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Apr 17, 2014

  1. Fix an issue in option --kmer-both-strand in sga filter: the command …

    …line option was not properly parse and set in the code
    authored April 17, 2014
  2. Merge branch 'master' of https://github.com/pradosj/sga

    authored April 17, 2014
  3. Add option --kmer-both-strand in sga filter, useful to filter out Ill…

    …umina reads having sequencing errors on one strand only
    authored April 17, 2014

Apr 11, 2014

  1. Jared Simpson

    Support reading from stdin in preprocess

    authored April 11, 2014

Apr 04, 2014

  1. Jared Simpson

    Merge pull request #70 from deltadev/patches

    sga overlap - "--prefix" option added.
    authored April 04, 2014

Apr 03, 2014

  1. deltadev

    Added --prefix option to sga overlap.

    authored April 03, 2014

Mar 10, 2014

  1. Jared Simpson

    Merge branch 'master' of https://github.com/jts/sga

    authored March 10, 2014
  2. Added AF filter and output file parameter

    authored February 07, 2014 jts committed March 10, 2014
  3. Added new alignment-based filters

    authored January 30, 2014 jts committed March 10, 2014
  4. Added an interactive mode to graphdiff for debugging

    authored January 29, 2014 jts committed March 10, 2014
  5. Jared Simpson

    used htslib instead of vcftools

    authored August 29, 2013
  6. Jared Simpson

    new options to variant-filters

    Conflicts:
    
    	src/bin/sga-variant-filters.pl
    authored March 10, 2014

Mar 05, 2014

  1. Jared Simpson

    index: Only allow one of -a or -d to defined. Closes #67

    authored March 05, 2014
  2. Jared Simpson

    preqc: added mode to quickly output basic read stats. Closes #64

    authored March 05, 2014

Mar 03, 2014

  1. Jared Simpson

    Merge pull request #68 from deltadev/sga-preqc-py-patch

    Made sga-preqc-report.py deal with bad json gracefully.
    authored March 03, 2014
  2. deltadev

    Made sga-preqc-report.py deal with bad json gracefully.

    authored March 03, 2014

Feb 27, 2014

  1. deltadev

    .gitignored SGA/sga.

    authored February 27, 2014
  2. deltadev

    Added some more build files to .gitignore.

    Also added config.h to .gitignore. This is platform specific so should
    prob. not be in vc either.
    authored February 27, 2014

Jan 17, 2014

  1. Jared Simpson

    v0.10.13

    authored January 17, 2014
  2. Jared Simpson

    Fix blank GC plot, remove unused plots

    authored January 17, 2014

Jan 06, 2014

  1. Jared Simpson

    Merge branch 'master' of git://github.com/travc/sga into travc-master

    authored January 06, 2014
  2. Jared Simpson

    Added a --enable-development flag to configure

    This flag will turn on -Werror to avoid compilation failures for users
    authored January 06, 2014

Dec 24, 2013

  1. travc

    sga-preqc-report.py : Fixed issue with matplotlib backend wanting a d…

    …isplay
    authored December 23, 2013
  2. travc

    sga-preqc-report.py Generally restructured so it outputs mutliple plo…

    …ts per page. One plot per page still available with -p option. Also takes -P <plotname> option for specific plots and more.
    authored December 23, 2013
  3. travc

    sga-preqc-report.py Generally restructured so it outputs mutliple plo…

    …ts per page. One plot per page still available with -p option. Also takes -P <plotname> option for specific plots and more.
    authored December 23, 2013
  4. travc

    Merge branch 'master' of https://github.com/travc/sga

    authored December 23, 2013
  5. travc

    sga-preqc-report.py Generally restructured so it outputs mutliple plo…

    …ts per page. One plot per page still available with -p option. Also takes -P <plotname> option for specific plots and more.
    authored December 23, 2013
  6. travc

    Merge branch 'master' of https://github.com/travc/sga

    authored December 23, 2013
  7. travc

    sga-preqc-report.py : Generally restructured so it outputs mutliple p…

    …lots per page. One plot per page still available with -p option. Also takes -P <plotname> option for specific plots and more.
    authored December 23, 2013
  8. travc

    Generally restructured so it outputs mutliple plots per page.

    One plot per page still available with -p option.
    Also takes -P <plotname> option for specific plots and more.
    authored December 23, 2013

Dec 18, 2013

  1. Jared Simpson

    Fix conditions for emitting convergence warning

    authored December 18, 2013
  2. Jared Simpson

    Merge branch 'master' of https://github.com/jts/sga

    authored December 18, 2013
  3. Jared Simpson

    Fix namespace issues and other warnings when compiling with clang

    authored December 18, 2013

Dec 17, 2013

  1. Jared Simpson

    Merge pull request #57 from mr-c/patch-1

    add a hotlink to src/README
    authored December 17, 2013
  2. Michael R. Crusoe

    add a hotlink to src/README

    authored December 16, 2013
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