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Update CHANGELOG.md
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gmcvicker authored Sep 4, 2016
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Version 0.2 - September 3, 2011
Version 0.2 - September 3, 2016
-----------

Version 0.2 of WASP is a major update to the code,
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of the pipline.

Changes include:
* re-wrote mapping scripts to make simpler and more modular
* re-wrote mapping test scripts and added of many tests
* fixed several mapping pipeline bugs related to paired-end reads
* find_intersecting_snps.py window size no longer required (is now
* re-wrote mapping scripts to make simpler and more modular
* re-wrote mapping test scripts and added of many tests
* fixed several mapping pipeline bugs related to paired-end reads
* find_intersecting_snps.py window size no longer required (is now
unlimited)
* find_intersecting_snps.py can now take HDF5 files as input
* find_intersecting_snps.py can now consider only haplotypes
* find_intersecting_snps.py can now take HDF5 files as input
* find_intersecting_snps.py can now consider only haplotypes
present in samples, rather than all possible allelic combinations
of SNPs overlapping reads.
* added get_as_counts.py script that outputs allele-specific read
* added get_as_counts.py script that outputs allele-specific read
counts at all polymorphic SNPs.
* snp2h5 now records sample info in output HDF5 files
* improved speed of many CHT pipeline steps
* improved stability of CHT dispersion parameter estimation
* added Snakemake workflows for both mapping and CHT pipelines
* snp2h5 now records sample info in output HDF5 files
* improved speed of many CHT pipeline steps
* improved stability of CHT dispersion parameter estimation
* added Snakemake workflows for both mapping and CHT pipelines


Version 0.1
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