* The sort command creates any needed temporary files alongside the final
  output file (similarly to the pre-1.3 behaviour), and now aborts when
  it detects a collision with another sort invocation's temporary files.

  When the -T PREFIX option specified is a directory (or when sorting to
  standard output), a random component is now added to temporary filenames
  to try to avoid collisions (#432, #523, #529, #535, PR #530).

* All samtools commands now check for I/O errors more carefully, especially
  when writing output files (#111, #253, #470, PR #467).

* Build fixes for 32-bit systems; be sure to run configure on such systems
  to enable large file support and access to 2GiB+ files.

* The fasta/fastq/bam2fq command no longer ignores reads when the -s option
  is used (#532).

* The fastq -O option no longer crashes on reads that do not have an OQ tag
  field (#517).

* The merge and sort commands now handle (unusual) BAM files that have no
  textual @SQ headers (#548, #550).

* Sorting files containing @CO headers no longer duplicates the comment
  headers, which previously happened on large sorts for which temporary
  files were needed (#563).

* The rmdup and view -l commands no longer crash on @RG headers that do not
  have a LB field (#538).

* Fixed miscellaneous issues #128, #130, #131, #489, and #514.