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Test zCall Pull Request#4

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jigold wants to merge 232 commits intojigold:wtsijigold/zCall:wtsifrom wtsi-npg:masterwtsi-npg/zCall:masterCopy head branch name to clipboard

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Commits on Jan 25, 2013

• Added notes on Git repository structure

  

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• Initial commit of src directory

  

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• Changed permissions to make executable

  

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• Initial commit

  

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Commits on Jan 28, 2013

• Added Makefile

  

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Commits on Jan 29, 2013

• Extensive refactoring, additional help text, added config file

  

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• Renamed calibration.py

  

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• Renamed to calibrationFromEGT.py

  

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• Validate arguments from argparse module and run on multiple zscores

  

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• Added 'config' command-line option

  

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• Initial commit

  

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• Install etc directory and .ini files

  

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• Exit if no PREFIX given for installation

  

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• Minor edits to git section

  

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• force recompiling of any .pyc files on install

  

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• Initial commit of new classes to evaluate concordance

  

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Commits on Jan 30, 2013

• Renamed and updated

  

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• Change verbose output, and skip existing threshold files

  

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• Extensive refactoring for concordance evaluation

  

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Commits on Jan 31, 2013

• Initial commit

  

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Commits on Feb 4, 2013

• Added headers to output file, --force option, reflect argument changes to other classes

  

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• bug fix in concordance counts; return inclusion rates only once

  

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• Add --force option to ensure overwrite

  

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Commits on Feb 5, 2013

• Added gain statistic

  

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• Edited comments

  

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• Added 'best z' calculation; minor refactoring

  

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• Added pydoc strings

  

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Commits on Feb 13, 2013

• Removed findConcordance, merged functionality into findMultipleConcordances; edited comments

  

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• fixed email address

  

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• Moved to new 'legacy' directory

  

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• Moved to new 'legacy' directory

  

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• Collect calibration/evaluation classes into a combined module

  

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• Moved classes into calibration.py, leaving script front-end

  

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• renamed as writeThresholdFiles.py

  

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Commits on Feb 15, 2013

• Edited comments

  

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• Change to .json input of GTC paths for calibration

  

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Commits on Feb 18, 2013

• Added getTotalSNPs method

  

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Commits on Feb 19, 2013

• Renamed

  

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• Renamed to evaluate.py

  

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• Initial commit

  

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• Modified to use ThresholdContainer

  

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Commits on Feb 20, 2013

• Extensive rewrite to support pipeline workflows

  

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• Corrected initial shebang line

  

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• Changed to use ThresholdContainer class

  

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• Modified to use SampleEvaluator class

  

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• Initial commit

  

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• Renamed/deleted files

  

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Commits on Feb 22, 2013

• Renamed

  

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• Renamed and added ThresholdContainer class

  

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• Deleted (contents moved into utilities.py)

  

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• Renamed

  

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Commits on Feb 26, 2013

• Update description and import statements

  

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• Edited comments

  

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• Edited argument description & updated imports

  

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• MetricEvaluator now has 1 output file instead of 2; edited comments

  

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• Initial commit

  

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• Removed unnecessary callsToStrings method

  

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• Renamed

  

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• Added getInputPath method

  

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• Moved constants/functions into SharedBase class and modified SampleEvaluator run method

  

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• Changed argument description

  

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• Write threshold .json index; modified import statements

  

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• Added main() method and bugfix in callsToBinary

  

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• Added SharedBase class

  

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Commits on Feb 27, 2013

• Renamed scripts directory to zcall

  

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• Removed .py suffix to prevent module import by pydoc

  

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• Renamed findThresholds and findMeanSD; remove unnecessary time import

  

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• Initial commit

  

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• Added html to ignore list

  

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• Initial commit

  

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Commits on Feb 28, 2013

• Initial commit of test data

  

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• Changed permissions

  

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• Initial commit

  

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• Added getMD5 function and modified test data locations

  

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Commits on Mar 1, 2013

• Fixed bug in merged results comparison

  

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• Revised ignore list

  

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• Removed excessively large test data files

  

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• Initial commit

  

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• Added bigdata directory path

  

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• Refactored and made more robust; added bigdata directory

  

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• Added option to round off threshold outputs in findThresholds

  

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• Added comment

  

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• Updated paths

  

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• Ignore test output directories

  

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• Edited comments and added README

  

