Test zCall Pull Request#4

Open

jigold wants to merge 232 commits intojigold:wtsifrom

wtsi-npg:master

Commits on Jan 25, 2013

Added notes on Git repository structure
Iain Bancarz
committed
Initial commit of src directory
Iain Bancarz
committed
Changed permissions to make executable
Iain Bancarz
committed
Initial commit
Iain Bancarz
committed

Commits on Jan 28, 2013

Added Makefile
Iain Bancarz
committed

Commits on Jan 29, 2013

Extensive refactoring, additional help text, added config file
Iain Bancarz
committed
Renamed calibration.py
Iain Bancarz
committed
Renamed to calibrationFromEGT.py
Iain Bancarz
committed
Validate arguments from argparse module and run on multiple zscores
Iain Bancarz
committed
Added 'config' command-line option
Iain Bancarz
committed
Initial commit
Iain Bancarz
committed
Install etc directory and .ini files
Iain Bancarz
committed
Exit if no PREFIX given for installation
Iain Bancarz
committed
Minor edits to git section
Iain Bancarz
committed
force recompiling of any .pyc files on install
Iain Bancarz
committed
Initial commit of new classes to evaluate concordance
Iain Bancarz
committed

Commits on Jan 30, 2013

Renamed and updated
Iain Bancarz
committed
Change verbose output, and skip existing threshold files
Iain Bancarz
committed
Extensive refactoring for concordance evaluation
Iain Bancarz
committed

Commits on Jan 31, 2013

Initial commit
Iain Bancarz
committed

Commits on Feb 4, 2013

Added headers to output file, --force option, reflect argument changes to other classes
Iain Bancarz
committed
bug fix in concordance counts; return inclusion rates only once
Iain Bancarz
committed
Add --force option to ensure overwrite
Iain Bancarz
committed

Commits on Feb 5, 2013

Added gain statistic
Iain Bancarz
committed
Edited comments
Iain Bancarz
committed
Added 'best z' calculation; minor refactoring
Iain Bancarz
committed
Added pydoc strings
Iain Bancarz
committed

Commits on Feb 13, 2013

Removed findConcordance, merged functionality into findMultipleConcordances; edited comments
Iain Bancarz
committed
fixed email address
Iain Bancarz
committed
Moved to new 'legacy' directory
Iain Bancarz
committed
Moved to new 'legacy' directory
Iain Bancarz
committed
Collect calibration/evaluation classes into a combined module
Iain Bancarz
committed
Moved classes into calibration.py, leaving script front-end
Iain Bancarz
committed
renamed as writeThresholdFiles.py
Iain Bancarz
committed

Commits on Feb 15, 2013

Edited comments
Iain Bancarz
committed
Change to .json input of GTC paths for calibration
Iain Bancarz
committed

Commits on Feb 18, 2013

Added getTotalSNPs method
Iain Bancarz
committed

Commits on Feb 19, 2013

Renamed
Iain Bancarz
committed
Renamed to evaluate.py
Iain Bancarz
committed
Initial commit
Iain Bancarz
committed
Modified to use ThresholdContainer
Iain Bancarz
committed

Commits on Feb 20, 2013

Extensive rewrite to support pipeline workflows
Iain Bancarz
committed
Corrected initial shebang line
Iain Bancarz
committed
Changed to use ThresholdContainer class
Iain Bancarz
committed
Modified to use SampleEvaluator class
Iain Bancarz
committed
Initial commit
Iain Bancarz
committed
Renamed/deleted files
Iain Bancarz
committed

Commits on Feb 22, 2013

Renamed
Iain Bancarz
committed
Renamed and added ThresholdContainer class
Iain Bancarz
committed
Deleted (contents moved into utilities.py)
Iain Bancarz
committed
Renamed
Iain Bancarz
committed

Commits on Feb 26, 2013

Update description and import statements
Iain Bancarz
committed
Edited comments
Iain Bancarz
committed
Edited argument description & updated imports
Iain Bancarz
committed
MetricEvaluator now has 1 output file instead of 2; edited comments
Iain Bancarz
committed
Initial commit
Iain Bancarz
committed
Removed unnecessary callsToStrings method
Iain Bancarz
committed
Renamed
Iain Bancarz
committed
Added getInputPath method
Iain Bancarz
committed
Moved constants/functions into SharedBase class and modified SampleEvaluator run method
Iain Bancarz
committed
Changed argument description
Iain Bancarz
committed
Write threshold .json index; modified import statements
Iain Bancarz
committed
Added main() method and bugfix in callsToBinary
Iain Bancarz
committed
Added SharedBase class
Iain Bancarz
committed

