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 output was added as a way to get easily-readable 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'