This minor release corrects an issue where the cht_data module was not included in the v0.2 release. This module is required by the fit_bnb_coefficients.py script.
Version 0.2 of WASP is a major update to the code, especially the mapping code. It fixes several bugs related to how paired-end reads are handled. For this reason it is strongly recommended that users switch to this version 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 unlimited)
- 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 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
- added qqplot.R script to CHT workflow
Initial version of WASP