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Commits on Mar 4, 2013

• Find modules dynamically instead of from hard-coded list

  

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• Generate html pydoc and install

  

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• Add findMeanSD and findThresholds to install list

  

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• Renamed

  

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Commits on Mar 6, 2013

• Enable start/end indices for list of GTC files

  

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• Print duratio

  

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• Test start/end indices for evaluation, rename calling script

  

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Commits on Mar 12, 2013

• Use JSON instead of .txt for input to evaluation merge

  

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• Updated input to merge test

  

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Commits on Mar 14, 2013

• Modify sys.path to import BPM module

  

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• Added getChromosomes, getPositions methods

  

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• Corrected bug in bytestring reversal; added method to sort calls in genomic order; added placeholder for .bim file writer

  

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Commits on Mar 18, 2013

• Initial commit

  

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• Moved Plink functionality into new PlinkHandler class

  

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Commits on Mar 19, 2013

• Added Plink reading functions

  

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• Initial commit

  

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Commits on Mar 20, 2013

• Minor rewording

  

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• Changed .bed file checksum

  

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• Edited comment

  

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• Changed outputs

  

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• Added destination directory argument

  

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• Initial commit

  

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• Fixed minor output bug

  

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• Output plink .bim and .fam

  

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• Test additional Plink outputs

  

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• Added basic logfile of zcall activity

  

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• initial commit of rough draft

  

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• Specify output directory and plink prefix as separate command line options

  

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Commits on Mar 21, 2013

• Moved loop to find multiple thresholds into ThresholdFinder class.

  

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• Improved parsing of start/end arguments

  

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• Reading of .json metric list moved from MetricEvaluator into mergeEvaluation.py

  

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• Fixed handling of gtc start/end indices; added functionality to support zCallComplete.py

  

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• Added functionality; first working version

  

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• Changed permissions

  

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• Added test for zCallComplete.py, and validatePlink method

  

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• Fixed bug in findBestZ (string vs. integer sort) and added verbose mode

  

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• Modified checksums and z range for zCallComplete test

  

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• Print duration in verbose mode; add verbosity support to finding best Z

  

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Commits on Mar 22, 2013

• Moved to main zcall module

  

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• Modifed documentation command

  

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• Prevent duplication of zcall module docs

  

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• Initial commit of convenience script to generate .ped files

  

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Commits on Mar 25, 2013

• Moved to legacy

  

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• New and simplified README

  

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• Fixed typos

  

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Commits on Mar 27, 2013

• Tidied up README

  

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• Deleted metrics.txt

  

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• Use main() method

  

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• Moved into zcall module

  

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• Remove obsolete code in src/legacy directory

  

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• Remove obsolete GTC json paths

  

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• Additional tidying

  

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• Removed unnecessary test gtc .json files

  

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• Modify help text

  

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• Modified comments

  

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• Changed to a short overview, most content moved to README_prototypes

  

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• Initial commit, material was previously in README

  

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• Corrected section numbering

  

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Commits on Mar 28, 2013

• Moved to README_extended

  

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Commits on Apr 2, 2013

• Added choice between binary and non-binary Plink output

  

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• Edited and added line breaks

  

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• Added line breaks

  

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Commits on Apr 3, 2013

• Initial commit

  

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• Initial commit

  

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• Ignore intermediate LaTeX output

  

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• Note on excluding QC failures

  

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• Initial entries for exended zcall

  

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Commits on Apr 30, 2013

• Changed log path default

  

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• Merge pull request #1 from iainrb/devel

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• Merge pull request #2 from wtsi-npg/devel

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Commits on May 2, 2013

• Gracefully handle ZeroDivisionError in findMAF

  

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Commits on May 7, 2013

• Merge pull request #3 from iainrb/devel

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• Merge branch 'devel'

  

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Commits on May 14, 2013

• If gender code not in .json, default to -9 instead of crashing

  

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• Initial commit

  

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• Note that gender codes are optional

  

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• Added option to write mean metric text

  

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Commits on May 15, 2013

• Change help text; bugfix in uri uniqueness check

  

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• Output sample count for evaluation in verbose mode

  

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• Support text output of mean concordance/gain

  

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Commits on May 17, 2013

• Added copyright text

  

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Commits on May 21, 2013

• Revise mean/sd sanity checks and heuristic for choosing z score

  

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Commits on May 22, 2013

• Initial commit of GPLv3 license

  