Commits on Feb 27, 2013

Renamed scripts directory to zcall
Iain Bancarz
committed
Removed .py suffix to prevent module import by pydoc
Iain Bancarz
committed
Renamed findThresholds and findMeanSD; remove unnecessary time import
Iain Bancarz
committed
Initial commit
Iain Bancarz
committed
Added html to ignore list
Iain Bancarz
committed
Initial commit
Iain Bancarz
committed

Commits on Feb 28, 2013

Initial commit of test data
Iain Bancarz
committed
Changed permissions
Iain Bancarz
committed
Initial commit
Iain Bancarz
committed
Added getMD5 function and modified test data locations
Iain Bancarz
committed

Commits on Mar 1, 2013

Fixed bug in merged results comparison
Iain Bancarz
committed
Revised ignore list
Iain Bancarz
committed
Removed excessively large test data files
Iain Bancarz
committed
Initial commit
Iain Bancarz
committed
Added bigdata directory path
Iain Bancarz
committed
Refactored and made more robust; added bigdata directory
Iain Bancarz
committed
Added option to round off threshold outputs in findThresholds
Iain Bancarz
committed
Added comment
Iain Bancarz
committed
Updated paths
Iain Bancarz
committed
Ignore test output directories
Iain Bancarz
committed
Edited comments and added README
Iain Bancarz
committed

Commits on Mar 4, 2013

Find modules dynamically instead of from hard-coded list
Iain Bancarz
committed
Generate html pydoc and install
Iain Bancarz
committed
Add findMeanSD and findThresholds to install list
Iain Bancarz
committed
Renamed
Iain Bancarz
committed

Commits on Mar 6, 2013

Enable start/end indices for list of GTC files
Iain Bancarz
committed
Print duratio
Iain Bancarz
committed
Test start/end indices for evaluation, rename calling script
Iain Bancarz
committed

Commits on Mar 12, 2013

Use JSON instead of .txt for input to evaluation merge
Iain Bancarz
committed
Updated input to merge test
Iain Bancarz
committed

Commits on Mar 14, 2013

Modify sys.path to import BPM module
Iain Bancarz
committed
Added getChromosomes, getPositions methods
Iain Bancarz
committed
Corrected bug in bytestring reversal; added method to sort calls in genomic order; added placeholder for .bim file writer
Iain Bancarz
committed

Commits on Mar 18, 2013

Initial commit
Iain Bancarz
committed
Moved Plink functionality into new PlinkHandler class
Iain Bancarz
committed

Commits on Mar 19, 2013

Added Plink reading functions
Iain Bancarz
committed
Initial commit
Iain Bancarz
committed

Commits on Mar 20, 2013

Minor rewording
Iain Bancarz
committed
Changed .bed file checksum
Iain Bancarz
committed
Edited comment
Iain Bancarz
committed
Changed outputs
Iain Bancarz
committed
Added destination directory argument
Iain Bancarz
committed
Initial commit
Iain Bancarz
committed
Fixed minor output bug
Iain Bancarz
committed
Output plink .bim and .fam
Iain Bancarz
committed
Test additional Plink outputs
Iain Bancarz
committed
Added basic logfile of zcall activity
Iain Bancarz
committed
initial commit of rough draft
Iain Bancarz
committed
Specify output directory and plink prefix as separate command line options
Iain Bancarz
committed

Commits on Mar 21, 2013

Moved loop to find multiple thresholds into ThresholdFinder class.
Iain Bancarz
committed
Improved parsing of start/end arguments
Iain Bancarz
committed
Reading of .json metric list moved from MetricEvaluator into mergeEvaluation.py
Iain Bancarz
committed
Fixed handling of gtc start/end indices; added functionality to support zCallComplete.py
Iain Bancarz
committed
Added functionality; first working version
Iain Bancarz
committed
Changed permissions
Iain Bancarz
committed
Added test for zCallComplete.py, and validatePlink method
Iain Bancarz
committed
Fixed bug in findBestZ (string vs. integer sort) and added verbose mode
Iain Bancarz
committed
Modified checksums and z range for zCallComplete test
Iain Bancarz
committed
Print duration in verbose mode; add verbosity support to finding best Z
Iain Bancarz
committed

