbreitwieser/kraken-hll 

    * 'master' of https://github.com/fbreitwieser/kraken-hll:
  Dump taxdb without ending separators (for kraken-report)
    @fbreitwieser
    fbreitwieser committed Oct 18, 2017
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Commits on Oct 23, 2017

  1. Update

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    fbreitwieser committed Oct 23, 2017
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Commits on Oct 25, 2017

  1. Update

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    fbreitwieser committed Oct 25, 2017
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  2. Many small changes to make it working for GCC 4.4 / C++0x

    @fbreitwieser
    fbreitwieser committed Oct 25, 2017
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Commits on Nov 5, 2017

  1. Make sure TaxDB is not copied

    @fbreitwieser
    fbreitwieser committed Nov 5, 2017
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  2. Fox parent map generation in taxDB

    @fbreitwieser
    fbreitwieser committed Nov 5, 2017
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  3. Add environment CPPFLAGS and LDFLAGS

    @fbreitwieser
    fbreitwieser committed Nov 5, 2017
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Commits on Nov 6, 2017

  1. Change name to KrakenHLL

    @fbreitwieser
    fbreitwieser committed Nov 6, 2017
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Commits on Nov 7, 2017

  1. Change name to KrakenHLL

    @fbreitwieser
    fbreitwieser committed Nov 7, 2017
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Commits on Nov 8, 2017

  1. Update

    @fbreitwieser
    fbreitwieser committed Nov 8, 2017
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  2. Merge branch 'master' of https://github.com/fbreitwieser/kraken-hll 

    * 'master' of https://github.com/fbreitwieser/kraken-hll:
  Change name to KrakenHLL
  Add environment CPPFLAGS and LDFLAGS
  Fox parent map generation in taxDB
  Make sure TaxDB is not copied
  Many small changes to make it working for GCC 4.4 / C++0x

Conflicts:
	tests/build-dbs.sh
    @fbreitwieser
    fbreitwieser committed Nov 8, 2017
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  3. Create taxDB if not present

    @fbreitwieser
    fbreitwieser committed Nov 8, 2017
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  4. Compute k-mer counts if not present

    @fbreitwieser
    fbreitwieser committed Nov 8, 2017
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  5. Merge branch 'master' of https://github.com/fbreitwieser/kraken-hll 

    * 'master' of https://github.com/fbreitwieser/kraken-hll:
  Update
  Change name to KrakenHLL

Conflicts:
	install_kraken.sh
	tests/build-dbs.sh
	tests/test-on-simulated-reads.sh
    @fbreitwieser
    fbreitwieser committed Nov 8, 2017
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  6. Fix indent

    @fbreitwieser
    fbreitwieser committed Nov 8, 2017
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  7. Merge branch 'master' of https://github.com/fbreitwieser/kraken-hll 

    * 'master' of https://github.com/fbreitwieser/kraken-hll:
  Compute k-mer counts if not present
  Create taxDB if not present
  Update
  Change name to KrakenHLL
    @fbreitwieser
    fbreitwieser committed Nov 8, 2017
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Commits on Nov 9, 2017

  1. Fix gzstream compilation, update on HLL

    @fbreitwieser
    fbreitwieser committed Nov 9, 2017
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  2. Fix gzstream building and licensing

    @fbreitwieser
    fbreitwieser committed Nov 9, 2017
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  3. Fix licensing

    @fbreitwieser
    fbreitwieser committed Nov 9, 2017
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  4. Merge branch 'master' of https://github.com/fbreitwieser/kraken-hll 

    * 'master' of https://github.com/fbreitwieser/kraken-hll:
  Fix gzstream building and licensing
  Fix gzstream compilation, update on HLL

Conflicts:
	src/hyperloglogplus.h
    @fbreitwieser
    fbreitwieser committed Nov 9, 2017
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  5. Fix taxonomy reporting order and percentage

    @fbreitwieser
    fbreitwieser committed Nov 9, 2017
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Commits on Nov 10, 2017

  1. Fixed HLL bug introduced by using vector for sparse representation

    @fbreitwieser
    fbreitwieser committed Nov 10, 2017
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  2. Fix Makefile

    @fbreitwieser
    fbreitwieser committed Nov 10, 2017
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Commits on Nov 11, 2017

  1. Allow setting custom precision

    @fbreitwieser
    fbreitwieser committed Nov 11, 2017
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