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Commits on Nov 13, 2017
  1. move fermil-nim here

    brentp committed Nov 13, 2017
Commits on Aug 4, 2017
  1. Merge pull request #20 from cviner/master

    brentp committed Aug 4, 2017
    Modify the output format to ease parsing
  2. Modify the output format:

    cviner committed Aug 4, 2017
    - Change the first column containing the guessed encodings to a
      comma-delimited list. Partially reverts output format changes
      introduced by 95adaa7. Resolves #19 (see discussion in #17).
    
    - Direct the main output to STDOUT, leaving comments or errors on
      STDERR. This was originally intended, but neglected, in 95adaa7.
Commits on Jul 13, 2017
  1. Merge pull request #16 from cviner/master

    brentp committed Jul 13, 2017
    Improved guess-encoding.py code and workflow (quality score heuristics unchanged)
Commits on Jul 12, 2017
  1. Made a number of minor improvements:

    cviner committed Jul 11, 2017
    - Permit input from a file provided as an argument, maintaining the ability to input via STDIN
    - Transparently permit input of a gzipped FASTQ, when provided with a FASTQ filename ending in '.gz'
    - Add useful '__future__' imports
    - Refactor print statements to use the new syntax and use '.format'
    - Enforce PEP8 compliance
    - Change exit code upon error to a non-zero value (1)
    - Minor refactoring, removing redundant traces
    - Add an appropriate shebang
    - Revise internal documentation, adding common use-cases
Commits on Mar 14, 2017
  1. off by 1 and header include

    brentp committed Mar 14, 2017
Commits on Feb 8, 2017
  1. stub out design

    brentp committed Feb 8, 2017
Commits on Feb 7, 2017
  1. 1kg-cnv

    brentp committed Feb 7, 2017
Commits on Jan 12, 2017
  1. Merge pull request #14 from rwanwork/master

    brentp committed Jan 12, 2017
    Added support for Illumina 1.8 data.
  2. Added support for Illumina 1.8 in guess-encoding.py . Also added a

    rwanwork committed Jan 12, 2017
    comment that explains that the maximum possible is actually 126.
Commits on Nov 28, 2016
  1. Merge pull request #13 from JureZmrzlikar/python3

    brentp committed Nov 28, 2016
    Make igv work with python3.
Commits on Nov 5, 2016
Commits on Sep 22, 2016
  1. start of concur

    brentp committed Sep 22, 2016
  2. initial commit of werelate

    brentp committed Sep 22, 2016
Commits on Sep 13, 2016
  1. add splicing to functional

    brentp committed Sep 13, 2016
Commits on Aug 22, 2016
  1. Merge pull request #11 from anarkia7115/patch-1

    brentp committed Aug 22, 2016
    change sanger range from 93 to 73
Commits on Aug 1, 2016
Commits on Jul 28, 2016
  1. add script to filter mosaic candidates to those that are functional (…

    brentp committed Jul 28, 2016
    …assuming VEP was run)
    
    and those that are in low allele freq in ExAC et al (from vcfanno).
Commits on Jul 21, 2016
  1. add mosaic script

    brentp committed Jul 21, 2016
Commits on Aug 7, 2014
  1. filter by QUAL

    brentp committed Aug 7, 2014
Commits on Aug 6, 2014
  1. smash info into first column

    brentp committed Aug 6, 2014
Commits on Aug 5, 2014
Commits on May 31, 2014
  1. Merge pull request #8 from simonohanlon101/patch-1

    brentp committed May 31, 2014
    Updated Sanger quality range
Commits on May 27, 2014
  1. Updated Sanger quality range

    simonohanlon101 committed May 27, 2014
    From the wiki
    
    >Sanger format can encode a Phred quality score from 0 to 93 using ASCII 33 to 126 (although in raw read data the Phred quality score rarely exceeds 60
    
    
    60 + 33 = 93. Using 73 means some high quality Sanger encoded data will not be determined (I had this issue having data with quality scores above 40).
Commits on Apr 11, 2014
Commits on Apr 10, 2014
  1. fix counting

    brentp committed Apr 10, 2014
  2. update readme

    brentp committed Apr 10, 2014
Commits on Nov 26, 2013
  1. add some filtering

    brentp committed Nov 26, 2013
  2. script to merge bed files

    brentp committed Nov 26, 2013
Commits on Jan 10, 2013
Commits on Jan 8, 2013