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ChangeLog
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2017-09-03 Yanxiao Zhang <[email protected]>
* version 1.1.19-1.1.21
* bugfixes
* changed read file method. Switch from reading the
left-most position to the read start position.
2017-03-06 Yanxiao Zhang <[email protected]>
* version 1.1.18
* fixed sveral runtime bugs
* Made compatible with python 3x
2016-08-08 Yanxiao Zhang <[email protected]>
* version 1.1.13
* fixed a bug if the bam file read is smaller 1000 reads.
* fixed a bug where 'no' for normalization will not run.
2016-07-14 Yanxiao Zhang <[email protected]>
* version 1.1.13
* added refine peak boundary back to the post-processing module
2016-06-27 Yanxiao Zhang <[email protected]>
* version 1.1.9-1.1.12
* hotfixes
* changes readme.
2016-05-31 Yanxiao Zhang <[email protected]>
* version 1.1.8
* added support for paired-end reads (bam and sam)
* v1.1.9
* check if the paired-end files are sorted by the read name.
2016-05-26 Yanxiao Zhang <[email protected]>
* version 1.1.7
* added back the inter-group normalization
* added a few exception handlers.
* check for files and directories before running PePr.
2016-05-24 Yanxiao Zhang <[email protected]>
* version 1.1.6
* added back the post-processing module
* make preprocessing and postprocessing modules separate console commands.
* added back fileParser.py to facilitate parser function reuse.
2016-05-23 Yanxiao Zhang <[email protected]>
* version 1.1.5
* added back 'removing duplicates'
2016-05 Yanxiao Zhang <[email protected]>
* version 1.1.1 - 1.1.4
* hotfixes.
2016-04-17 Yanxiao Zhang <[email protected]>
* version 1.1.0
* A few major changes
* PePr now separated into three steps: (1) preprocessing (2)
peak-calling (3) post-processing. step 3 is no longer required.
* Instead of command line options, can take parameter file as input
now, and will output parameters into a file so users can reproduce the
results or fine-tune the parameters using that file.
* Shift size estimation method changed
* Added multiprocessing. Now can run in parallel mode.
* Memory usage significantly reduced because reads are no longer
completed loaded into memory.
* No longer needed to sort and index bam files for reading.
2015-08-05 Yanxiao Zhang <[email protected]>
* Bug fixes for the refining peak width.
2015-04-07 Yanxiao Zhang <[email protected]>
* Change dependencies on Numpy and Scipy to
'numpy>=1.6.0'
'scipy>=0.14.0'
2015-03-24 Yanxiao Zhang <[email protected]>
* version 1.0.7
* refactor a few functions, now should work with python 3.4.
* change dependency to numpy==1.6.0 and scipy==0.14.0, which is the working version under development.
2015-01-27 Yanxiao Zhang <[email protected]>
* version 1.0.6
* enable custom normalization or NO normalization.
* fixed the filename list bug.
* add a message when PePr finishes running
2014-12-02 Yanxiao Zhang <[email protected]>
* version 1.0.5
* from now on, users can submit differential analysis without input samples.
2014-11-21 Yanxiao Zhang <[email protected]>
* sigTest.py: fixed the coordinates overflow error in the post-processing step.
2014-08-22 Yanxiao Zhang <[email protected]>
* classDef.py: Added a few exception handlers for invalid input
parameters.
2014-04-23 Yanxiao Zhang <[email protected]>
* setup.py: Added. Made PePr into a python package and uploaded it up to the PyPI repository.
2014-04-04 Yanxiao Zhang <[email protected]>
* sigTest.py: Removed the previous method that filter out the peaks without any strand lag; added a method to remove artefacts that either have same peak shape in ChIP and background, or are dominated by reads at less than three positions.
2014-04-01 Yanxiao Zhang <[email protected]>
* Version 1.0.1
* Major changes:
Added support for BAM format (requring pysam module);
Changed the normalization strategy (NCIS and modified TMM for input and ChIP samples respectively);
For differential analysis, will subtract input reads from ChIP reads after normalization; Improved the peak-calling speed;
No longer requires a pre-specified genome.
* classDef.py: Added a new class Parameters.
* fileParser.py: Added BAM format parser.
* sigTest.py: implemented a new method for estimating over-dispersion parameter.
* windowSize.py: Added new normalization: NCIS for input and modified TMM for ChIP samples.
* genomeData.py: Deleted. Chromosome and genome size will be established directly from the data.
2014-02-05 Yanxiao Zhang <[email protected]>
* Version 1.0.0
* optParser.py: Added diff option to allow the user to do automatical sample swap for differential analysis instead of running the program twice.
* shiftSize.py, sigTests.py: some functions changed accordingly to do sample swap.
2012-10-09 Yanxiao Zhang <[email protected]>
* Version 0.9.0
* sigTests.py: Added optional post-processing steps: (1) Estimating the shift size for every peak and remove peaks that have shift size less than 5bp+readlength (2) refine the peak boundary to minimally contain the core region that are warranted by reads.
* Cleaned deprecated functions.
2012-09-28 Yanxiao Zhang <[email protected]>
* sigTests.py: Revised the dispersion parameter estiamtion method to leverage the local information to increase the precision of estiamtion. Deleted the code from edgeR.
2012-03-19 Yanxiao Zhang <[email protected]>
* windowsize.py: New window size estiamtion method
* shiftsize.py: New shift size estiamtion method
* sigTests.py: Using the log transformed wald test instead of the original wald test.
* clasDef.py: Added function to estimate and remove redundant reads.
2012-01-24 Yanxiao Zhang <[email protected]>
* genomeData.py: Added support to genome build mm9, dm3
2011-10-25 Yanxiao Zhang <[email protected]>
* The first draft version of the program.
* classDef.py, fileParser.py, genomeData.py, logConfig.py, misc.py, optParser.py, PePr.py, shiftSize.py, sigTests.py, windowSize.py: files created