samtools/samtools — pull request #20 by peterjc (2012-10-26 14:58:17+00:00)
Title: Raise error if give @HD SO:coordinate to 'samtools fixmate'

The (minimal) documentation does tell you 'samtools fixmate' requires query name sorted reads (in fact grouped by query name is enough), but doesn't actually raise an error if given coordinate sorted reads (it just silently fails to fix them).

This change raises an explicit error if the @HD line contains SO:coordinate, and expands the usage text slightly.