samtools/htslib — pull request #100 by jkbonfield (2014-06-02 14:23:35+00:00)
Title: Removal of bogus CRAM warnings.

Removed bogus "Unable to find ref name"* errors when converting a SAM
file UR:local/path/name syntax and without finding an MD5 reference to
use. The code previously went on to work fine as a subsequent refs2id
call worked.

This is avoided in Staden io_lib by the use of a scram_set_refs()
function which is called on the result of a scram_get_refs() call on a
SAM/BAM file, returning NULL and then resetting fd->refs to NULL.

We have no such call in HTSlib, but can resolve it by a smarter
implementation of cram_load_reference().