Commits on Mar 22, 2013

Moved to main zcall module
Iain Bancarz
committed
Modifed documentation command
Iain Bancarz
committed
Prevent duplication of zcall module docs
Iain Bancarz
committed
Initial commit of convenience script to generate .ped files
Iain Bancarz
committed

Commits on Mar 25, 2013

Moved to legacy
Iain Bancarz
committed
New and simplified README
Iain Bancarz
committed
Fixed typos
Iain Bancarz
committed

Commits on Mar 27, 2013

Tidied up README
Iain Bancarz
committed
Deleted metrics.txt
Iain Bancarz
committed
Use main() method
Iain Bancarz
committed
Moved into zcall module
Iain Bancarz
committed
Remove obsolete code in src/legacy directory
Iain Bancarz
committed
Remove obsolete GTC json paths
Iain Bancarz
committed
Additional tidying
Iain Bancarz
committed
Removed unnecessary test gtc .json files
Iain Bancarz
committed
Modify help text
Iain Bancarz
committed
Modified comments
Iain Bancarz
committed
Changed to a short overview, most content moved to README_prototypes
Iain Bancarz
committed
Initial commit, material was previously in README
Iain Bancarz
committed
Corrected section numbering
Iain Bancarz
committed

Commits on Mar 28, 2013

Moved to README_extended
Iain Bancarz
committed

Commits on Apr 2, 2013

Added choice between binary and non-binary Plink output
Iain Bancarz
committed
Edited and added line breaks
Iain Bancarz
committed
Added line breaks
Iain Bancarz
committed

Commits on Apr 3, 2013

Initial commit
Iain Bancarz
committed
Initial commit
Iain Bancarz
committed
Ignore intermediate LaTeX output
Iain Bancarz
committed
Note on excluding QC failures
Iain Bancarz
committed
Initial entries for exended zcall
Iain Bancarz
committed

Commits on Apr 30, 2013

Changed log path default
Iain Bancarz
committed
Merge pull request #1 from iainrb/devel
Iain Bancarz
committed
Merge pull request #2 from wtsi-npg/devel
Iain Bancarz
committed

Commits on May 2, 2013

Gracefully handle ZeroDivisionError in findMAF
Iain Bancarz
committed

Commits on May 7, 2013

Merge pull request #3 from iainrb/devel
Iain Bancarz
committed
Merge branch 'devel'
Iain Bancarz
committed

Commits on May 14, 2013

If gender code not in .json, default to -9 instead of crashing
Iain Bancarz
committed
Initial commit
Iain Bancarz
committed
Note that gender codes are optional
Iain Bancarz
committed
Added option to write mean metric text
Iain Bancarz
committed

Commits on May 15, 2013

Change help text; bugfix in uri uniqueness check
Iain Bancarz
committed
Output sample count for evaluation in verbose mode
Iain Bancarz
committed
Support text output of mean concordance/gain
Iain Bancarz
committed

Commits on May 17, 2013

Added copyright text
Iain Bancarz
committed

Commits on May 21, 2013

Revise mean/sd sanity checks and heuristic for choosing z score
Iain Bancarz
committed

Commits on May 22, 2013

Initial commit of GPLv3 license
Iain Bancarz
committed
Merge pull request #4 from iainrb/devel
Iain Bancarz
committed
Merge branch 'devel'
Iain Bancarz
committed

Commits on May 29, 2013

Added --profile option to run Python profiler
Iain Bancarz
committed

Commits on May 30, 2013

Add --profile option
Iain Bancarz
committed

Commits on Jun 3, 2013

Convert findMeanSD script to a method in calibration.py
Iain Bancarz
committed
Replaced findThresholds script with method in calibration.py
Iain Bancarz
committed
Split findMeanSD into smaller and more manageable methods
Iain Bancarz
committed
Edited comments
Iain Bancarz
committed

