HDF5 output file formats (cmp.h5, bas.h5) were deprecated in v3.0 and replaced by industry standard BAM formats. Because there is no way to convert BAM formats back to bas/cmp.h5 formats, SMALR should be able to detect when BAM files are input and support using them for single-molecule methylation detection.
A summary of the new BAM file structures can be found here.
HDF5 output file formats (cmp.h5, bas.h5) were deprecated in v3.0 and replaced by industry standard BAM formats. Because there is no way to convert BAM formats back to bas/cmp.h5 formats, SMALR should be able to detect when BAM files are input and support using them for single-molecule methylation detection.
A summary of the new BAM file structures can be found here.