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Update CHANGELOG.md
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CHANGELOG.md

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Version 0.2 - September 3, 2011
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Version 0.2 - September 3, 2016
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Version 0.2 of WASP is a major update to the code,
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of the pipline.
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Changes include:
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* re-wrote mapping scripts to make simpler and more modular
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* re-wrote mapping test scripts and added of many tests
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* fixed several mapping pipeline bugs related to paired-end reads
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* find_intersecting_snps.py window size no longer required (is now
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* re-wrote mapping scripts to make simpler and more modular
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* re-wrote mapping test scripts and added of many tests
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* fixed several mapping pipeline bugs related to paired-end reads
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* find_intersecting_snps.py window size no longer required (is now
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unlimited)
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* find_intersecting_snps.py can now take HDF5 files as input
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* find_intersecting_snps.py can now consider only haplotypes
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* find_intersecting_snps.py can now take HDF5 files as input
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* find_intersecting_snps.py can now consider only haplotypes
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present in samples, rather than all possible allelic combinations
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of SNPs overlapping reads.
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* added get_as_counts.py script that outputs allele-specific read
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* added get_as_counts.py script that outputs allele-specific read
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counts at all polymorphic SNPs.
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* snp2h5 now records sample info in output HDF5 files
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* improved speed of many CHT pipeline steps
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* improved stability of CHT dispersion parameter estimation
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* added Snakemake workflows for both mapping and CHT pipelines
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* snp2h5 now records sample info in output HDF5 files
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* improved speed of many CHT pipeline steps
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* improved stability of CHT dispersion parameter estimation
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* added Snakemake workflows for both mapping and CHT pipelines
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Version 0.1

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