Commits on Jun 4, 2013

Bugfix in arguments to runMultiple
Iain Bancarz
committed
Write profile output to file
Iain Bancarz
committed
Removed obsolete scripts
Iain Bancarz
committed

Commits on Jun 5, 2013

Write pstats to named temporary file (pasted from cython branch)
Iain Bancarz
committed

Commits on Jun 7, 2013

Added option to activate profiling by default in config.ini
Iain Bancarz
committed

Commits on Jun 12, 2013

Removed cython imports, previously added in error
Iain Bancarz
committed

Commits on Jun 17, 2013

Commits on Jun 18, 2013

Bugfix for output array length in callsToBinary
Iain Bancarz
committed

Commits on Jun 19, 2013

Fix minor bug in handling --text argument with profiler
Iain Bancarz
committed
Changed copyright notice for multiple authors
Iain Bancarz
committed

Commits on Jun 20, 2013

Use class in utilities.py for generic argument validation
Iain Bancarz
committed
Merge pull request #5 from iainrb/devel
Iain Bancarz
committed
Merge branch 'devel'
Iain Bancarz
committed

Commits on Jun 21, 2013

Bugfix for profile args
Iain Bancarz
committed
Print additional information on JSON parse error
Iain Bancarz
committed
Merge pull request #6 from iainrb/devel
Iain Bancarz
committed
Merge pull request #7 from wtsi-npg/devel
Iain Bancarz
committed

Commits on Jun 25, 2013

Moved some plink functionality to the plinktools module
Iain Bancarz
committed

Commits on Jul 2, 2013

Merge pull request #8 from iainrb/devel
Iain Bancarz
committed
Merge branch 'devel'
Iain Bancarz
committed

Commits on Sep 23, 2013

Initial commit
Iain Bancarz
committed
Updated Rscript path to 0.3.0; works on both farm2 and farm3
Iain Bancarz
committed
Updatd prerequisites
Iain Bancarz
committed
Check for NaN/INF values and assign no-call if found
Iain Bancarz
committed
Change ImportError message
Iain Bancarz
committed

Commits on Oct 2, 2013

Catch ZeroDivisionError in normalization
Iain Bancarz
committed
Changed error message
Iain Bancarz
committed
Merge pull request #9 from iainrb/devel
Iain Bancarz
committed

Commits on Nov 6, 2013

Initial commit
Iain Bancarz
committed

Commits on Nov 8, 2013

Implement normalization to Illumina TOP strand
Iain Bancarz
committed

Commits on Jan 6, 2014

Added markdown for headings
Iain Bancarz
committed
Renamed
Iain Bancarz
committed
Added markdown
Iain Bancarz
committed
Renamed
Iain Bancarz
committed
Add tearDown() to delete test output; update checksums for non-normalized manifest
Iain Bancarz
committed
Remove manifest normalization
Iain Bancarz
committed
Deleted
Iain Bancarz
committed
Add subsection on strand normalization
Iain Bancarz
committed

Commits on Jan 7, 2014

Edited comments
Iain Bancarz
committed
Minor edits to README docs
Iain Bancarz
committed
fixed typos
Iain Bancarz
committed
Fixed typos and list of scripts
Iain Bancarz
committed
Merge pull request #10 from iainrb/devel
Iain Bancarz
committed

Commits on Jan 8, 2014

Announce deletion of output directory to stdout
Iain Bancarz
committed

Commits on Jan 30, 2014

Bugfix; correct number of no-calls for padding to integer number of bytes
Iain Bancarz
committed
Updated locations of test data
Iain Bancarz
committed
Added test of zCallComplete.py with alternate manifest
Iain Bancarz
committed
Initial commit
Iain Bancarz
committed
Merge pull request #11 from iainrb/devel
Keith James
committed

Commits on Jan 31, 2014

Merge pull request #13 from wtsi-npg/release-0.4.4
Iain Bancarz
committed

Commits on Mar 25, 2014

Updated test data and changed data location
iainrb
committed

Commits on Mar 27, 2014

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

Commits on Mar 28, 2014

Allow user to configure representation of missing data in Plink .fam output
iainrb
committed
Merge pull request #14 from iainrb/devel
Keith James
committed
Merge pull request #16 from wtsi-npg/release-0.4.5
Iain Bancarz
committed