SAM/BAM format v1.5 extensions for de novo assemblies.The current version is a terse three pages (trying to meet an "application note" page limit), but nevertheless should clarify the intended usage of these parts of the SAM/BAM specification.
Peter J. A. Cock, James K. Bonfield, Bastien Chevreux, Heng Li.
bioRxiv DOI: 10.1101/020024
This manuscript has been in progress since 2012, in parallel with the associated file format change discussions all held openly on the samtools-devel mailing list, and "samtools depad" work on GitHub.
My apologies to my co-authors, the long delays are my fault. After getting useful comments from an internal pre-submission review (thank you to colleagues at the James Hutton Institute), I should have posted the current preprint back in February. Better late than never.
Also, thank you to Nick Loman for a discussion in 2011 which was one of the motivations in making this effort in the first place.
Also relevant are some of my blog posts from late 2011, with screenshots illustrating SAM/BAM files with a padded reference, vs SAM/BAM files with an un-padded reference.
If there are queries about the file format itself, please raise them on the samtools-devel mailing list. I'm happy to receive comments about the manuscript itself by email directly.