samtools/htslib — pull request #101 by jkbonfield (2014-06-02 16:48:09+00:00)
Title: Samtools view -T for CRAM

sam_hdr_write() now calls cram_load_reference if
hts_set_fai_filename() has been called. Also refs_load_fai() now
copes with being given foo.fa or foo.fa.fai and does the right thing.

https://github.com/samtools/samtools/issues/144