I have an aligned .bam file and a reference .fasta file. I'd like to convert the .bam and .fasta from an unpadded representation to a padded one (with 'padded' and 'unpadded' as defined in the SAM spec). Are there tools that can do this either across the entire .bam and reference sequence, or alternatively just for reads that overlap a particular region?
Ps. I know samtools had a pad2unpad (aka. depad) tool at one point. Perhaps there is something similar for going the opposite direction?