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• Merge pull request #4 from iainrb/devel

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• Merge branch 'devel'

  

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Commits on May 29, 2013

• Added --profile option to run Python profiler

  

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Commits on May 30, 2013

• Add --profile option

  

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Commits on Jun 3, 2013

• Convert findMeanSD script to a method in calibration.py

  

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• Replaced findThresholds script with method in calibration.py

  

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• Split findMeanSD into smaller and more manageable methods

  

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• Edited comments

  

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Commits on Jun 4, 2013

• Bugfix in arguments to runMultiple

  

  Iain Bancarz

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• Write profile output to file

  

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• Removed obsolete scripts

  

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Commits on Jun 5, 2013

• Write pstats to named temporary file (pasted from cython branch)

  

  Iain Bancarz

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Commits on Jun 7, 2013

• Added option to activate profiling by default in config.ini

  

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Commits on Jun 12, 2013

• Removed cython imports, previously added in error

  

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Commits on Jun 17, 2013

• Replace 'for range' with 'while' and list append with assignment, for greater efficiency

  

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• Replace 'for range' with 'while', list append with assignment, and file with StringIO, for greater efficiency

  

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Commits on Jun 18, 2013

• Bugfix for output array length in callsToBinary

  

  Iain Bancarz

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Commits on Jun 19, 2013

• Fix minor bug in handling --text argument with profiler

  

  Iain Bancarz

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• Changed copyright notice for multiple authors

  

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Commits on Jun 20, 2013

• Use class in utilities.py for generic argument validation

  

  Iain Bancarz

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• Merge pull request #5 from iainrb/devel

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• Merge branch 'devel'

  

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Commits on Jun 21, 2013

• Bugfix for profile args

  

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• Print additional information on JSON parse error

  

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• Merge pull request #6 from iainrb/devel

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• Merge pull request #7 from wtsi-npg/devel

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Commits on Jun 25, 2013

• Moved some plink functionality to the plinktools module

  

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Commits on Jul 2, 2013

• Merge pull request #8 from iainrb/devel

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• Merge branch 'devel'

  

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Commits on Sep 23, 2013

• Initial commit

  

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• Updated Rscript path to 0.3.0; works on both farm2 and farm3

  

  Iain Bancarz

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• Updatd prerequisites

  

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• Check for NaN/INF values and assign no-call if found

  

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• Change ImportError message

  

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Commits on Oct 2, 2013

• Catch ZeroDivisionError in normalization

  

  Iain Bancarz

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• Changed error message

  

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• Merge pull request #9 from iainrb/devel

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Commits on Nov 6, 2013

• Initial commit

  

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Commits on Nov 8, 2013

• Implement normalization to Illumina TOP strand

  

  Iain Bancarz

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Commits on Jan 6, 2014

• Added markdown for headings

  

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• Renamed

  

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• Added markdown

  

  Iain Bancarz

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• Renamed

  

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• Add tearDown() to delete test output; update checksums for non-normalized manifest

  

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• Remove manifest normalization

  

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• Deleted

  

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• Add subsection on strand normalization

  

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Commits on Jan 7, 2014

• Edited comments

  

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• Minor edits to README docs

  

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• fixed typos

  

  Iain Bancarz

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• Fixed typos and list of scripts

  

  Iain Bancarz

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• Merge pull request #10 from iainrb/devel

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Commits on Jan 8, 2014

• Announce deletion of output directory to stdout

  

  Iain Bancarz

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Commits on Jan 30, 2014

• Bugfix; correct number of no-calls for padding to integer number of bytes

  

  Iain Bancarz

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• Updated locations of test data

  

  Iain Bancarz

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• Added test of zCallComplete.py with alternate manifest

  

  Iain Bancarz

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• Initial commit

  

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• Merge pull request #11 from iainrb/devel

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Commits on Jan 31, 2014

• Merge pull request #13 from wtsi-npg/release-0.4.4

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Commits on Mar 25, 2014

• Updated test data and changed data location

  

  iainrb

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Commits on Mar 27, 2014

• Change placeholder value from -9 to 0 in Plink .fam output

  

  iainrb

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Commits on Mar 28, 2014

• Allow user to configure representation of missing data in Plink .fam output

  

  iainrb

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• Merge pull request #14 from iainrb/devel

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• Merge pull request #16 from wtsi-npg/release-0.4.5

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