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CHANGELOG.md

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Version 0.3.4 - April 30, 2019

This release fixes some issues with the bam2h5.py script.

Changes to bam2h5.py include:

  • Correct counting of reads with indels in bam2h5.py (pull request from MingshiGao)
  • Fix txtfile output from bam2h5.py, which was outputting incorrect genotypes when multiple samples present in haplotype file. Note that this txt file was added as a way to get human-readible allele-specific counts and the incorrect genotypes in the file were not actually used by the WASP pipeline.
  • Default to uint16 datatype rather than uint8 so that counts are no longer thresholded at 255
  • Silence warnings printed when using chromosomes that do not start with 'chr'

Version 0.3.3 - September 14, 2018

This release contains a single bugfix:

  • Fixes to ref/alt/other allele match reporting in find_intersecting_snps.py which was broken during py2 to py3 conversion.

Version 0.3.2 - September 13, 2018

This release fixes a minor bug in snp2h5 that could occur if haplotypes were not specified.

Version 0.3.1 - August 31, 2018

This release makes several improvements/fixes to read filtering by the mapping pipeline. Several of these improvements were suggested by Alex Dobin for using WASP with the STAR mapper.

Changes include:

  • find_intersecting_snps.py was modified to handle dependence of alleles when both reads from a read pair overlap the same variant(s). Previously the reads that were generated for remapping were treated independently, however if read1 has alternate allele for a given SNP, so should read2 if it overlaps the same SNPs.
  • snp2h5 was altered to add a new phase carray to haplotype.h5 containing phase information from the VCF. find_intersecting_snps.py will now use the phase information from haplotype.h5 to calculate new haplotypes with all possible allelic combinations at unphased sites, resulting in more reads being generated for remapping. If phase information is not provided in haplotype.h5, all sites will be assumed unphased.
  • Supplementary and secondary alignments are now filtered by find_intersecting_snps and filter_remapped_reads
  • Reads whose CIGAR flags change after the remapping step are now discarded, even if they map to the same start position.
  • snp2h5 will now try to add/remove 'chr' from the chromosome name read from the VCF file if the original name does not match any chromosomes in the chromInfo file.

Version 0.3.0 - July 3, 2018

This release moves the codebase from Python2 to Python3 and includes several additional improvements.

Changes include:

  • Switch to Python3 from Python2
  • Switch to PyTables version 3
  • General cleanup of code to conform to PEP8 style
  • Better matching of VCF files to chromosomes in snp2h5 (uses name of chromosome within VCF, rather than relying on filename)
  • add --txt_counts option to bam2h5.py as a simple way to obtain a file with allele-specific counts. The bam2h5.py should now be used instead of the get_as_counts.py script (which double counts reads that overlap multiple SNPs).

Version 0.2.2 - November 15, 2017

This release incorporates several modifications/fixes that have been made to the master branch over the past year.

Changes include:

  • check first 2 bytes of input files to decide if they are gzipped rather than relying on .gz filename extension
  • fix bug in which unmapped reads in BAM were causing find_intersecting_snps.py to crash
  • fix bug in which some cigar codes caused find_intersecting_snps to crash because of typo in snptable
  • fix bug related to soft-clipped reads (switch to use pysam 'query_sequence' instead of 'query' attribute)
  • added check for pysam version to rmdup_pe and find_intersecting_snps.py
  • added check for pytables version to find_intersecting_snps.py
  • rescale count totals in CHT so that alpha and beta estimates stay in reasonable range
  • allow empty header lines in VCF parsing
  • change max SNP identifier length from 16 to 255
  • include much more information in output table from combined haplotype test such as SNP info, total numbers of AS reads, etc.
  • warn and gracefully handle situation where there are no matching samples on a chromosome

Version 0.2.1 - September 5, 2016

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 - September 3, 2016

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

Version 0.1

Initial version of WASP